Browse by Research Area

Abdelilah-Seyfried, Salim

Genie: literature-based gene prioritization at multi genomic scale.
Fontaine, J.F., Priller, F., Barbosa-Silva, A. and Andrade-Navarro, M.A.
Nucleic Acids Research 39 (Suppl 2): W455-W461. July 2011

Cell tracking using photoconvertible proteins during zebrafish development.
Lombardo, V.A., Sporbert, A. and Abdelilah-Seyfried, S.
Journal of Visualized Experiments (67): e4350. 28 September 2012

Akalin, Altuna (BIMSB)

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

Nucleic Acids Research 44 (D1): D27-D37. 4 January 2016

Transcriptional features of genomic regulatory blocks.
Akalin, A., Fredman, D., Arner, E, Dong, X, Bryne, JC, Suzuki, H., Daub, CO, Hayashizaki, Y and Lenhard, B
Genome Biology 10 (4): R38. 19 April 2009

Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia.
Akalin, A., Garrett-Bakelman, F.E., Kormaksson, M., Busuttil, J., Zhang, L., Khrebtukova, I., Milne, T.A., Huang, Y., Biswas, D., Hess, J.L., Allis, C.D., Roeder, R.G., Valk, P.J.M., Loewenberg, B., Delwel, R., Fernandez, H.F., Paietta, E., Tallman, M.S., Schroth, G.P., Mason, C.E., Melnick, A. and Figueroa, M.E.
PLoS Genetics 8 (6): e1002781. 21 June 2012

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles.
Akalin, A., Kormaksson, M., Li, S., Garrett-Bakelman, F.E., Figueroa, M.E., Melnick, A. and Mason, C.E.
Genome Biology 13 (10): R87. 3 October 2012

Computational genomics with R.
Akalin, A.
Chapman and Hall/CRC Computational Biology Series . CRC Press LLC, Milton. ISBN 9781498781855 2020

genomation: a toolkit to summarize, annotate and visualize genomic intervals.
Akalin, A., Franke, V., Vlahoviček, K., Mason, C.E. and Schübeler, D.
Bioinformatics 31 (7): 1127-1129. 1 April 2015

Enhancing biomarker-based oncology trial matching using large language models.
Al Khoury, N., Shaik, M., Wurmus, R. and Akalin, A.
bioRxiv : 2024.09.13.612922. 19 September 2024

Predicting the binding affinity of MHC class II peptides.
Altiparmak, F., Akalin, A. and Ferhatosmanoglu, H.
Computational Systems Bioinformatics 2006 : 331-334. August 2006

The role of respiratory microbiota in the protection against viral diseases: respiratory commensal bacteria as next-generation probiotics for COVID-19.
Andrade, B.G.N., Cuadrat, R.R.C., Tonetti, F.R., Kitazawa, H. and Villena, J.
Bioscience of Microbiota, Food and Health 41 (3): 94-102. 1 July 2022

Putative mobilized colistin resistance genes in the human gut microbiome.
Andrade, B.G.N., Goris, T., Afli, H., Coutinho, F.H., Dávila, A.M.R. and Cuadrat, R.R.C.
BMC Microbiology 21 : 220. 22 July 2021

The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators.
Appel, L.M., Franke, V., Benedum, J., Grishkovskaya, I., Strobl, X., Polyansky, A., Ammann, G., Platzer, S., Neudolt, A., Wunder, A., Walch, L., Kaiser, S., Zagrovic, B., Djinovic-Carugo, K., Akalin, A. and Slade, D.
Nature Communications 14 (1): 166. 11 January 2023

PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC.
Appel, L.M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A., Kaufmann, T., Schoeberl, U.E., Puchinger, M.G., Kostrhon, S., Ebenwaldner, C., Sebesta, M., Beltzung, E., Mechtler, K., Lin, G., Vlasova, A., Leeb, M., Pavri, R., Stark, A., Akalin, A., Stefl, R., Bernecky, C., Djinovic-Carugo, K. and Slade, D.
Nature Communications 12 (1): 6078. 19 October 2021

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.
Baranasic, D., Hörtenhuber, M., Balwierz, P.J., Zehnder, T., Mukarram, A.K., Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., Wragg, J., D'Orazio, F.M., Relic, D., Pachkov, M., Díaz, N., Hernández-Rodríguez, B., Chen, Z., Stoiber, M., Dong, M., Stevens, I., Ross, S.E., Eagle, A., Martin, R., Obasaju, O., Rastegar, S., McGarvey, A.C., Kopp, W., Chambers, E., Wang, D., Kim, H.R., Acemel, R.D., Naranjo, S., Łapiński, M., Chong, V., Mathavan, S., Peers, B., Sauka-Spengler, T., Vingron, M., Carninci, P., Ohler, U., Lacadie, S.A., Burgess, S.M., Winata, C., van Eeden, F., Vaquerizas, J.M., Gómez-Skarmeta, J.L., Onichtchouk, D., Brown, B.J., Bogdanovic, O., van Nimwegen, E., Westerfield, M., Wardle, F.C, Daub, C.O., Lenhard, B. and Müller, F.
Nature Genetics 54 (7): 1037-1050. July 2022

Multi-omics alleviates the limitations of panel sequencing for cancer drug response prediction.
Baranovskii, A., Gündüz, I.B., Franke, V., Uyar, B. and Akalin, A.
Cancers 14 (22): 5604. 15 November 2022

Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation.
Baubec, T., Colombo, D.F., Wirbelauer, C., Schmidt, J., Burger, L., Krebs, A.R., Akalin, A. and Schübeler, D.
Nature 520 (7546): 243-247. 9 April 2015

The SPOC proteins DIDO3 and PHF3 co-regulate gene expression and neuronal differentiation.
Benedum, J., Franke, V., Appel, L.M., Walch, L., Bruno, M., Schneeweiss, R., Gruber, J., Oberndorfer, H., Frank, E., Strobl, X., Polyansky, A., Zagrovic, B., Akalin, A. and Slade, D.
Nature Communications 14 (1): 7912. 30 November 2023

Zebrafish enhancer detection (ZED) vector: a new tool to facilitate transgenesis and the functional analysis of cis-regulatory regions in zebrafish.
Bessa, J., Tena, J.J., de la Calle-Mustienes, E., Fernandez-Minan, A., Naranjo, S., Fernandez, A., Montoliu, L., Akalin, A., Lenhard, B., Casares, F. and Gomez-Skarmeta, J.L.
Developmental Dynamics 238 (9): 2409-2417. September 2009

DoRiNA 2.0-upgrading the doRiNA database of RNA interactions in post-transcriptional regulation.
Blin, K., Dieterich, C., Wurmus, R., Rajewsky, N., Landthaler, M. and Akalin, A.
Nucleic Acids Research 43 (Database issue): D160-D167. 28 January 2015

The histone H4 lysine 20 demethylase DPY-21 regulates the dynamics of condensin DC binding.
Breimann, L., Morao, A.K., Kim, J., Jimenez, D.S., Maryn, N., Bikkasani, K., Carrozza, M.J., Albritton, S.E., Kramer, M., Street, L.A., Cerimi, K., Schumann, V.F., Bahry, E., Preibisch, S., Woehler, A. and Ercan, S.
Journal of Cell Science 135 (2): jcs258818. January 2022

Alternative 3' UTRs direct localization of functionally diverse protein isoforms in neuronal compartments.
Ciolli Mattioli, C., Rom, A., Franke, V., Imami, K., Arrey, G., Terne, M., Woehler, A., Akalin, A., Ulitsky, I. and Chekulaeva, M.
Nucleic Acids Research 47 (5): 2560-2573. 18 March 2019

Reproducible and user-controlled software environments in HPC with Guix.
Courtes, L. and Wurmus, R.
Lecture Notes in Computer Science 9523 : 579-591. 2015

Association of the human gut microbiota with vascular stiffness.
Cuadrat, R.R.C., Goris, T., Birukov, A., Eichelmann, F., Andrade, B.G.N., Bang, C., Franke, A., Wittenbecher, C. and Schulze, M.B.
Scientific Reports 13 (1): 13348. 16 August 2023

Cardiovascular disease biomarkers derived from circulating cell-free DNA methylation.
Cuadrat, R.R.C., Kratzer, A., Arnal, H.G., Rathgeber, A.C., Wreczycka, K., Blume, A., Gündüz, I.B., Ebenal, V., Mauno, T., Osberg, B., Moobed, M., Hartung, J., Jakobs, K., Seppelt, C., Meteva, D., Haghikia, A., Leistner, D.M., Landmesser, Ulf and Akalin, A.
NAR Genomics and Bioinformatics 5 (2): lqad061. June 2023

PDGFA-associated protein 1 protects mature B lymphocytes from stress-induced cell death and promotes antibody gene diversification.
Delgado-Benito, V., Berruezo-Llacuna, M., Altwasser, R., Winkler, W., Sundaravinayagam, D., Balasubramanian, S., Caganova, M., Graf, R., Rahjouei, A., Henke, M.T., Driesner, M., Keller, L., Prigione, A., Janz, M., Akalin, A. and Di Virgilio, M.
Journal of Experimental Medicine 217 (10): e20200137. 5 October 2020

Nuclear organization in the spinal cord depends on motor neuron lamination orchestrated by catenin and afadin function.
Dewitz, C., Pimpinella, S., Hackel, P., Akalin, A., Jessell, T.M. and Zampieri, N.
Cell Reports 22 (7): 1681-1694. 13 February 2018

Identifying tumor cells at the single-cell level using machine learning.
Dohmen, J., Baranovskii, A., Ronen, J., Uyar, B., Franke, V. and Akalin, A.
Genome Biology 23 (1): 123. 30 May 2022

Translog, a web browser for studying the expression divergence of homologous genes.
Dong, X., Akalin, A., Sharma, Y. and Lenhard, B.
BMC Bioinformatics 11 (Suppl 1): S59. 18 January 2010

Complex loci in human and mouse genomes.
Engstroem, P.G., Suzuki, H., Ninomiya, N., Akalin, A., Sessa, L., Lavorgna, G., Brozzi, A., Luzi, L., Tan, S.L., Yang, L., Kunarso, G., Ng, E.L.C., Batalov, S., Wahlestedt, C., Kai, C., Kawai, J., Carninci, P., Hayashizaki, Y., Wells, C., Bajic, V.B., Orlando, V., Reid, J.F., Lenhard, B. and Lipovich, L.
PLoS Genetics 2 (4): 564-577. 28 April 2006

RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation.
Ferrai, C., Torlai Triglia, E., Risner-Janiczek, J.R., Rito, T., Rackham, O.J.L., De Santiago, I., Kukalev, A., Nicodemi, M., Akalin, A., Li, M., Ungless, M.A. and Pombo, A.
Molecular Systems Biology 13 (10): 946. 16 October 2017

The SEQC2 epigenomics quality control (EpiQC) study.
Foox, J., Nordlund, J., Lalancette, C., Gong, T., Lacey, M., Lent, S., Langhorst, B.W., Ponnaluri, V.K.C., Williams, L., Padmanabhan, K.R., Cavalcante, R., Lundmark, A., Butler, D., Mozsary, C., Gurvitch, J., Greally, J.M., Suzuki, M., Menor, M., Nasu, M., Alonso, A., Sheridan, C., Scherer, A., Bruinsma, S., Golda, G., Muszynska, A., Łabaj, P.P., Campbell, M.A., Wos, F., Raine, A., Liljedahl, U., Axelsson, T., Wang, C., Chen, Z., Yang, Z., Li, J., Yang, X., Wang, H., Melnick, A., Guo, S., Blume, A., Franke, V., Ibanez de Caceres, I., Rodriguez-Antolin, C., Rosas, R., Davis, J.W., Ishii, J., Megherbi, D.B., Xiao, W., Liao, W., Xu, J., Hong, H., Ning, B., Tong, W., Akalin, A., Wang, Y., Deng, Y. and Mason, C.E.
Genome Biology 22 (1): 332. 6 December 2021

A multimorphic mutation in IRF4 causes human autosomal dominant combined immunodeficiency.
Fornes, O., Jia, A., Kuehn, H.S., Min, Q., Pannicke, U., Schleussner, N., Thouenon, R., Yu, Z., de Los Angeles Astbury, M., Biggs, C.M., Galicchio, M., Garcia-Campos, J.A., Gismondi, S., Gonzalez Villarreal, G., Hildebrand, K.J., Hönig, M., Hou, J., Moshous, D., Pittaluga, S., Qian, X., Rozmus, J., Schulz, A.S., Staines-Boone, A.T., Sun, B., Sun, J., Uwe, S., Venegas-Montoya, E., Wang, W., Wang, X., Ying, W., Zhai, X., Zhou, Q., Akalin, A., André, I., Barth, T.F.E., Baumann, B., Brüstle, A., Burgio, G., Bustamante, J.C., Casanova, J.L., Casarotto, M.G., Cavazzana, M., Chentout, L., Cockburn, I.A., Costanza, M., Cui, C., Daumke, O., Del Bel, K.L., Eibel, H., Feng, X., Franke, V., Gebhardt, J.C.M., Götz, A., Grunwald, S., Hoareau, B., Hughes, T.R., Jacobsen, E.M., Janz, M., Jolma, A., Lagresle-Peyrou, C., Lai, N., Li, Y., Lin, S., Lu, H.Y., Lugo-Reyes, S.O., Meng, X., Möller, P., Moreno-Corona, N., Niemela, J.E., Novakovsky, G., Perez-Caraballo, J.J., Picard, C., Poggi, L., Puig-Lombardi, M.E., Randall, K.L., Reisser, A., Schmitt, Y., Seneviratne, S., Sharma, M., Stoddard, J., Sundararaj, S., Sutton, H., Tran, L.Q., Wang, Y., Wasserman, W.W., Wen, Z., Winkler, W., Xiong, E., Yang, A.W.H., Yu, M., Zhang, L., Zhang, H., Zhao, Q., Zhen, X., Enders, A., Kracker, S., Martinez-Barricarte, R., Mathas, S., Rosenzweig, S.D., Schwarz, K., Turvey, S.E. and Wang, J.Y.
Science Immunology 8 (79): eade7953. January 2023

Parallel genetics of regulatory sequences using scalable genome editing in vivo.
Froehlich, J.J., Uyar, B., Herzog, M., Theil, K., Glažar, P., Akalin, A. and Rajewsky, N.
Cell Reports 35 (2): 108988. 13 April 2021

Evaluating large language model workflows in clinical decision support: referral, triage, and diagnosis.
Gaber, F., Shaik, M., Franke, V. and Akalin, A.
medRxiv : 2024.09.27.24314505. 28 September 2024

Rapid inflammasome activation is attenuated in post-myocardial infarction monocytes.
Giral, H., Franke, V., Moobed, M., Müller, M.F., Lübking, L., James, D.M., Hartung, J., Kuschnerus, K., Meteva, D., Seppelt, C., Jakob, P., Klingenberg, R., Kränkel, N., Leistner, D., Zeller, T., Blankenberg, S., Zimmermann, F., Haghikia, A., Lüscher, T.F., Akalin, A., Landmesser, U. and Kratzer, A.
Frontiers in Immunology 13 : 857455. 26 April 2022

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.
Grüning, B.A., Fallmann, J., Yusuf, D., Will, S., Erxleben, A., Eggenhofer, F., Houwaart, T., Batut, B., Videm, P., Bagnacani, A., Wolfien, M., Lott, S.C., Hoogstrate, Y., Hess, W.R., Wolkenhauer, O., Hoffmann, S., Akalin, A., Ohler, U., Stadler, P.F. and Backofen, R.
Nucleic Acids Research 45 (W1): W560-W566. 3 July 2017

Two independent transcription initiation codes overlap on vertebrate core promoters.
Haberle, V., Li, N., Hadzhiev, Y., Plessy, C., Previti, C., Nepal, C., Gehrig, J., Dong, X., Akalin, A., Suzuki, A.M., van IJcken, W.F.J., Armant, O., Ferg, M., Strähle, U., Carninci, P., Müller, F. and Lenhard, B.
Nature 507 (7492): 381-385. 20 March 2014

Dolosigranulum pigrum modulates immunity against SARS-CoV-2 in respiratory epithelial cells.
Islam, M.A., Albarracin, L., Melnikov, V., Andrade, B.G.N., Cuadrat, R.R.C., Kitazawa, H. and Villena, J.
Pathogens 10 (6): 634. 21 May 2021

Immunobiotic Lactobacilli improve resistance of respiratory epithelial cells to SARS-CoV-2 infection.
Islam, M.A., Albarracin, L., Tomokiyo, M., Valdez, J.C., Sacur, J., Vizoso-Pinto, M.G., Andrade, B.G.N., Cuadrat, R.C., Kitazawa, H. and Villena, J.
Pathogens 10 (9): 1197. September 2021

Long non-coding RNAs defining major subtypes of B cell precursor acute lymphoblastic leukemia.
James, A.R., Schroeder, M.P., Neumann, M., Bastian, L., Eckert, C., Gökbuget, N., Tanchez, J.O., Schlee, C., Isaakidis, K., Schwartz, S., Burmeister, T., von Stackelberg, A., Rieger, M.A., Göllner, S., Horstman, M., Schrappe, M., Kirschner-Schwabe, R., Brüggemann, M., Müller-Tidow, C., Serve, H., Akalin, A. and Baldus, C.D.
Journal of Hematology & Oncology 12 (1): 8. 14 January 2019

scMaui: a widely applicable deep learning framework for single-cell multiomics integration in the presence of batch effects and missing data.
Jeong, Y., Ronen, J., Kopp, W., Lutsik, P. and Akalin, A.
BMC Bioinformatics 25 (1): 257. 6 August 2024

Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling.
Karabacak Calviello, A., Hirsekorn, A., Wurmus, R., Yusuf, D. and Ohler, U.
Genome Biology 20 (1): 42. 21 February 2019

Cytosolic nucleic acid sensors and interferon beta-1 activation drive radiation-induced anti-tumour immune effects in human pancreatic cancer cells.
Kerschbaum-Gruber, S., Kleinwächter, A., Popova, K., Kneringer, A., Appel, L.M., Stasny, K., Röhrer, A., Dias, A.B., Benedum, J., Walch, L., Postl, A., Barna, S., Kratzer, B., Pickl, W.F., Akalin, A., Horvat, F., Franke, V., Widder, J., Georg, D. and Slade, D.
Frontiers in Immunology 15 : 1286942. 20 September 2024

Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates.
Kikuta, H., Laplante, M., Navratilova, P., Komisarczuk, A.Z., Engstroem, P.G., Fredman, D., Akalin, A., Caccamo, M., Sealy, I., Howe, K., Ghislain, J., Pezeron, G., Mourrain, P., Ellingsen, S., Oates, A.C., Thisse, C., Thisse, B., Foucher, I., Adolf, B., Geling, A., Lenhard, B. and Becker, T.S.
Genome Research 17 (5): 545-555. May 2007

Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells.
Kim, M., Franke, V., Brandt, B., Lowenstein, E.D., Schöwel, V., Spuler, S., Akalin, A. and Birchmeier, C.
Nature Communications 11 : 6375. 11 December 2020

Transcriptional repression of NFKBIA triggers constitutive IKK- and proteasome-independent p65/RelA activation in senescence.
Kolesnichenko, M., Mikuda, N., Höpken, U.E., Kärgel, E., Uyar, B., Tufan, A.B., Milanovic, M., Sun, W., Krahn, I., Schleich, K., von Hoff, L., Hinz, M., Willenbrock, M., Jungmann, S., Akalin, A., Lee, S., Schmidt-Ullrich, R., Schmitt, C.A. and Scheidereit, C.
EMBO Journal 40 (6): e104296. 15 March 2021

FACT sets a barrier for cell fate reprogramming in Caenorhabditis elegans and human cells.
Kolundzic, E., Ofenbauer, A., Bulut, S.I., Uyar, B., Baytek, G., Sommermeier, A., Seelk, S., He, M., Hirsekorn, A., Vucicevic, D., Akalin, A., Diecke, S., Lacadie, S.A. and Tursun, B.
Developmental Cell 46 (5): 611-626. 10 September 2018

Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning.
Kopp, W., Akalin, A. and Ohler, U.
Nature Machine Intelligence 4 (2): 162-168. February 2022

Deep learning for genomics using Janggu.
Kopp, W., Monti, R., Tamburrini, A., Ohler, U. and Akalin, A.
Nature Communications 11 (1): 3488. 13 July 2020

Social networks and protest participation: evidence from 130 million Twitter users.
Larson, J.M., Nagler, J., Ronen, J. and Tucker, J.A.
American Journal of Political Science 63 (3): 690-705. July 2019

Spatio-temporal, optogenetic control of gene expression in organoids.
Legnini, I., Emmenegger, L., Zappulo, A., Wurmus, R., Oliveras Martinez, A., Cerda Jara, C., Boltengagen, A., Hessler, T., Mastrobuoni, G., Rybak-Wolf, A., Kempa, S., Zinzen, R.P., Woehler, A. and Rajewsky, N.
bioRxiv : 2021.09.26.461850v3. 9 February 2022

An optimized algorithm for detecting and annotating regional differential methylation.
Li, S., Garrett-Bakelman, F.E., Akalin, A., Zumbo, P., Levine, R., To, B.L., Lewis, I.D., Brown, A.L., D'Andrea, R.J., Melnick, A. and Mason, C.E.
BMC Bioinformatics 14 (Suppl 5): S10. 2013

Predicting lethal courses in critically ill COVID-19 patients using a machine learning model trained on patients with non-COVID-19 viral pneumonia.
Lichtner, G., Balzer, F., Haufe, S., Giesa, N., Schiefenhövel, F., Schmieding, M., Jurth, C., Kopp, W., Akalin, A., Schaller, S.J., Weber-Carstens, S., Spies, C. and von Dincklage, F.
Scientific Reports 11 (1): 13205. 24 June 2021

Induction of sarcomas by mutant IDH2.
Lu, C., Venneti, S., Akalin, A., Fang, F., Ward, P.S., Dematteo, R.G., Intlekofer, A.M., Chen, C., Ye, J., Hameed, M., Nafa, K., Agaram, N.P., Cross, J.R., Khanin, R., Mason, C.E., Healey, J.H., Lowe, S.W., Schwartz, G.K., Melnick, A. and Thompson, C.B.
Genes & Development 27 (18): 1986-1998. 15 September 2013

Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos.
McGarvey, A.C., Kopp, W., Vučićević, D., Mattonet, K., Kempfer, R., Hirsekorn, A., Bilić, I., Gil, M., Trinks, A., Merks, A.M., Panáková, D., Pombo, A., Akalin, A., Junker, J.P., Stainier, D.Y.R., Garfield, D., Ohler, U. and Lacadie, S.A.
Cell Genomics 2 (1): 100083. 13 January 2022

Lymphocyte access to lymphoma is impaired by high endothelial venule regression.
Menzel, L., Zschummel, M., Crowley, T., Franke, V., Grau, M., Ulbricht, C., Hauser, A., Siffrin, V., Bajénoff, M., Acton, S.E., Akalin, A., Lenz, G., Willimsky, G., Höpken, U.E. and Rehm, A.
Cell Reports 37 (4): 109878. 26 October 2021

Degrons in cancer.
Meszaros, B., Kumar, M., Gibson, T.J., Uyar, B. and Dosztanyi, Z.
Science Signaling 10 (470): eaak9982. 14 March 2017

Mutations in disordered regions can cause disease by creating dileucine motifs.
Meyer, K., Kirchner, M., Uyar, B., Cheng, J.Y., Russo, G., Hernandez-Miranda, L.R., Szymborska, A., Zauber, H., Rudolph, I.M., Willnow, T.E., Akalin, A., Haucke, V., Gerhardt, H., Birchmeier, C., Kühn, R., Krauss, M., Diecke, S., Pascual, J.M. and Selbach, M.
Cell 175 (1): 239-253. 20 September 2018

The IκB kinase complex is a regulator of mRNA stability.
Mikuda, N., Kolesnichenko, M., Beaudette, P., Popp, O., Uyar, B., Sun, W., Tufan, A.B., Perder, B., Akalin, A., Chen, W., Mertins, P., Dittmar, G., Hinz, M. and Scheidereit, C.
EMBO Journal 37 (24): e98658. 14 December 2018

Deciphering human ribonucleoprotein regulatory networks.
Mukherjee, N., Wessels, H.H., Lebedeva, S., Sajek, M., Ghanbari, M., Garzia, A., Munteanu, A., Yusuf, D., Farazi, T., Hoell, J.I., Akat, K.M., Akalin, A., Tuschl, T. and Ohler, U.
Nucleic Acids Research 47 (2): 570-581. 25 January 2019

Political knowledge and misinformation in the era of social media: evidence from the 2015 UK election.
Munger, K., Egan, P.J., Nagler, J., Ronen, J. and Tucker, J.
British Journal of Political Science 52 (1): 107 - 127. January 2022

Differential evolution of the 13 Atlantic salmon Hox clusters.
Mungpakdee, S., Seo, H.C., Angotzi, A.R., Dong, X., Akalin, A. and Chourrout, D.
Molecular Biology and Evolution 25 (7): 1333-1343. July 2008

Single-molecule analysis reveals agonist-specific dimer formation of µ-opioid receptors.
Möller, J., Isbilir, A., Sungkaworn, T., Osberg, B., Karathanasis, C., Sunkara, V., Grushevskyi, E.O., Bock, A., Annibale, P., Heilemann, M., Schütte, C. and Lohse, M.J.
Nature Chemical Biology 16 (9): 946-954. September 2020

The conserved histone chaperone LIN-53 is required for normal lifespan and maintenance of muscle integrity in Caenorhabditis elegans.
Müthel, S., Uyar, B., He, M., Krause, A., Vitrinel, B., Bulut, S., Vasiljevic, D., Marchal, I., Kempa, S., Akalin, A. and Tursun, B.
Aging Cell 18 (6): e13012. December 2019

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis.
Nepal, C., Hadzhiev, Y., Previti, C., Haberle, V., Li, N., Takahashi, H., Suzuki, A.M.M., Sheng, Y., Abdelhamid, R.F., Anand, S., Gehrig, J., Akalin, A., Kockx, C.E.M., van der Sloot, A.A.J., van Ijcken, W.F.J., Armant, O., Rastegar, S., Watson, C., Strähle, U., Stupka, E., Carninci, P., Lenhard, B. and Müller, F.
Genome Research 23 (11): 1938-1950. November 2013

NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements.
Pascarella, G., Lazarevic, D., Plessy, C., Bertin, N., Akalin, A., Vlachouli, C., Simone, R., Faulkner, G.J., Zucchelli, S., Kawai, J., Daub, C.O., Hayashizaki, Y., Lenhard, B., Carninci, P. and Gustincich, S.
Frontiers in Cellular Neuroscience 8 : 41. 18 February 2014

Promoter architecture of mouse olfactory receptor genes.
Plessy, C., Pascarella, G., Bertin, N., Akalin, A., Carrieri, C., Vassalli, A., Lazarevic, D., Severin, J., Vlachouli, C., Simone, R., Faulkner, G.J., Kawai, J., Daub, C.O., Zucchelli, S., Hayashizaki, Y., Mombaerts, P., Lenhard, B., Gustincich, S. and Carninci, P.
Genome Research 22 (3): 486-497. March 2012

Cis-regulatory characterization of sequence conservation surrounding the Hox4 genes.
Punnamoottil, B., Herrmann, C., Pascual-Anaya, J., D'Aniello, S., Garcia-Fernandez, J., Akalin, A., Becker, T.S. and Rinkwitz, S.
Developmental Biology 340 (2): 269-282. 15 April 2010

Functional annotation of human long noncoding RNAs via molecular phenotyping.
Ramilowski, J.A., Yip, C.W., Agrawal, S., Chang, J.C., Ciani, Y., Kulakovskiy, I.V., Mendez, M., Ooi, J.L.C., Ouyang, J.F., Parkinson, N., Petri, A., Roos, L., Severin, J., Yasuzawa, K., Abugessaisa, I., Akalin, A., Antonov, I.V., Arner, E., Bonetti, A., Bono, H., Borsari, B., Brombacher, F., Cameron, C.J.F., Cannistraci, C.V., Cardenas, R., Cardon, M., Chang, H., Dostie, J., Ducoli, L., Favorov, A., Fort, A., Garrido, D., Gil, N., Gimenez, J., Guler, R., Handoko, L., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, K., Hayatsu, N., Heutink, P., Hirose, T., Imada, E.L., Itoh, M., Kaczkowski, B., Kanhere, A., Kawabata, E., Kawaji, H., Kawashima, T., Kelly, S.T., Kojima, M., Kondo, N., Koseki, H., Kouno, T., Kratz, A., Kurowska-Stolarska, M., Kwon, A.T.J., Leek, J., Lennartsson, A., Lizio, M., López-Redondo, F., Luginbühl, J., Maeda, S., Makeev, V.J., Marchionni, L., Medvedeva, Y.A., Minoda, A., Müller, F., Muñoz-Aguirre, M., Murata, M., Nishiyori, H., Nitta, K.R., Noguchi, S., Noro, Y., Nurtdinov, R., Okazaki, Y., Orlando, V., Paquette, D., Parr, C.J.C., Rackham, O.J.L., Rizzu, P., Sánchez Martinez, D.F., Sandelin, A., Sanjana, P., Semple, C.A.M., Shibayama, Y., Sivaraman, D.M., Suzuki, T., Szumowski, S.C., Tagami, M., Taylor, M.S., Terao, C., Thodberg, M., Thongjuea, S., Tripathi, V., Ulitsky, I., Verardo, R., Vorontsov, I.E., Yamamoto, C., Young, R.S., Baillie, J.K., Forrest, A.R.R., Guigó, R., Hoffman, M.M., Hon, C.C., Kasukawa, T., Kauppinen, S., Kere, J., Lenhard, B., Schneider, C., Suzuki, H., Yagi, K., de Hoon, M.J.L., Shin, J.W. and Carninci, P.
Genome Research 30 (7): 1060-1072. July 2020

DNA hydroxymethylation profiling reveals that WT1 mutations result in loss of TET2 function in acute myeloid leukemia.
Rampal, R., Akalin, A., Madzo, J., Vasanthakumar, A., Pronier, E., Patel, J., Li, Y., Ahn, J., Abdel-Wahab, O., Shih, A., Lu, C., Ward, P.S., Tsai, J.J., Hricik, T., Tosello, V., Tallman, J.E., Zhao, X., Daniels, D., Dai, Q., Ciminio, L., Aifantis, I., He, C., Fuks, F., Tallman, M.S., Ferrando, A., Nimer, S., Paietta, E., Thompson, C.B., Licht, J.D., Mason, C.E., Godley, L.A., Melnick, A., Figueroa, M.E. and Levine, R.L.
Cell Reports 9 (5): 1841-1855. 11 December 2014

An atlas of combinatorial transcriptional regulation in mouse and man.
Ravasi, T., Suzuki, H., Cannistraci, C.V., Katayama, S., Bajic, V.B., Tan, K., Akalin, A., Schmeier, S., Kanamori-Katayama, M., Bertin, N., Carninci, P., Daub, C.O., Forrest, A.R.R., Gough, J., Grimmond, S., Han, J.H., Hashimoto, T., Hide, W., Hofmann, O., Kamburov, A., Kaur, M., Kawaji, H., Kubosaki, A., Lassmann, T., van Nimwegen, E., MacPherson, C.R., Ogawa, C., Radovanovic, A., Schwartz, A., Teasdale, R.D., Tegner, J., Lenhard, B., Teichmann, S.A., Arakawa, T., Ninomiya, N., Murakami, K., Tagami, M., Fukuda, S., Imamura, K., Kai, C., Ishihara, R., Kitazume, Y., Kawai, J., Hume, D.A., Ideker, T. and Hayashizaki, Y.
Cell 140 (5): 744-752. 5 March 2010

netSmooth: network-smoothing based imputation for single cell RNA-seq.
Ronen, J. and Akalin, A.
F1000Research 7 : 8. 10 July 2018

Evaluation of colorectal cancer subtypes and cell lines using deep learning.
Ronen, J., Hayat, S. and Akalin, A.
Life Science Alliance 2 (6): 201900517. December 2019

Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions.
Royo, J.L., Hidalgo, C., Roncero, Y., Seda, M.A., Akalin, A., Lenhard, B., Casares, F. and Gomez-Skarmeta, J.L.
PLoS ONE 6 (9): e24824. 13 September 2011

Pathogenic mutations of human phosphorylation sites affect protein–protein interactions.
Rrustemi, T., Meyer, K., Roske, Y., Uyar, B., Akalin, A., Imami, K., Ishihama, Y., Daumke, O. and Selbach, M.
Nature Communications 15 (1): 3146. 11 April 2024

CompassDock: Comprehensive accurate assessment approach for deep learning-based molecular docking in inference and fine-tuning.
Sariguen, A., Franke, V., Uyar, B. and Akalin, A.
arXiv : 2406.06841. 1 October 2024

Transcriptional reprogramming by mutated IRF4 in lymphoma.
Schleussner, N., Cauchy, P., Franke, V., Giefing, M., Fornes, O., Vankadari, N., Assi, S.A., Costanza, M., Weniger, M.A., Akalin, A., Anagnostopoulos, I., Bukur, T., Casarotto, M.G., Damm, F., Daumke, O., Edginton-White, B., Gebhardt, J.C.M., Grau, M., Grunwald, S., Hansmann, M.L., Hartmann, S., Huber, L., Kärgel, E., Lusatis, S., Noerenberg, D., Obier, N., Pannicke, U., Fischer, A., Reisser, A., Rosenwald, A., Schwarz, K., Sundararaj, S., Weilemann, A., Winkler, W., Xu, W., Lenz, G., Rajewsky, K., Wasserman, W.W., Cockerill, P.N., Scheidereit, C., Siebert, R., Küppers, R., Grosschedl, R., Janz, M., Bonifer, C. and Mathas, S.
Nature Communications 14 (1): 6947. 7 November 2023

Oncogene inactivation-induced senescence facilitates tumor relapse.
Schmitt, P., Hönig, K., Milojkovic, A., Anders, K., Schröck, E., Sauer, S., Uyar, B., Akalin, A., Martínez-Reyes, I. and Blankenstein, T.
bioRxiv : 2024.07.13.603369. 17 July 2024

Disintegration of the NuRD complex in primary human muscle stem cells in critical illness myopathy.
Schneider, J., Sundaravinayagam, D., Blume, A., Marg, A., Grunwald, S., Metzler, E., Escobar, H., Müthel, S., Wang, H., Wollersheim, T., Weber-Carstens, S., Akalin, A., Di Virgilio, M., Tursun, B. and Spuler, S.
International Journal of Molecular Sciences 24 (3): 2772. 1 February 2023

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages.
Schroder, K., Irvine, K.M., Taylor, M.S., Bokil, N.J., Le Cao, K.A., Masterman, K.A., Labzin, L.I., Semple, C.A., Kapetanovic, R., Fairbairn, L., Akalin, A., Faulkner, G.J., Baillie, J.K., Gongora, M., Daub, C.O., Kawaji, H., McLachlan, G.J., Goldman, N., Grimmond, S.M., Carninci, P., Suzuki, H., Hayashizaki, Y., Lenhard, B., Hume, D.A. and Sweet, M.J.
Proceedings of the National Academy of Sciences of the United States of America 109 (16): E944-E953. 17 April 2012

SARS-CoV-2 infection dynamics revealed by wastewater sequencing analysis and deconvolution.
Schumann, V.F., de Castro Cuadrat, R.R., Wyler, E., Wurmus, R., Deter, A., Quedenau, C., Dohmen, J., Faxel, M., Borodina, T., Blume, A., Freimuth, J., Meixner, M., Grau, J.H., Liere, K., Hackenbeck, T., Zietzschmann, F., Gnirss, R., Böckelmann, U., Uyar, B., Franke, V., Barke, N., Altmüller, J., Rajewsky, N., Landthaler, M. and Akalin, A.
Science of the Total Environment 853 : 158931. 20 December 2022

Crowdsourcing digital health measures to predict Parkinson's disease severity: the Parkinson's Disease Digital Biomarker DREAM Challenge.
Sieberts, S.K., Schaff, J., Duda, M., Pataki, B.Á., Sun, M., Snyder, P., Daneault, J.F., Parisi, F., Costante, G., Rubin, U., Banda, P., Chae, Y., Chaibub Neto, E., Dorsey, E.R., Aydın, Z., Chen, A., Elo, L.L., Espino, C., Glaab, E., Goan, E., Golabchi, F.N., Görmez, Y., Jaakkola, M.K., Jonnagaddala, J., Klén, R., Li, D., McDaniel, C., Perrin, D., Perumal, T.M., Rad, N.M., Rainaldi, E., Sapienza, S., Schwab, P., Shokhirev, N., Venäläinen, M.S., Vergara-Diaz, G., Zhang, Y., Wang, Y., Guan, Y., Brunner, D., Bonato, P., Mangravite, L.M. and Omberg, L.
NPJ Digital Medicine 4 (1): 53. 19 March 2021

Functional interplay of Epstein-Barr virus oncoproteins in a mouse model of B cell lymphomagenesis.
Sommermann, T., Yasuda, T., Ronen, J., Wirtz, T., Weber, T., Sack, U., Caeser, R., Zhang, J., Li, X., Chu, V.T., Jauch, A., Unger, K., Hodson, D.J., Akalin, A. and Rajewsky, K.
Proceedings of the National Academy of Sciences of the United States of America 117 (25): 14421-14432. 23 June 2020

Scalable workflows and reproducible data analysis for genomics.
Strozzi, F., Janssen, R., Wurmus, R., Crusoe, M.R., Githinji, G., Di Tommaso, P., Belhachemi, D., Möller, S., Smant, G., de Ligt, J. and Prins, P.
Methods in Molecular Biology 1910 : 723-745. 2019

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.
Suzuki, H, Forrest, ARR, van Nimwegen, E, Daub, CO, Balwierz, PJ, Irvine, KM, Lassmann, T, Ravasi, T, Hasegawa, Y, de Hoon, MJL, Katayama, S, Schroder, K, Carninci, P, Tomaru, Y, Kanamori-Katayama, M, Kubosaki, A, Akalin, A., Ando, Y, Arner, E, Asada, M, Asahara, H, Bailey, T, Bajic, VB, Bauer, D, Beckhouse, AG, Bertin, N, Björkegren, J, Brombacher, F, Bulger, E, Chalk, AM, Chiba, J, Cloonan, N, Dawe, A, Dostie, J, Engstroem, PG, Essack, M, Faulkner, GJ, Fink, JL, Fredman, D, Fujimori, K, Furuno, M, Gojobori, T, Gough, J, Grimmond, SM, Gustafsson, M, Hashimoto, M, Hashimoto, T, Hatakeyama, M, Heinzel, S, Hide, W, Hofmann, O, Hörnquist, M, Huminiecki, L, Ikeo, K, Imamoto, N, Inoue, S, Inoue, Y, Ishihara, R, Iwayanagi, T, Jacobsen, A, Kaur, M, Kawaji, H, Kerr, MC, Kimura, R, Kimura, S, Kimura, Y, Kitano, H, Koga, H, Kojima, T, Kondo, S, Konno, T, Krogh, A, Kruger, A, Kumar, A, Lenhard, B, Lennartsson, A, Lindow, M, Lizio, M, Macpherson, C, Maeda, N, Maher, CA, Maqungo, M, Mar, J, Matigian, NA, Matsuda, H, Mattick, JS, Meier, S, Miyamoto, S, Miyamoto-Sato, E, Nakabayashi, K, Nakachi, Y, Nakano, M, Nygaard, S, Okayama, T, Okazaki, Y, Okuda-Yabukami, H, Orlando, V, Otomo, J, Pachkov, M, Petrovsky, N, Plessy, C, Quackenbush, J, Radovanovic, A, Rehli, M, Saito, R, Sandelin, A, Schmeier, S, Schönbach, C, Schwartz, AS, Semple, CA, Sera, M, Severin, J, Shirahige, K, Simons, C, St Laurent, G, Suzuki, M, Suzuki, T, Sweet, MJ, Taft, RJ, Takeda, S, Takenaka, Y, Tan, K, Taylor, MS, Teasdale, RD, Tegnér, J, Teichmann, S, Valen, E, Wahlestedt, C, Waki, K, Waterhouse, A, Wells, CA, Winther, O, Wu, L, Yamaguchi, K, Yanagawa, H, Yasuda, J, Zavolan, M, Hume, DA, Arakawa, T, Fukuda, S, Imamura, K, Kai, C, Kaiho, A, Kawashima, T, Kawazu, C, Kitazume, Y, Kojima, M, Miura, H, Murakami, K, Murata, M, Ninomiya, N, Nishiyori, H, Noma, S, Ogawa, C, Sano, T, Simon, C, Tagami, M, Takahashi, Y, Kawai, J and Hayashizaki, Y
Nature Genetics 41 (5): 553-562. May 2009

A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons.
Szabó, D., Franke, V., Bianco, S., Batiuk, M.Y., Paul, E.J., Kukalev, A., Pfisterer, U.G., Irastorza-Azcarate, I., Chiariello, A.M., Demharter, S., Zea-Redondo, L., Lopez-Atalaya, J.P., Nicodemi, M., Akalin, A., Khodosevich, K., Ungless, M.A., Winick-Ng, W. and Pombo, A.
bioRxiv : 2024.05.10.593308. 12 May 2024

DNA virus infections shape transposable elements activity in vitro and in vivo.
Tan, J., Franke, V., Neugebauer, E., Lagisquet, J., Kuderna, A.K., Walter, S., Landthaler, M., Ensser, A., Stamminger, T., Gramberg, T., Akalin, A., Wyler, E. and Full, F.
bioRxiv : 2024.04.18.589901. 19 April 2024

Flexynesis: A deep learning framework for bulk multi-omics data integration for precision oncology and beyond.
Uyar, B., Savchyn, T., Wurmus, R., Sarigun, A., Shaik, M.M., Franke, V. and Akalin, A.
bioRxiv : 2024.07.16.603606. 18 July 2024

Single-cell analyses of aging, inflammation and senescence.
Uyar, B., Palmer, D., Kowald, A., Escobar, H.M., Barrantes, I., Möller, S., Akalin, A. and Fuellen, G.
Ageing Research Reviews 64 : 101156. December 2020

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.
Uyar, B., Yusuf, D., Wurmus, R., Rajewsky, N., Ohler, U. and Akalin, A.
Nucleic Acids Research 45 (10): e91. 2 June 2017

The association between salt taste perception, mediterranean diet and metabolic syndrome: a cross-sectional study.
Veček, N.N., Mucalo, L., Dragun, R., Miličević, T., Pribisalić, A., Patarčić, I., Hayward, C., Polašek, O. and Kolčić, I.
Nutrients 12 (4): 1164. April 2020

Herpesviral induction of germline transcription factor DUX4 is critical for viral gene expression.
Walter, S., Franke, V., Drayman, N., Wyler, E., Tay, S., Landthaler, M., Akalin, A., Ensser, A. and Full, F.
bioRxiv : 2021.03.24.436599. 24 March 2021

Global identification of functional microRNA-mRNA interactions in Drosophila.
Wessels, H.H., Lebedeva, S., Hirsekorn, A., Wurmus, R., Akalin, A., Mukherjee, N. and Ohler, U.
Nature Communications 10 (1): 1626. 9 April 2019

Cell-type specialization is encoded by specific chromatin topologies.
Winick-Ng, W., Kukalev, A., Harabula, I., Zea-Redondo, L., Szabó, D., Meijer, M., Serebreni, L., Zhang, Y., Bianco, S., Chiariello, A.M., Irastorza-Azcarate, I., Thieme, C.J., Sparks, T.M., Carvalho, S., Fiorillo, L., Musella, F., Irani, E., Triglia, E.T., Kolodziejczyk, A.A., Abentung, A., Apostolova, G., Paul, E.J., Franke, V., Kempfer, R., Akalin, A., Teichmann, S.A., Dechant, G., Ungless, M.A., Nicodemi, M., Welch, L., Castelo-Branco, G. and Pombo, A.
Nature 599 (7886): 684-691. 25 November 2021

HOT or not: examining the basis of high-occupancy target regions.
Wreczycka, K., Franke, V., Uyar, B., Wurmus, R., Bulut, S., Tursun, B. and Akalin, A.
Nucleic Acids Research : gkz460. 20 June 2019

Strategies for analyzing bisulfite sequencing data.
Wreczycka, K., Gosdschan, A., Yusuf, D., Grüning, B., Assenov, Y. and Akalin, A.
Journal of Biotechnology 261 : 105-115. 10 November 2017

PiGx: reproducible genomics analysis pipelines with GNU Guix.
Wurmus, R., Uyar, B., Osberg, B., Franke, V., Gosdschan, A., Wreczycka, K., Ronen, J. and Akalin, A.
GigaScience 7 (12): giy123. 1 December 2018

Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program.
Wyler, E., Franke, V., Menegatti, J., Kocks, C., Boltengagen, A., Praktiknjo, S., Walch-Rückheim, B., Bosse, J., Rajewsky, N., Grässer, F., Akalin, A. and Landthaler, M.
Nature Communications 10 (1): 4878. 25 October 2019

Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection.
Wyler, E., Menegatti, J., Franke, V., Kocks, C., Boltengagen, A., Hennig, T., Theil, K., Rutkowski, A., Ferrai, C., Baer, L., Kermas, L., Friedel, C., Rajewsky, N., Akalin, A., Dölken, L., Grässer, F. and Landthaler, M.
Genome Biology 18 (1): 209. 31 October 2017

Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy.
Wyler, E., Mösbauer, K., Franke, V., Diag, A., Gottula, L.T., Arsiè, R., Klironomos, F., Koppstein, D., Hönzke, K., Ayoub, S., Buccitelli, C., Hoffmann, K., Richter, A., Legnini, I., Ivanov, A., Mari, T., Del Giudice, S., Papies, J., Praktiknjo, S., Meyer, T.F., Müller, M.A., Niemeyer, D., Hocke, A., Selbach, M., Akalin, A., Rajewsky, N., Drosten, C. and Landthaler, M.
iScience 24 (3): 102151. 19 March 2021

RNA localization is a key determinant of neurite-enriched proteome.
Zappulo, A., van den Bruck, D., Ciolli Mattioli, C., Franke, V., Imami, K., McShane, E., Moreno-Estelles, M., Calviello, L., Filipchyk, A., Peguero-Sanchez, E., Müller, T., Woehler, A., Birchmeier, C., Merino, E., Rajewsky, N., Ohler, U., Mazzoni, E.O., Selbach, M., Akalin, A. and Chekulaeva, M.
Nature Communications 8 (1): 583. 19 September 2017

Autocrine LTA signaling drives NF-κB and JAK-STAT activity and myeloid gene expression in Hodgkin lymphoma.
von Hoff, L., Kärgel, E., Franke, V., McShane, E., Schulz-Beiss, K.W., Patone, G., Schleussner, N., Kolesnichenko, M., Hübner, N., Daumke, O., Selbach, M., Akalin, A., Mathas, S. and Scheidereit, C.
Blood 133 (13): 1489-1494. 28 March 2019

Altmüller, Janine (BIMSB/BIH)

Mapping the human genetic architecture of COVID-19.

Nature 600 (7889): 472-477. December 2021

Fine mapping and chromosome walking towards the Ror1 locus in barley (Hordeum vulgare L.).
Acevedo-Garcia, J., Collins, N.C., Ahmadinejad, N., Ma, L., Houben, A., Bednarek, P., Benjdia, M., Freialdenhoven, A., Altmüller, J., Nürnberg, P., Reinhardt, R., Schulze-Lefert, P. and Panstruga, R.
Theoretical and Applied Genetics 126 (12): 2969-2982. December 2013

A mechanistic classification of clinical phenotypes in neuroblastoma.
Ackermann, S., Cartolano, M., Hero, B., Welte, A., Kahlert, Y., Roderwieser, A., Bartenhagen, C., Walter, E., Gecht, J., Kerschke, L., Volland, R., Menon, R., Heuckmann, J.M., Gartlgruber, M., Hartlieb, S., Henrich, K.O., Okonechnikov, K., Altmüller, J., Nürnberg, P., Lefever, S., de Wilde, B., Sand, F., Ikram, F., Rosswog, C., Fischer, J., Theissen, J., Hertwig, F., Singhi, A.D., Simon, T., Vogel, W., Perner, S., Krug, B., Schmidt, M., Rahmann, S., Achter, V., Lang, U., Vokuhl, C., Ortmann, M., Büttner, R., Eggert, A., Speleman, F., O'Sullivan, R.J., Thomas, R.K., Berthold, F., Vandesompele, J., Schramm, A., Westermann, F., Schulte, J.H., Peifer, M. and Fischer, M.
Science 362 (6419): 1165-1170. 7 December 2018

Exome sequencing identifies biallelic MSH3 germline mutations as a recessive subtype of colorectal adenomatous polyposis.
Adam, R., Spier, I., Zhao, B., Kloth, M., Marquez, J., Hinrichsen, I., Kirfel, J., Tafazzoli, A., Horpaopan, S., Uhlhaas, S., Stienen, D., Friedrichs, N., Altmüller, J., Laner, A., Holzapfel, S., Peters, S., Kayser, K., Thiele, H., Holinski-Feder, E., Marra, G., Kristiansen, G., Nöthen, M.M., Büttner, R., Möslein, G., Betz, R.C., Brieger, A., Lifton, R.P. and Aretz, S.
American Journal of Human Genetics 99 (2): 337-51. 4 August 2016

Genetic heterogeneity in Pakistani microcephaly families revisited.
Ahmad, I., Baig, S.M., Abdulkareem, A.R., Hussain, M.S., Sur, I., Toliat, M.R., Nürnberg, G., Dalibor, N., Moawia, A., Waseem, S.S., Asif, M., Nagra, H., Sher, M., Khan, M.M.A., Hassan, I., Rehman, S.U., Thiele, H., Altmüller, J., Noegel, A.A. and Nürnberg, P.
Clinical Genetics 92 (1): 62-68. July 2017

A novel MAP3K20 mutation causing centronuclear myopathy-6 with fiber-type disproportion in a Pakistani family.
Ahmad, I., Khan, A., Noor Ul Ayan, H., Budde, B., Altmüller, J., Korejo, A.A., Nürnberg, G., Thiele, H., Tariq, M., Nürnberg, P. and Erdmann, J.
Journal of Human Genetics 11 October 2022

The interleukin-11 receptor variant p.W307R results in craniosynostosis in humans.
Ahmad, I., Lokau, J., Kespohl, B., Malik, N.A., Baig, S.M., Hartig, R., Behme, D., Schwab, R., Altmüller, J., Jameel, M., Mucha, S., Thiele, H., Tariq, M., Nürnberg, P., Erdmann, J. and Garbers, C.
Scientific Reports 13 (1): 13479. 18 August 2023

Late diagnosis of a truncating WISP3 mutation entails a severe phenotype of progressive pseudorheumatoid dysplasia.
Alawbathani, S., Kawalia, A., Karakaya, M., Altmüller, J., Nürnberg, P. and Cirak, S.
Cold Spring Harbor Molecular Case Studies 4 (1): a002139. 19 December 2017

Integrative and comparative genomic analyses identify clinically relevant pulmonary carcinoid groups and unveil the supra-carcinoids.
Alcala, N., Leblay, N., Gabriel, A.A.G., Mangiante, L., Hervas, D., Giffon, T., Sertier, A.S., Ferrari, A., Derks, J., Ghantous, A., Delhomme, T.M., Chabrier, A., Cuenin, C., Abedi-Ardekani, B., Boland, A., Olaso, R., Meyer, V., Altmuller, J., Le Calvez-Kelm, F., Durand, G., Voegele, C., Boyault, S., Moonen, L., Lemaitre, N., Lorimier, P., Toffart, A.C., Soltermann, A., Clement, J.H., Saenger, J., Field, J.K., Brevet, M., Blanc-Fournier, C., Galateau-Salle, F., Le Stang, N., Russell, P.A., Wright, G., Sozzi, G., Pastorino, U., Lacomme, S., Vignaud, J.M., Hofman, V., Hofman, P., Brustugun, O.T., Lund-Iversen, M., Thomas de Montpreville, V., Muscarella, L.A., Graziano, P., Popper, H., Stojsic, J., Deleuze, J.F., Herceg, Z., Viari, A., Nuernberg, P., Pelosi, G., Dingemans, A.M.C., Milione, M., Roz, L., Brcic, L., Volante, M., Papotti, M.G., Caux, C., Sandoval, J., Hernandez-Vargas, H., Brambilla, E., Speel, E.J.M., Girard, N., Lantuejoul, S., McKay, J.D., Foll, M. and Fernandez-Cuesta, L.
Nature Communications 10 (1): 3407. 20 August 2019

Single-nucleus and spatial transcriptome reveal adrenal homeostasis in normal and tumoural adrenal glands.
Altieri, B., Secener, A.K., Sai, S., Fischer, C., Sbiera, S., Arampatzi, P., Kircher, S., Herterich, S., Landwehr, L.S., Vitcetz, S.N., Braeuning, C., Fassnacht, M., Ronchi, C.L. and Sauer, S.
Clinical and Translational Medicine 14 (8): e1798. August 2024

Genomewide scans of complex human diseases: true linkage is hard to find.
Altmüller, J., Palmer, L.J., Fischer, G., Scherb, H. and Wjst, M.
American Journal of Human Genetics 69 (5): 936-50. November 2001

Enrichment of target sequences for next-generation sequencing applications in research and diagnostics.
Altmüller, J., Budde, B.S. and Nürnberg, P.
Biological Chemistry 395 (2): 231-237. 1 February 2014

Mutational profiling in the peripheral blood leukocytes of patients with systemic mast cell activation syndrome using next-generation sequencing.
Altmüller, J., Haenisch, B., Kawalia, A., Menzen, M., Nöthen, M.M., Fier, H. and Molderings, G.J.
Immunogenetics 69 (6): 359-369. June 2017

A systematic comparison of two new releases of exome sequencing products: the aim of use determines the choice of product.
Altmüller, J., Motameny, S., Becker, C., Thiele, H., Chatterjee, S., Wollnik, B. and Nürnberg, P.
Biological Chemistry 397 (8): 791-801. 1 August 2016

Mutations in AP3D1 associated with immunodeficiency and seizures define a new type of Hermansky-Pudlak syndrome.
Ammann, S., Schulz, A., Krägeloh-Mann, I., Dieckmann, N.M.G., Niethammer, K., Fuchs, S., Eckl, K.M., Plank, R., Werner, R., Altmüller, J., Thiele, H., Nürnberg, P., Bank, J., Strauss, A., von Bernuth, H., Zur Stadt, U., Grieve, S., Griffiths, G.M., Lehmberg, K., Hennies, H.C. and Ehl, S.
Blood 127 (8): 997-1006. 25 February 2016

De novo whole genome assembly of the Roborovski dwarf hamster (Phodopus roborovskii) genome, an animal model for severe/critical COVID-19.
Andreotti, S., Altmüller, J., Quedenau, C., Borodina, T., Nouailles, G., Teixeira Alves, L.G., Landthaler, M., Bieniara, M., Trimpert, J. and Wyler, E.
Genome Biology and Evolution 14 (7): evac100. July 2022

Floral induction in Arabidopsis by FLOWERING LOCUS T requires direct repression of BLADE-ON-PETIOLE genes by the homeodomain protein PENNYWISE.
Andrés, F., Romera-Branchat, M., Martínez-Gallegos, R., Patel, V., Schneeberger, K., Jang, S., Altmüller, J., Nürnberg, P. and Coupland, G.
Plant Physiology 169 (3): 2187-2199. November 2015

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients.
Aschenbrenner, A.C., Mouktaroudi, M., Krämer, B., Oestreich, M., Antonakos, N., Nuesch-Germano, M., Gkizeli, K., Bonaguro, L., Reusch, N., Baßler, K., Saridaki, M., Knoll, R., Pecht, T., Kapellos, T.S., Doulou, S., Kröger, C., Herbert, M., Holsten, L., Horne, A., Gemünd, I.D., Rovina, N., Agrawal, S., Dahm, K., van Uelft, M., Drews, A., Lenkeit, L., Bruse, N., Gerretsen, J., Gierlich, J., Becker, M., Händler, K., Kraut, M., Theis, H., Mengiste, S., Domenico, E., Schulte-Schrepping, J., Seep, L., Raabe, J., Hoffmeister, C., ToVinh, M., Keitel, V., Rieke, G., Talevi, V., Skowasch, D., Aziz, N.A., Pickkers, P., van de Veerdonk, F.L., Netea, M.G., Schultze, J.L., Kox, M., Breteler, M.M.B., Nattermann, J., Koutsoukou, A., Giamarellos-Bourboulis, E.J. and Ulas, T.
Genome Medicine 13 (1): 7. 13 January 2021

Attenuated BMP1 function compromises osteogenesis, leading to bone fragility in humans and zebrafish.
Asharani, P.V., Keupp, K., Semler, O., Wang, W., Li, Y., Thiele, H., Yigit, G., Pohl, E., Becker, J., Frommolt, P., Sonntag, C., Altmüller, J., Zimmermann, K., Greenspan, D.S., Akarsu, N.A., Netzer, C., Schönau, E., Wirth, R., Hammerschmidt, M., Nürnberg, P., Wollnik, B. and Carney, T.J.
American Journal of Human Genetics 90 (4): 661-74. 6 April 2012

De novo variants of CSNK2B cause a new intellectual disability-craniodigital syndrome by disrupting the canonical Wnt signaling pathway.
Asif, M., Kaygusuz, E., Shinawi, M., Nickelsen, A., Hsieh, T.C., Wagle, P., Budde, B., Hochscherf, J., Abdullah, U., Höning, S., Nienberg, C., Lindenblatt, D., Noegel, A.A., Altmüller, J., Thiele, H., Motameny, S., Fleischer, N., Segal, I., Pais, L., Tinschert, S., Samra, N.G., Savatt, J.M., Rudy, N.L., De Luca, C., Fortugno, P., White, S.M., Krawitz, P., Hurst, A.C.E., Niefind, K., Jose, J., Brancati, F., Nürnberg, P. and Hussain, M.S.
Human Genetics and Genomics Advances 3 (3): 100111. 14 July 2022

A novel missense variant of SCN4A co-segregates with congenital essential tremor in a consanguineous Kurdish family.
Asif, M., Mocanu, I.D., Abdullah, U., Höhne, W., Altmüller, J., Makhdoom, E.U.H., Thiele, H., Baig, S.M., Nürnberg, P., Graul-Neumann, L. and Hussain, M.S.
American Journal of Medical Genetics A 188 (4): 1251-1258. April 2022

Post-COVID syndrome in non-hospitalised patients with COVID-19: a longitudinal prospective cohort study.
Augustin, M., Schommers, P., Stecher, M., Dewald, F., Gieselmann, L., Gruell, H., Horn, C., Vanshylla, K., Cristanziano, V.D., Osebold, L., Roventa, M., Riaz, T., Tschernoster, N., Altmueller, J., Rose, L., Salomon, S., Priesner, V., Luers, J.C., Albus, C., Rosenkranz, S., Gathof, B., Fätkenheuer, G., Hallek, M., Klein, F., Suárez, I. and Lehmann, C.
The Lancet Regional Health - Europe 6 : 100122. July 2021

Expanding the spectrum of EEF1D neurodevelopmental disorders: biallelic variants in the guanine exchange domain.
Averdunk, L., Al-Thihli, K., Surowy, H., Lüdecke, H.J., Drechsler, M., Yigit, G., Smorag, L., Hallak, B.A., Li, Y., Altmüller, J., Guthoff, T., Wallot, M., Nürnberg, P., Wollnik, B., Abou Jamra, R., Al-Maawali, A. and Wieczorek, D.
Clinical Genetics 103 (4): 484-491. April 2023

A microRNA screen reveals that elevated hepatic ectodysplasin A expression contributes to obesity-induced insulin resistance in skeletal muscle.
Awazawa, M., Gabel, P., Tsaousidou, E., Nolte, H., Krüger, M., Schmitz, J., Ackermann, P.J., Brandt, C., Altmüller, J., Motameny, S., Wunderlich, F.T., Kornfeld, J.W., Blüher, M. and Brüning, J.C.
Nature Medicine 23 (12): 1466-1473. 1 December 2017

A homozygous nonsense mutation identified in COL7A1 in a family with autosomal recessive dystrophic epidermolysis bullosa.
Ayub, M., Xiong, X., Anwer, S., Altmüller, J., Naeem, M., Hassan, N., Khan, K., Motameny, S., Khaliq, S., Rehman, F.U., Uddin, S.A., Wali, A., Betz, R. and Basit, S.
Journal of medicine and life 17 (9): 892-896. 9 September 2024

In situ Patch-seq analysis of microglia reveals a lack of stress genes as found in FACS-isolated microglia.
Bakina, O., Conrad, T., Mitic, N., Vidal, R.O., Obrusnik, T., Sai, S., Nolte, C., Semtner, M. and Kettenmann, H.
PLoS ONE 19 (7): e0302376. 11 July 2024

Ultra-rapid emergency genomic diagnosis of Donahue syndrome in a preterm infant within 17 hours.
Bamborschke, D., Özdemir, Ö., Kreutzer, M., Motameny, S., Thiele, H., Kribs, A., Dötsch, J., Altmüller, J., Nürnberg, P. and Cirak, S.
American Journal of Medical Genetics A 185 (1): 90-96. January 2021

Three-layered proteomic characterization of a novel ACTN4 mutation unravels its pathogenic potential in FSGS.
Bartram, M.P., Habbig, S., Pahmeyer, C., Höhne, M., Weber, L.T., Thiele, H., Altmüller, J., Kottoor, N., Wenzel, A., Krueger, M., Schermer, B., Benzing, T., Rinschen, M.M. and Beck, B.B.
Human Molecular Genetics 25 (6): 1152-1164. 15 March 2016

Deficiency for the ubiquitin ligase UBE3B in a blepharophimosis-ptosis-intellectual-disability syndrome.
Basel-Vanagaite, L., Dallapiccola, B., Ramirez-Solis, R., Segref, A., Thiele, H., Edwards, A., Arends, M.J., Miró, X., White, J.K., Désir, J., Abramowicz, M., Dentici, M.L., Lepri, F., Hofmann, K., Har-Zahav, A., Ryder, E., Karp, N.A., Estabel, J., Gerdin, A.K.B., Podrini, C., Ingham, N.J., Altmüller, J., Nürnberg, G., Frommolt, P., Abdelhak, S., Pasmanik-Chor, M., Konen, O., Kelley, R.I., Shohat, M., Nürnberg, P., Flint, J., Steel, K.P., Hoppe, T., Kubisch, C., Adams, D.J. and Borck, G.
American Journal of Human Genetics 91 (6): 998-1010. 7 December 2012

Pathogenicity of POFUT1 in Dowling-Degos disease: additional mutations and clinical overlap with reticulate acropigmentation of kitamura.
Basmanav, F.B., Fritz, G., Lestringant, G.G., Pachat, D., Hoffjan, S., Fischer, J., Wehner, M., Wolf, S., Thiele, H., Altmüller, J., Pulimood, S.A., Rütten, A., Kruse, R., Hanneken, S., Frank, J., Danda, S., Bygum, A. and Betz, R.C.
Journal of Investigative Dermatology 135 (2): 615-618. February 2015

Mutations in POGLUT1, encoding protein o-glucosyltransferase 1, cause autosomal-dominant Dowling-Degos disease.
Basmanav, F.B., Oprisoreanu, A.M., Pasternack, S.M., Thiele, H., Fritz, G., Wenzel, J., Größer, L., Wehner, M., Wolf, S., Fagerberg, C., Bygum, A., Altmüller, J., Rütten, A., Parmentier, L., El Shabrawi-Caelen, L., Hafner, C., Nürnberg, P., Kruse, R., Schoch, S., Hanneken, S. and Betz, R.C.
American Journal of Human Genetics 94 (1): 135-143. 2 January 2014

Gain-of-function mutations in KCNN3 encoding the small-conductance Ca(2+)-activated K(+) channel SK3 cause Zimmermann-Laband syndrome.
Bauer, C.K., Schneeberger, P.E., Kortüm, F., Altmüller, J., Santos-Simarro, F., Baker, L., Keller-Ramey, J., White, S.M., Campeau, P.M., Gripp, K.W. and Kutsche, K.
American Journal of Human Genetics 104 (6): 1139-1157. 6 June 2019

Mutation of POC1B in a severe syndromic retinal ciliopathy.
Beck, B.B., Phillips, J.B., Bartram, M.P., Wegner, J., Thoenes, M., Pannes, A., Sampson, J., Heller, R., Göbel, H., Koerber, F., Neugebauer, A., Hedergott, A., Nürnberg, G., Nürnberg, P., Thiele, H., Altmüller, J., Toliat, M.R., Staubach, S., Boycott, K.M., Valente, E.M., Janecke, A.R., Eisenberger, T., Bergmann, C., Tebbe, L., Wang, Y., Wu, Y., Fry, A.M., Westerfield, M., Wolfrum, U. and Bolz, H.J.
Human Mutation 35 (10): 1153-1162. October 2014

Deep ion sequencing of amplicon adapter ligated libraries: a novel tool in molecular diagnostics of formalin fixed and paraffin embedded tissues.
Becker, K., Vollbrecht, C., Koitzsch, U., Koenig, K., Fassunke, J., Huss, S., Nuernberg, P., Heukamp, L.C., Buettner, R., Odenthal, M., Altmueller, J. and Merkelbach-Bruse, S.
Journal of Clinical Pathology 66 (9): 803-806. 1 September 2013

Genetic information from discordant sibling pairs points to ESRP2 as a candidate trans-acting regulator of the CF modifier gene SCNN1B.
Becker, T., Pich, A., Tamm, S., Hedtfeld, S., Ibrahim, M., Altmüller, J., Dalibor, N., Toliat, M.R., Janciauskiene, S., Tümmler, B. and Stanke, F.
Scientific Reports 10 (1): 22447. 31 December 2020

Inhibition of TFG function causes hereditary axon degeneration by impairing endoplasmic reticulum structure.
Beetz, C., Johnson, A., Schuh, A.L., Thakur, S., Varga, R.E., Fothergill, T., Hertel, N., Bomba-Warczak, E., Thiele, H., Nürnberg, G., Altmüller, J., Saxena, R., Chapman, E.R., Dent, E.W., Nürnberg, P. and Audhya, A.
Proceedings of the National Academy of Sciences of the United States of America 110 (13): 5091-5096. 26 March 2013

Apoptotic cleavage of DNA in human lymphocyte chromatin shows high sequence specificity.
Bettecken, T., Frenkel, Z.M., Altmüller, J., Nürnberg, P. and Trifonov, E.N.
Journal of Biomolecular Structure & Dynamics 30 (2): 211-6. 12 June 2012

Exome-wide analysis of mutational burden in patients with typical and atypical Rolandic epilepsy.
Bobbili, D.R., Lal, D., May, P., Reinthaler, E.M., Jabbari, K., Thiele, H., Nothnagel, M., Jurkowski, W., Feucht, M., Nürnberg, P., Lerche, H., Zimprich, F., Krause, R., Neubauer, B.A., Reinthaler, E.M., Zimprich, F., Feucht, M., Steinböck, H., Neophytou, B., Geldner, J., Gruber-Sedlmayr, U., Haberlandt, E., Ronen, G.M., Altmüller, J., Lal, D., Nürnberg, P., Sander, T., Thiele, H., Krause, R., May, P., Balling, R., Lerche, H. and Neubauer, B.A.
European Journal of Human Genetics 26 (2): 258-264. February 2018

Exon junction complexes suppress spurious splice sites to safeguard transcriptome integrity.
Boehm, V., Britto-Borges, T., Steckelberg, A.L., Singh, K.K., Gerbracht, J.V., Gueney, E., Blazquez, L., Altmüller, J., Dieterich, C. and Gehring, N.H.
Molecular Cell 72 (3): 482-495. 1 November 2018

SMG5-SMG7 authorize nonsense-mediated mRNA decay by enabling SMG6 endonucleolytic activity.
Boehm, V., Kueckelmann, S., Gerbracht, J.V., Kallabis, S., Britto-Borges, T., Altmüller, J., Krüger, M., Dieterich, C. and Gehring, N.H.
Nature Communications 12 (1): 3965. 25 June 2021

A comparison of metabolic labeling and statistical methods to infer genome-wide dynamics of RNA turnover.
Boileau, E., Altmüller, J., Naarmann-de Vries, I.S. and Dieterich, C.
Briefings in Bioinformatics 22 (6): bbab219. November 2021

Full-length spatial transcriptomics reveals the unexplored isoform diversity of the myocardium post-MI.
Boileau, E., Li, X., Naarmann-de Vries, I.S., Becker, C., Casper, R., Altmüller, J., Leuschner, F. and Dieterich, C.
Frontiers in Genetics 13 : 912572. 22 July 2022

eIF2γ mutation that disrupts eIF2 complex integrity links intellectual disability to impaired translation initiation.
Borck, G., Shin, B.S., Stiller, B., Mimouni-Bloch, A., Thiele, H., Kim, J.R., Thakur, M., Skinner, C., Aschenbach, L., Smirin-Yosef, P., Har-Zahav, A., Nürnberg, G., Altmüller, J., Frommolt, P., Hofmann, K., Konen, O., Nürnberg, P., Munnich, A., Schwartz, C.E., Gothelf, D., Colleaux, L., Dever, T.E., Kubisch, C. and Basel-Vanagaite, L.
Molecular Cell 48 (4): 641-6. 30 November 2012

BRF1 mutations alter RNA polymerase III–dependent transcription and cause neurodevelopmental anomalies.
Borck, G., Hög, F., Dentici, M.L., Tan, P.L., Sowada, N., Medeira, A., Gueneau, L., Thiele, H., Kousi, M., Lepri, F., Wenzeck, L., Blumenthal, I., Radicioni, A., Schwarzenberg, T.L., Mandriani, B., Fischetto, R., Morris-Rosendahl, D.J., Altmüller, J., Reymond, A., Nürnberg, P., Merla, G., Dallapiccola, B., Katsanis, N., Cramer, P. and Kubisch, C.
Genome Research 25 (2): 155-166. February 2015

Label-free protein-RNA interactome analysis identifies khsrp signaling downstream of the p38/Mk2 kinase complex as a critical modulator of cell cycle progression.
Boucas, J., Fritz, C., Schmitt, A., Riabinska, A., Thelen, L., Peifer, M., Leeser, U., Nuernberg, P., Altmüller, J., Gaestel, M., Dieterich, C. and Reinhardt, H.C.
PLoS ONE 10 (5): e0125745. 2015

Heterozygous HNRNPU variants cause early onset epilepsy and severe intellectual disability.
Bramswig, N.C., Lüdecke, H.J., Hamdan, F.F., Altmüller, J., Beleggia, F., Elcioglu, N.H., Freyer, C., Gerkes, E.H., Demirkol, Y.K., Knupp, K.G., Kuechler, A., Li, Y., Lowenstein, D.H., Michaud, J.L., Park, K., Stegmann, A.P.A., Veenstra-Knol, H.E., Wieland, T., Wollnik, B., Engels, H., Strom, T.M., Kleefstra, T. and Wieczorek, D.
Human Genetics 136 (7): 821-834. July 2017

Mutations in multiple components of the nuclear pore complex cause nephrotic syndrome.
Braun, D.A., Lovric, S., Schapiro, D., Schneider, R., Marquez, J., Asif, M., Hussain, M.S., Daga, A., Widmeier, E., Rao, J., Ashraf, S., Tan, W., Lusk, C.P., Kolb, A., Jobst-Schwan, T., Schmidt, J.M., Hoogstraten, C.A., Eddy, K., Kitzler, T.M., Shril, S., Moawia, A., Schrage, K., Khayyat, A.I.A., Lawson, J.A., Gee, H.Y., Warejko, J.K., Hermle, T., Majmundar, A.J., Hugo, H., Budde, B., Motameny, S., Altmüller, J., Noegel, A. A., Fathy, H.M., Gale, D.P., Waseem, S.S., Khan, A., Kerecuk, L., Hashmi, S., Mohebbi, N., Ettenger, R., Serdaroğlu, E., Alhasan, K.A., Hashem, M., Goncalves, S., Ariceta, G., Ubetagoyena, M., Antonin, W., Baig, S.M., Alkuraya, F.S., Shen, Q., Xu, H., Antignac, C., Lifton, R.P., Mane, S., Nürnberg, P., Khokha, M.K. and Hildebrandt, F.
Journal of Clinical Investigation 128 (10): 4313-4328. 1 October 2018

Micro-RNA networks in T-cell prolymphocytic leukemia reflect T-cell activation and shape DNA damage response and survival pathways.
Braun, T., Glass, M., Wahnschaffe, L., Otte, M., Mayer, P., Franitza, M., Altmüller, J., Hallek, M., Hüttelmaier, S., Schrader, A. and Herling, M.
Haematologica 107 (1): 187-200. January 2022

Noncanonical function of AGO2 augments T-cell receptor signaling in T-cell prolymphocytic leukemia.
Braun, T., Stachelscheid, J., Bley, N., Oberbeck, S., Otte, M., Müller, T.A., Wahnschaffe, L., Glaß, M., Ommer, K., Franitza, M., Gathof, B., Altmüller, J., Hallek, M., Auguin, D., Hüttelmaier, S., Schrader, A. and Herling, M.
Cancer Research 82 (9): 1818-1831. 1 May 2022

Claudin-10a deficiency shifts proximal tubular Cl(-) permeability to cation selectivity via claudin-2 redistribution.
Breiderhoff, T., Himmerkus, N., Meoli, L., Fromm, A., Sewerin, S., Kriuchkova, N., Nagel, O., Ladilov, Y., Krug, S., Quintanova, C., Stumpp, M., Garbe-Schönberg, D., Westernströer, U., Merkel, C., Brinkhus, M., Altmüller, J., Schweiger, M., Mueller, D., Mutig, K., Morawski, M., Halbritter, J., Milatz, S., Bleich, M. and Günzel, D.
Journal of the American Society of Nephrology 33 (4): 699-717. April 2022

Mutations in plasmalemma vesicle-associated protein cause severe syndromic protein-losing enteropathy.
Broekaert, I.J., Becker, K., Gottschalk, I., Körber, F., Dötsch, J., Thiele, H., Altmüller, J., Nürnberg, P., Hünseler, C. and Cirak, S.
Journal of Medical Genetics 55 (9): 637-640. September 2018

Coregulation of gene expression by White collar 1 and phytochrome in Ustilago maydis.
Brych, A., Haas, F.B., Parzefall, K., Panzer, S., Schermuly, J., Altmüller, J., Engelsdorf, T., Terpitz, U., Rensing, S.A., Kiontke, S. and Batschauer, A.
Fungal Genetics and Biology 152 : 103570. July 2021

Mitochondrial respiratory chain function promotes extracellular matrix integrity in cartilage.
Bubb, K., Holzer, T., Nolte, J.L., Krüger, M., Wilson, R., Schlötzer-Schrehardt, U., Brinckmann, J., Altmüller, J., Aszodi, A., Fleischhauer, L., Clausen-Schaumann, H., Probst, K. and Brachvogel, B.
Journal of Biological Chemistry 297 (4): 101224. October 2021

Comprehensive molecular analysis of 61 Egyptian families with hereditary nonsyndromic hearing loss.
Budde, B.S., Aly, M.A., Mohamed, M.R., Breß, A., Altmüller, J., Motameny, S., Kawalia, A., Thiele, H., Konrad, K., Becker, C., Toliat, M.R., Nürnberg, G., Sayed, E.A.F., Mohamed, E.S., Pfister, M. and Nürnberg, P.
Clinical Genetics 98 (1): 32-42. July 2020

Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA.
Bundschuh, R., Altmüller, J., Becker, C., Nürnberg, P. and Gott, J.M.
Nucleic Acids Research 39 (14): 6044-55. 1 August 2011

Mutation-induced LZTR1 polymerization provokes cardiac pathology in recessive Noonan syndrome.
Busley, A.V., Gutiérrez-Gutiérrez, Ó., Hammer, E., Koitka, F., Mirzaiebadizi, A., Steinegger, M., Pape, C., Böhmer, L., Schroeder, H., Kleinsorge, M., Engler, M., Cirstea, I.C., Gremer, L., Willbold, D., Altmüller, J., Marbach, F., Hasenfuss, G., Zimmermann, W.H., Ahmadian, M.R., Wollnik, B. and Cyganek, L.
Cell Reports 43 (7): 114448. 23 July 2024

WARS1 and SARS1: two tRNA synthetases implicated in autosomal recessive microcephaly.
Bögershausen, N., Krawczyk, H.E., Jamra, R.A., Lin, S.J., Yigit, G., Hüning, I., Polo, A.M., Vona, B., Huang, K., Schmidt, J., Altmüller, J., Luppe, J., Platzer, K., Dörgeloh, B.B., Busche, A., Biskup, S., Mendes, M.I., Smith, D.E.C., Salomons, G.S., Zibat, A., Bültmann, E., Nürnberg, P., Spielmann, M., Lemke, J.R., Li, Y., Zenker, M., Varshney, G.K., Hillen, H.S., Kratz, C.P. and Wollnik, B.
Human Mutation 43 (10): 1454-1471. October 2022

Recessive TRAPPC11 mutations cause a disease spectrum of limb girdle muscular dystrophy and myopathy with movement disorder and intellectual disability.
Bögershausen, N., Shahrzad, N., Chong, J.X., von Kleist-Retzow, J.C., Stanga, D., Li, Y., Bernier, F.P., Loucks, C.M., Wirth, R., Puffenberger, E.G., Hegele, R.A., Schreml, J., Lapointe, G., Keupp, K., Brett, C.L., Anderson, R., Hahn, A., Innes, A.M., Suchowersky, O., Mets, M.B., Nürnberg, G., McLeod, D.R., Thiele, H., Waggoner, D., Altmüller, J., Boycott, K.M., Schoser, B., Nürnberg, P., Ober, C., Heller, R., Parboosingh, J.S., Wollnik, B., Sacher, M. and Lamont, R.E.
American Journal of Human Genetics 93 (1): 181-190. 11 July 2013

Intramyocardial sprouting tip cells specify coronary arterialization.
Cano, E., Schwarzkopf, J., Kanda, M., Lindberg, E.L., Hollfinger, I., Pogontke, C., Braeuning, C., Fischer, C., Hübner, N. and Gerhardt, H.
Circulation Research 135 (6): 671-684. 30 August 2024

Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells.
Chamorro González, R., Conrad, T., Stöber, M.C., Xu, R., Giurgiu, M., Rodriguez-Fos, E., Kasack, K., Brückner, L., van Leen, E., Helmsauer, K., Dorado Garcia, H., Stefanova, M.E., Hung, K.L., Bei, Y., Schmelz, K., Lodrini, M., Mundlos, S., Chang, H.Y., Deubzer, H.E., Sauer, S., Eggert, A., Schulte, J.H., Schwarz, R.F., Haase, K., Koche, R.P. and Henssen, A.G.
Nature Genetics 55 (5): 880-890. May 2023

R-loops trigger the release of cytoplasmic ssDNAs leading to chronic inflammation upon DNA damage.
Chatzidoukaki, O., Stratigi, K., Goulielmaki, E., Niotis, G., Akalestou-Clocher, A., Gkirtzimanaki, K., Zafeiropoulos, A., Altmüller, J., Topalis, P. and Garinis, G.A.
Science Advances 7 (47): eabj5769. 19 November 2021

XPF interacts with TOP2B for R-loop processing and DNA looping on actively transcribed genes.
Chatzinikolaou, G., Stratigi, K., Siametis, A., Goulielmaki, E., Akalestou-Clocher, A., Tsamardinos, I., Topalis, P., Austin, C., Bouwman, B.A.M., Crosetto, N., Altmüller, J. and Garinis, G.A.
Science Advances 9 (45): eadi2095. 10 November 2023

Ectodysplasin signalling genes and phenotypic evolution in sculpins (Cottus).
Cheng, J., Sedlazek, F., Altmüller, J. and Nolte, A.W.
Proceedings of the Royal Society of London Series B-Biological Sciences 282 (1815): 20150746. 22 September 2015

Single cell‐ and spatial 'omics revolutionize physiology.
Conrad, T. and Altmüller, J.
Acta Physiologica 235 (4): e13848. August 2022

Determination of primary microRNA processing in clinical samples by targeted pri-miR-sequencing.
Conrad, T., Ntini, E., Lang, B., Cozzuto, L., Andersen, J.B., Marquardt, J.U., Ponomarenko, J., Tartaglia, G.G. and Vang Orom, U.A.
RNA 26 (11): 1726-1730. November 2020

Maximizing transcription of nucleic acids with efficient T7 promoters.
Conrad, T., Plumbom, I., Alcobendas, M., Vidal, R. and Sauer, S.
Communications Biology 3 (1): 439. 14 August 2020

Ecological transcriptomics – a non-lethal sampling approach for endangered fire salamanders.
Czypionka, T., Krugman, T., Altmüller, J., Blaustein, L., Steinfartz, S., Templeton, A.R., Nolte, A.W. and Leder, E.
Methods in Ecology and Evolution 6 (12): 1417-1425. December 2015

Novel mutations in KMT2B offer pathophysiological insights into childhood-onset progressive dystonia.
Dafsari, H.S., Sprute, R., Wunderlich, G., Daimagüler, H.S., Karaca, E., Contreras, A., Becker, K., Schulze-Rhonhof, M., Kiening, K., Karakulak, T., Kloss, M., Horn, A., Pauls, A., Nürnberg, P., Altmüller, J., Thiele, H., Assmann, B., Koy, A. and Cirak, S.
Journal of Human Genetics 64 (8): 803-813. August 2019

Clinical and genetic characterization of PYROXD1-related myopathy patients from Turkey.
Daimagüler, H.S., Akpulat, U., Özdemir, Ö., Yis, U., Güngör, S., Talim, B., Diniz, G., Baydan, F., Thiele, H., Altmüller, J., Nürnberg, P. and Cirak, S.
American Journal of Medical Genetics A 185 (6): 1678-1690. 14 May 2021

Detailed stratified GWAS analysis for severe COVID-19 in four European populations.
Degenhardt, F., Ellinghaus, D., Juzenas, S., Lerga-Jaso, J., Wendorff, M., Maya-Miles, D., Uellendahl-Werth, F., ElAbd, H., Rühlemann, M.C., Arora, J., Özer, O., Lenning, O.B., Myhre, R., Vadla, M.S., Wacker, E.M., Wienbrandt, L., Ortiz, A.B., de Salazar, A., Chercoles, A.G., Palom, A., Ruiz, A., Garcia-Fernandez, A.E., Blanco-Grau, A., Mantovani, A., Zanella, A., Holten, A.R., Mayer, A., Bandera, A., Cherubini, A., Protti, A., Aghemo, A., Gerussi, A., Ramirez, A., Braun, A., Nebel, A., Barreira, A., Lleo, A., Teles, A., Kildal, A.B., Biondi, A., Caballero-Garralda, A., Ganna, A., Gori, A., Glück, A., Lind, A., Tanck, A., Hinney, A., Nolla, A.C., Fracanzani, A.L., Peschuck, A., Cavallero, A., Dyrhol-Riise, A.M., Ruello, A., Julià, A., Muscatello, A., Pesenti, A., Voza, A., Rando-Segura, A., Solier, A., Schmidt, A., Cortes, B., Mateos, B., Nafria-Jimenez, B., Schaefer, B., Jensen, B., Bellinghausen, C., Maj, C., Ferrando, C., Horra, C., Quereda, C., Skurk, C., Thibeault, C., Scollo, C., Herr, C., Spinner, C.D., Gassner, C., Lange, C., Hu, C., Paccapelo, C., Lehmann, C., Angelini, C., Cappadona, C., Azuure, C., Bianco, C., Cea, C., Sancho, C., Hoff, D.A.L., Galimberti, D., Prati, D., Haschka, D., Jiménez, D., Pestaña, D., Toapanta, D., Muñiz-Diaz, E., Azzolini, E., Sandoval, E., Binatti, E., Scarpini, E., Helbig, E.T., Casalone, E., Urrechaga, E., Paraboschi, E.M., Pontali, E., Reverter, E., Calderón, E.J., Navas, E., Solligård, E., Contro, E., Arana-Arri, E., Aziz, F., Garcia, F., Sánchez, F.G., Ceriotti, F., Martinelli-Boneschi, F., Peyvandi, F., Kurth, F., Blasi, F., Malvestiti, F., Medrano, F.J., Mesonero, F., Rodriguez-Frias, F., Hanses, F., Müller, F., Hemmrich-Stanisak, G., Bellani, G., Grasselli, G., Pezzoli, G., Costantino, G., Albano, G., Cardamone, G., Bellelli, G., Citerio, G., Foti, G., Lamorte, G., Matullo, G., Baselli, G., Kurihara, H., Neb, H., My, I., Kurth, I., Hernández, I., Pink, I., Rojas, I., Galván-Femenia, I., Holter, J.C., Afset, J.E., Heyckendorf, J., Kässens, J., Damås, J.K., Rybniker, J., Altmüller, J., Ampuero, J., Martín, J., Erdmann, J., Banales, J.M., Badia, J.R., Dopazo, J., Schneider, J., Bergan, J., Barretina, J., Walter, J., Quero, J.H., Goikoetxea, J., Delgado, J., Guerrero, J.M., Fazaal, J., Kraft, J., Schröder, J., Risnes, K., Banasik, K., Müller, K.E., Gaede, K.I., Garcia-Etxebarria, K., Tonby, K., Heggelund, L., Izquierdo-Sanchez, L., Bettini, L.Rachele, Sumoy, L., Sander, L.E., Lippert, L.J., Terranova, L., Nkambule, L., Knopp, L., Gustad, L.T., Garbarino, L., Santoro, L., Téllez, L., Roade, L., Ostadreza, M., Intxausti, M., Kogevinas, M., Riveiro-Barciela, M., Berger, M.M., Schaefer, M., Niemi, M.E.K., Gutiérrez-Stampa, M.A., Carrabba, M., Figuera Basso, M.E., Valsecchi, M.G., Hernandez-Tejero, M., Vehreschild, M.J.G.T, Manunta, M., Acosta-Herrera, M., D'Angiò, M., Baldini, M., Cazzaniga, M., Grimsrud, M.M., Cornberg, M., Nöthen, M.M., Marquié, M., Castoldi, M., Cordioli, M., Cecconi, M., D'Amato, M., Augustin, M., Tomasi, M., Boada, M., Dreher, M., Seilmaier, M.J., Joannidis, M., Wittig, M., Mazzocco, M., Ciccarelli, M., Rodríguez-Gandía, M., Bocciolone, M., Miozzo, M., Ayo, N.I., Blay, N., Chueca, N., Montano, N., Braun, N., Ludwig, N., Marx, N., Martínez, N., Cornely, O.A., Witzke, O., Palmieri, O., Faverio, P., Preatoni, P., Bonfanti, P., Omodei, P., Tentorio, P., Castro, P., Rodrigues, P.M., España, P.P., Hoffmann, P., Rosenstiel, P., Schommers, P., Suwalski, P., Pablo, R., Ferrer, R., Bals, R., Gualtierotti, R., Gallego-Durán, R., Nieto, R., Carpani, R., Morilla, R., Badalamenti, S., Haider, S., Ciesek, S., May, S., Bombace, S., Marsal, S., Pigazzini, S., Klein, S., Pelusi, S., Wilfling, S., Bosari, S., Volland, S., Brunak, S., Raychaudhuri, S., Schreiber, S., Heilmann-Heimbach, S., Aliberti, S., Ripke, S., Dudman, S., Wesse, T., Zheng, T., Bahmer, T., Eggermann, T., Illig, T., Brenner, T., Pumarola, T., Feldt, T., Folseraas, T., Cejudo, T.G., Landmesser, U., Protzer, U., Hehr, U., Rimoldi, V., Monzani, V., Skogen, V., Keitel, V., Kopfnagel, V., Friaza, V., Andrade, V., Moreno, V., Albrecht, W., Peter, W., Poller, W., Farre, X., Yi, X., Wang, X., Khodamoradi, Y., Karadeniz, Z., Latiano, A., Goerg, S., Bacher, P., Koehler, P., Tran, F., Zoller, H., Schulte, E.C., Heidecker, B., Ludwig, K.U., Fernández, J., Romero-Gómez, M., Albillos, A., Invernizzi, P., Buti, M., Duga, S., Bujanda, L., Hov, J.R., Lenz, T.L., Asselta, R., Cid, R., Valenti, L., Karlsen, T.H., Cáceres, M. and Franke, A.
Human Molecular Genetics 31 (23): 3945-3966. 1 December 2022

Exonic microdeletions of the gephyrin gene impair GABAergic synaptic inhibition in patients with idiopathic generalized epilepsy.
Dejanovic, B., Lal, D., Catarino, C.B., Arjune, S., Belaidi, A.A., Trucks, H., Vollmar, C., Surges, R., Kunz, W.S., Motameny, S., Altmüller, J., Köhler, A., Neubauer, B.A., Nürnberg, P., Noachtar, S., Schwarz, G. and Sander, T.
Neurobiology of Disease 67 : 88-96. July 2014

Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin.
Dennenmoser, S., Sedlazeck, F.J., Iwaszkiewicz, E., Li, X.Y., Altmüller, J. and Nolte, A.W.
Molecular Ecology 26 (18): 4712-4724. 26 September 2017

Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish.
Dennenmoser, S., Sedlazeck, F.J., Schatz, M.C, Altmüller, J., Zytnicki, M. and Nolte, A.W.
Molecular Ecology 28 (6): 1491-1505. March 2019

Update on the ACTG1-associated Baraitser–Winter cerebrofrontofacial syndrome.
Di Donato, N., Kuechler, A., Vergano, S., Heinritz, W., Bodurtha, J., Merchant, S.R., Breningstall, G., Ladda, R., Sell, S., Altmüller, J., Bögershausen, N., Timms, A.E., Hackmann, K., Schrock, E., Collins, S., Olds, C., Rump, A. and Dobyns, W.B.
American Journal of Medical Genetics Part A 170 (10): 2644-2651. October 2016

Mutations in EXOSC2 are associated with a novel syndrome characterised by retinitis pigmentosa, progressive hearing loss, premature ageing, short stature, mild intellectual disability and distinctive gestalt.
Di Donato, N., Neuhann, T., Kahlert, A.K., Klink, B., Hackmann, K., Neuhann, I., Novotna, B., Schallner, J., Krause, C., Glass, I.A., Parnell, S.E., Benet-Pages, A., Nissen, A.M., Berger, W., Altmüller, J., Thiele, H., Weber, B.H.F., Schrock, E., Dobyns, W.B., Bier, A. and Rump, A.
Journal of Medical Genetics 53 (6): 419-425. June 2016

T- and L-type calcium channels maintain calcium oscillations in the murine zona glomerulosa.
Dinh, H.A., Volkert, M., Secener, A.K., Scholl, U.I. and Stölting, G.
Hypertension 81 (4): 811-822. April 2024

A second cohort of CHD3 patients expands the molecular mechanisms known to cause Snijders Blok-Campeau syndrome.
Drivas, T.G., Li, D., Nair, D., Alaimo, J.T., Alders, M., Altmüller, J., Barakat, T.S., Bebin, E.M., Bertsch, N.L., Blackburn, P.R., Blesson, A., Bouman, A.M., Brockmann, K., Brunelle, P., Burmeister, M., Cooper, G.M., Denecke, J., Dieux-Coëslier, A., Dubbs, H., Ferrer, A., Gal, D., Bartik, L.E., Gunderson, L.B., Hasadsri, L., Jain, M., Karimov, C., Keena, B., Klee, E.W., Kloth, K., Lace, B., Macchiaiolo, M., Marcadier, J.L., Milunsky, J.M., Napier, M.P., Ortiz-Gonzalez, X.R., Pichurin, P.N., Pinner, J., Powis, Z., Prasad, C., Radio, F.C., Rasmussen, K.J., Renaud, D.L., Rush, E.T., Saunders, C., Selcen, D., Seman, A.R., Shinde, D.N., Smith, E.D., Smol, T., Snijders Blok, L., Stoler, J.M., Tang, S., Tartaglia, M., Thompson, M.L., van de Kamp, J.M., Wang, J., Weise, D., Weiss, K., Woitschach, R., Wollnik, B., Yan, H., Zackai, E.H., Zampino, G., Campeau, P. and Bhoj, E.
European Journal of Human Genetics 28 (10): 1422-1431. October 2020

Uncovering the contribution of moderate-penetrance susceptibility genes to breast cancer by whole-exome sequencing and targeted enrichment sequencing of candidate genes in women of European ancestry.
Dumont, M., Weber-Lassalle, N., Joly-Beauparlant, C., Ernst, C., Droit, A., Feng, B.J., Dubois, S., Collin-Deschesnes, A.C., Soucy, P., Vallée, M., Fournier, F., Lemaçon, A., Adank, M.A., Allen, J., Altmüller, J., Arnold, N., Ausems, M.G.E.M., Berutti, R., Bolla, M.K., Bull, S., Carvalho, S., Cornelissen, S., Dufault, M.R., Dunning, A.M., Engel, C., Gehrig, A., Geurts-Giele, W.R.R., Gieger, C., Green, J., Hackmann, K., Helmy, M., Hentschel, J., Hogervorst, F.B.L., Hollestelle, A., Hooning, M.J., Horváth, J., Ikram, M.A., Kaulfuß, S., Keeman, R., Kuang, D., Luccarini, C., Maier, W., Martens, J.W.M., Niederacher, D., Nürnberg, P., Ott, C.E., Peters, A., Pharoah, P.D.P., Ramirez, A., Ramser, J., Riedel-Heller, S., Schmidt, G., Shah, M., Scherer, M., Stäbler, A., Strom, T.M., Sutter, C., Thiele, H., van Asperen, C.J., van der Kolk, L., van der Luijt, R.B., Volk, A.E., Wagner, M., Waisfisz, Q., Wang, Q., Wang-Gohrke, S., Weber, B.H.F., Devilee, P., Tavtigian, S., Bader, G.D., Meindl, A., Goldgar, D.E., Andrulis, I.L., Schmutzler, R.K., Easton, D.F., Schmidt, M.K., Hahnen, E. and Simard, J.
Cancers 14 (14): 3363. 11 July 2022

Cystatin M/E variant causes autosomal dominant keratosis follicularis spinulosa decalvans by dysregulating cathepsins L and V.
Eckl, K.M., Gruber, R., Brennan, L., Marriott, A., Plank, R., Moosbrugger-Martinz, V., Blunder, S., Schossig, A., Altmüller, J., Thiele, H., Nürnberg, P., Zschocke, J., Hennies, H.C. and Schmuth, M.
Frontiers in Genetics 12 : 689940. July 2021

Impaired epidermal ceramide synthesis causes autosomal recessive congenital ichthyosis and reveals the importance of ceramide acyl chain length.
Eckl, K.M., Tidhar, R., Thiele, H., Oji, V., Hausser, I., Brodesser, S., Preil, M.L., Önal-Akan, A., Stock, F., Müller, D., Becker, K., Casper, R., Nürnberg, G., Altmüller, J., Nürnberg, P., Traupe, H., Futerman, A.H. and Hennies, H.C.
Journal of Investigative Dermatology 133 (9): 2202-2211. September 2013

Homozygous and compound-heterozygous mutations in TGDS cause Catel-Manzke syndrome.
Ehmke, N., Caliebe, A., Koenig, R., Kant, S.G., Stark, Z., Cormier-Daire, V., Wieczorek, D., Gillessen-Kaesbach, G., Hoff, K., Kawalia, A., Thiele, H., Altmüller, J., Fischer-Zirnsak, B., Knaus, A., Zhu, N., Heinrich, V., Huber, C., Harabula, I., Spielmann, M., Horn, D., Kornak, U., Hecht, J., Krawitz, P.M., Nürnberg, P., Siebert, R., Manzke, H. and Mundlos, S.
American Journal of Human Genetics 95 (6): 763-70. 4 December 2014

De novo mutations in SLC25A24 cause a craniosynostosis syndrome with hypertrichosis, progeroid appearance, and mitochondrial dysfunction.
Ehmke, N., Graul-Neumann, L., Smorag, L., Koenig, R., Segebrecht, L., Magoulas, P., Scaglia, F., Kilic, E., Hennig, A.F., Adolphs, N., Saha, N., Fauler, B., Kalscheuer, V.M., Hennig, F., Altmüller, J., Netzer, C., Thiele, H., Nürnberg, P., Yigit, G., Jäger, M., Hecht, J., Krüger, U., Mielke, T., Krawitz, P.M., Horn, D., Schuelke, M., Mundlos, S., Bacino, C.A., Bonnen, P.E., Wollnik, B., Fischer-Zirnsak, B. and Kornak, U.
American Journal of Human Genetics 101 (5): 833-843. 2 November 2017

Homozygous nonsense mutation of WTN10B gene in a Moroccan family with split-hand foot malformation identified by exome sequencing: a case report.
Elalaoui, S.C., Fejjal, N., Li, Y., Thiele, H., Altmüller, J., Guaoua, S., Nürnberg, P., Wollnik, B., Sefiani, A. and Ratbi, I.
Pan African Medical Journal 39 : 21. May 2021

Mutant phosphodiesterase 3A protects from hypertension-induced cardiac damage.
Ercu, M., Mücke, M.B., Pallien, T., Markó, L., Sholokh, A., Schächterle, C., Aydin, A., Kidd, A., Walter, S., Esmati, Y., McMurray, B.J., Lato, D.F., Sunaga-Franze, D.Y., Dierks, P.H., Flores, B.I.M., Walker-Gray, R., Gong, M., Merticariu, C., Zühlke, K., Russwurm, M., Liu, T., Batolomaeus, T.U.P., Pautz, S., Schelenz, S., Taube, M., Napieczynska, H., Heuser, A., Eichhorst, J., Lehmann, M., Miller, D.C., Diecke, S., Qadri, F., Popova, E., Langanki, R., Movsesian, M.A., Herberg, F.W., Forslund, S.K., Müller, D.N., Borodina, T., Maass, P.G., Bähring, S., Hübner, N., Bader, M. and Klussmann, E.
Circulation 146 (23): 1758-1778. 6 December 2022

Germline C1GALT1C1 mutation causes a multisystem chaperonopathy.
Erger, F., Aryal, R.P., Reusch, B., Matsumoto, Y., Meyer, R., Zeng, J., Knopp, C., Noel, M., Muerner, L., Wenzel, A., Kohl, S., Tschernoster, N., Rappl, G., Rouvet, I., Schröder-Braunstein, J., Seibert, F.S., Thiele, H., Häusler, M.G., Weber, L.T., Büttner-Herold, M., Elbracht, M., Cummings, S.F., Altmüller, J., Habbig, S., Cummings, R.D. and Beck, B.B.
Proceedings of the National Academy of Sciences of the United States of America 120 (22): e2211087120. 30 May 2023

cfNOMe - a single assay for comprehensive epigenetic analyses of cell-free DNA.
Erger, F., Nörling, D., Borchert, D., Leenen, E., Habbig, S., Wiesener, M.S., Bartram, M.P., Wenzel, A., Becker, C., Toliat, M.R., Nürnberg, P., Beck, B.B. and Altmüller, J.
Genome Medicine 12 (1): 54. 24 June 2020

Association of ALPL and ENPP1 gene polymorphisms with bone strength related skeletal traits in a Chuvashian population.
Ermakov, S., Toliat, M.R., Cohen, Z., Malkin, I., Altmüller, J., Livshits, G. and Nürnberg, P.
Bone 46 (5): 1244-50. May 2010

Transposable elements and introgression introduce genetic variation in the invasive ant Cardiocondyla obscurior.
Errbii, M., Keilwagen, J., Hoff, K.J., Steffen, R., Altmüller, J., Oettler, J. and Schrader, L.
Molecular Ecology 30 (23): 6211-6228. December 2021

Expanding the spectrum of FAT1 nephropathies by novel mutations that affect hippo signaling.
Fabretti, F., Tschernoster, N., Erger, F., Hedergott, A., Buescher, A.K., Dafinger, C., Reusch, B., Köntges, V.K., Kohl, S., Bartram, M.P., Weber, L.T., Thiele, H., Altmueller, J., Schermer, B., Beck, B.B. and Habbig, S.
Kidney International Reports 6 (5): 1368-1378. May 2021

Self-organizing 3D human trunk neuromuscular organoids.
Faustino Martins, J.M., Fischer, C., Urzi, A., Vidal, R., Kunz, S., Ruffault, P.L., Kabuss, L., Hube, I., Gazzerro, E., Birchmeier, C., Spuler, S., Sauer, S. and Gouti, M.
Cell Stem Cell 26 (2): 172-186. 6 February 2020

Dominant SCN2A mutation causes familial episodic ataxia and impairment of speech development.
Fazeli, W., Becker, K., Herkenrath, P., Düchting, C., Körber, F., Landgraf, P., Nürnberg, P., Altmüller, J., Thiele, H., Koy, A., Liebau, M.C., Simon, T., Dötsch, J. and Cirak, S.
Neuropediatrics 49 (6): 379-384. December 2018

A TUBB6 mutation is associated with autosomal dominant non-progressive congenital facial palsy, bilateral ptosis and velopharyngeal dysfunction.
Fazeli, W., Herkenrath, P., Stiller, B., Neugebauer, A., Fricke, J., Lang-Roth, R., Nürnberg, G., Thoenes, M., Becker, J., Altmüller, J., Volk, A.E., Kubisch, C. and Heller, R.
Human Molecular Genetics 26 (20): 4055-4066. 15 October 2017

Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids.
Fernandez-Cuesta, L., Peifer, M., Lu, X., Sun, R., Ozretić, L., Seidal, D., Zander, T., Leenders, F., George, J., Müller, C., Dahmen, I., Pinther, B., Bosco, G., Konrad, K., Altmüller, J., Nürnberg, P., Achter, V., Lang, U., Schneider, P.M., Bogus, M., Soltermann, A., Brustugun, O.T., Helland, Å., Solberg, S., Lund-Iversen, M., Ansén, S., Stoelben, E., Wright, G.M., Russell, P., Wainer, Z., Solomon, B., Field, J.K., Hyde, R., Davies, M.P., Heukamp, L.C., Petersen, I., Perner, S., Lovly, C., Cappuzzo, F., Travis, W.D., Wolf, J., Vingron, M., Brambilla, E., Haas, S.A., Buettner, R. and Thomas, R.K.
Nature Communications 5 : 3518. 27 March 2014

CD74–NRG1 fusions in lung adenocarcinoma.
Fernandez-Cuesta, L., Plenker, D., Osada, H., Sun, R., Menon, R., Leenders, F., Ortiz-Cuaran, S., Peifer, M., Bos, M., Daßler, J., Malchers, F., Schöttle, J., Vogel, W., Dahmen, I., Koker, M., Ullrich, R.T., Wright, G.M., Russell, P.A., Wainer, Z., Solomon, B., Brambilla, E., Nagy-Mignotte, H., Moro-Sibilot, D., Brambilla, C.G., Lantuejoul, S., Altmüller, J., Becker, C., Nürnberg, P., Heuckmann, J.M., Stoelben, E., Petersen, I., Clement, J.H., Sänger, J., Muscarella, L.A., la Torre, A., Fazio, V.M., Lahortiga, I., Perera, T., Ogata, S., Parade, M., Brehmer, D., Vingron, M., Heukamp, L.C., Buettner, R., Zander, T., Wolf, J., Perner, S., Ansén, S., Haas, S.A., Yatabe, Y. and Thomas, R.K.
Cancer Discovery 4 (4): 415-22. 1 April 2014

Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data.
Fernandez-Cuesta, L., Sun, R., Menon, R., George, J., Lorenz, S., Meza-Zepeda, L.A., Peifer, M., Plenker, D., Heuckmann, J.M., Leenders, F., Zander, T., Dahmen, I., Koker, M., Schöttle, J., Ullrich, R.T., Altmüller, J., Becker, C., Nürnberg, P., Seidel, H., Böhm, D., Göke, F., Ansén, S., Russell, P.A., Wright, G.M., Wainer, Z., Solomon, B., Petersen, I., Clement, J.H., Sänger, J., Brustugun, O.T., Helland, Å., Solberg, S., Lund-Iversen, M., Buettner, R., Wolf, J., Brambilla, E., Vingron, M., Perner, S., Haas, S.A. and Thomas, R.K.
Genome Biology 16 : 7. 5 January 2015

MTBP phosphorylation controls DNA replication origin firing.
Ferreira, P., Höfer, V., Kronshage, N., Marko, A., Reusswig, K.U., Tetik, B., Dießel, C., Köhler, K., Tschernoster, N., Altmüller, J., Schulze, N., Pfander, B. and Boos, D.
Scientific Reports 11 (1): 4242. 19 February 2021

Signals trigger state-specific transcriptional programs to support diversity and homeostasis in immune cells.
Fischer, C., Metsger, M., Bauch, S., Vidal, R., Böttcher, M., Grote, P., Kliem, M. and Sauer, S.
Science Signaling 12 (581): eaao5820. 14 May 2019

RNA-Seq analysis of human trigeminal and dorsal root ganglia with a focus on chemoreceptors.
Flegel, C., Schöbel, N., Altmüller, J., Becker, C., Tannapfel, A., Hatt, H. and Gisselmann, G.
PLoS ONE 10 (6): e0128951. 2015

Characterization of the olfactory receptors expressed in human spermatozoa.
Flegel, C., Vogel, F., Hofreuter, A., Schreiner, B.S.P., Osthold, S., Veitinger, S., Becker, C., Brockmeyer, N.H., Muschol, M., Wennemuth, G., Altmüller, J., Hatt, H. and Gisselmann, G.
Frontiers in Molecular Biosciences 2 : 73. 2015

Characterization of non-olfactory GPCRs in human sperm with a focus on GPR18.
Flegel, C., Vogel, F., Hofreuter, A., Wojcik, S., Schoeder, C., Kieć-Kononowicz, K., Brockmeyer, N.H., Müller, C.E., Becker, C., Altmüller, J., Hatt, H. and Gisselmann, G.
Scientific Reports 6 : 32255. 30 August 2016

Unstable TTTTA/TTTCA expansions in MARCH6 are associated with Familial Adult Myoclonic Epilepsy type 3.
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Nature Communications 10 (1): 4919. 29 October 2019

Potential contribution of ancient introgression to the evolution of a derived reproductive strategy in ricefishes.
Flury, J.M., Meusemann, K., Martin, S., Hilgers, L., Spanke, T., Böhne, A., Herder, F., Mokodongan, D., Altmüller, J., Wowor, D., Misof, B., Nolte, A.W. and Schwarzer, J.
Genome Biology and Evolution 15 (8): evad138. 29 August 2023

Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and aging.
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bioRxiv : 2021.08.02.454573v1. 28 November 2021

Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and development.
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Communications Biology 6 (1): 40. 13 January 2023

Spermidine reduces neuroinflammation and soluble amyloid beta in an Alzheimer’s disease mouse model.
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Journal of Neuroinflammation 19 (1): 172. 2 July 2022

Specific chromatin changes mark lateral organ founder cells in the Arabidopsis inflorescence meristem.
Frerichs, A., Engelhorn, J., Altmüller, J., Gutierrez-Marcos, J. and Werr, W.
Journal of Experimental Botany 70 (15): 3867-3879. 1 August 2019

Dissecting HSV-1-induced host shut-off at RNA level.
Friedel, C.C., Whisnant, A.W., Djakovic, L., Rutkowski, A.J., Friedl, M.S., Kluge, M., Williamson, J.C., Sai, S., Oliveira Vidal, R., Sauer, S., Hennig, T., Prusty, B., Lehner, P.J., Matheson, N.J., Erhard, F. and Dölken, L.
bioRxiv : 2020.05.20.106039. 20 May 2020

Dissecting herpes simplex virus 1-induced host shutoff at the RNA level.
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Journal of Virology 95 (3): e01399-20. 13 January 2021

Assessing the enrichment performance in targeted resequencing experiments.
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Human Mutation 33 (4): 635-41. April 2012

Interferon regulatory factor 4 plays a pivotal role in the development of aGVHD-associated colitis.
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OncoImmunology 13 (1): 2296712. 2024

Human brain organoids assemble functionally integrated bilateral optic vesicles.
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Cell Stem Cell 28 (10): 1740-1757.e8. October 2021

CHD2 variants are a risk factor for photosensitivity in epilepsy.
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Brain 138 (5): 1198-1207. May 2015

Intellectual disability associated with craniofacial dysmorphism, cleft palate, and congenital heart defect due to a de novo MEIS2 mutation: a clinical longitudinal study.
Gangfuß, A., Yigit, G., Altmüller, J., Nürnberg, P., Czeschik, J.C., Wollnik, B., Bögershausen, N., Burfeind, P., Wieczorek, D., Kaiser, F., Roos, A., Kölbel, H., Schara-Schmidt, U. and Kuechler, A.
American Journal of Medical Genetics A 185 (4): 1216-1221. April 2021

CLUH regulates mitochondrial biogenesis by binding mRNAs of nuclear-encoded mitochondrial proteins.
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Journal of Cell Biology 207 (2): 213-223. 27 October 2014

Benign infantile seizures and paroxysmal dyskinesia caused by an SCN8A mutation.
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Annals of Neurology 79 (3): 428-436. March 2016

Comprehensive genomic profiles of small cell lung cancer.
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Nature 524 (7563): 47-53. 6 August 2015

Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors.
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Nature Communications 9 (1): 1048. 13 March 2018

CASC3 promotes transcriptome-wide activation of nonsense-mediated decay by the exon junction complex.
Gerbracht, J.V., Boehm, V., Britto-Borges, T., Kallabis, S., Wiederstein, J.L., Ciriello, S., Aschemeier, D.U., Krüger, M., Frese, C.K., Altmüller, J., Dieterich, C. and Gehring, N.H.
Nucleic Acids Research 48 (15): 8626-8644. 4 September 2020

Biallelic mutations in ADPRHL2, encoding ADP-ribosylhydrolase 3, lead to a degenerative pediatric stress-induced epileptic ataxia syndrome.
Ghosh, S.G., Becker, K., Huang, H., Dixon-Salazar, T., Chai, G., Salpietro, V., Al-Gazali, L., Waisfisz, Q., Wang, H., Vaux, K.K., Stanley, V., Manole, A., Akpulat, U., Weiss, M.M., Efthymiou, S., Hanna, M.G., Minetti, C., Striano, P., Pisciotta, L., De Grandis, E., Altmüller, J., Weixler, L., Nürnberg, P., Thiele, H., Yis, U., Okur, T.D., Polat, A.I., Amiri, N., Doosti, M., Karimani, E.G., Toosi, M.B., Haddad, G., Karakaya, M., Wirth, B., van Hagen, J.M., Wolf, N.I., Maroofian, R., Houlden, H., Cirak, S. and Gleeson, J.G.
American Journal of Human Genetics 103 (3): 431-439. 6 September 2018

A novel remitting leukodystrophy associated with a variant in FBP2.
Gizak, A., Diegmann, S., Dreha-Kulaczewski, S., Wiśniewski, J., Duda, P., Ohlenbusch, A., Huppke, B., Henneke, M., Höhne, W., Altmüller, J., Thiele, H., Nürnberg, P., Rakus, D., Gärtner, J. and Huppke, P.
Brain Communications 3 (2): fcab036. 11 March 2021

Parallel habitat acclimatization is realized by the expression of different genes in two closely related salamander species (genus Salamandra).
Goedbloed, D.J., Czypionka, T., Altmüller, J., Rodriguez, A., Küpfer, E., Segev, O., Blaustein, L., Templeton, A.R., Nolte, A.W. and Steinfartz, S.
Heredity 119 (6): 429-437. December 2017

Association of the interleukin-1 receptor antagonist gene with asthma.
Gohlke, H., Illig, T., Bahnweg, M., Klopp, N., André, E., Altmüller, J., Herbon, N., Werner, M., Knapp, M., Pescollderungg, L., Boner, A., Malerba, G., Pignatti, P.F. and Wjst, M.
American Journal of Respiratory and Critical Care Medicine 169 (11): 1217-23. 1 June 2004

Identification of a novel mutation in RIPK4 in a kindred with phenotypic features of Bartsocas-Papas and CHAND syndromes.
Gollasch, B., Basmanav, F.B., Nanda, A., Fritz, G., Mahmoudi, H., Thiele, H., Wehner, M., Wolf, S., Altmüller, J., Nürnberg, P., Frank, J. and Betz, R.C.
American Journal of Medical Genetics Part A 167 (11): 2555-2562. November 2015

Neuronal activity regulates DROSHA via autophagy in spinal muscular atrophy.
Gonçalves, I.C.G., Brecht, J., Thelen, M.P., Rehorst, W.A., Peters, M., Lee, H.J., Motameny, S., Torres-Benito, L., Ebrahimi-Fakhari, D., Kononenko, N.L., Altmüller, J., Vilchez, D., Sahin, M., Wirth, B. and Kye, M.J.
Scientific Reports 8 (1): 7907. 21 May 2018

Tissue-infiltrating macrophages mediate an exosome-based metabolic reprogramming upon DNA damage.
Goulielmaki, E., Ioannidou, A., Tsekrekou, M., Stratigi, K., Poutakidou, I.K., Gkirtzimanaki, K., Aivaliotis, M., Evangelou, K., Topalis, P., Altmüller, J., Gorgoulis, V.G., Chatzinikolaou, G. and Garinis, G.A.
Nature Communications 11 (1): 42. 2 January 2020

The splicing factor XAB2 interacts with ERCC1-XPF and XPG for R-loop processing.
Goulielmaki, E., Tsekrekou, M., Batsiotos, N., Ascensão-Ferreira, M., Ledaki, E., Stratigi, K., Chatzinikolaou, G., Topalis, P., Kosteas, T., Altmüller, J., Demmers, J.A., Barbosa-Morais, N.L. and Garinis, G.A.
Nature Communications 12 (1): 3153. 26 May 2021

The complete mitochondrial transcript of the red tail loach Yasuhikotakia modesta as assembled from RNAseq (Teleostei: Botiidae).
Grau, J.H., Hilgers, L., Altmüller, J., Šlechtová, V. and Bohlen, J.
Mitochondrial DNA Part B Resources 2 (1): 46-47. 2 February 2017

Transcriptome of iPSC-derived neuronal cells reveals a module of co-expressed genes consistently associated with autism spectrum disorder.
Griesi-Oliveira, K., Fogo, M.S., Pinto, B.G.G., Alves, A.Y., Suzuki, A.M., Morales, A.G., Ezquina, S., Sosa, O.J., Sutton, G.J., Sunaga-Franze, D.Y., Bueno, A.P., Seabra, G., Sardinha, L., Costa, S.S., Rosenberg, C., Zachi, E.C., Sertie, A.L., Martins-de-Souza, D., Reis, E.M., Voineagu, I. and Passos-Bueno, M.R.
Molecular Psychiatry 26 (5): 1589-1605. May 2021

Combined targeted resequencing of cytosine DNA methylation and mutations of DNA repair genes with potential use for poly(ADP-ribose) polymerase 1 inhibitor sensitivity testing.
Grimm, C., Fischer, A., Farrelly, A.M., Kalachand, R., Castiglione, R., Wasserburger, E., Hussong, M., Schultheis, Anne M, Altmüller, J., Thiele, H., Reinhardt, H.C., Hauschulz, K., Hennessy, B.T., Herwig, R., Lienhard, M., Buettner, R. and Schweiger, M.R.
Journal of Molecular Diagnostics 21 (2): 198-213. March 2019

Sequence variants affecting eosinophil numbers associate with asthma and myocardial infarction.
Gudbjartsson, D.F., Bjornsdottir, U.S., Halapi, E., Helgadottir, A., Sulem, P., Jonsdottir, G.M., Thorleifsson, G., Helgadottir, H., Steinthorsdottir, V., Stefansson, H., Williams, C., Hui, J., Beilby, J., Warrington, N.M., James, A., Palmer, L.J., Koppelman, G.H., Heinzmann, A., Krueger, M., Boezen, H.M., Wheatley, A., Altmuller, J., Shin, H.D., Uh, S.T., Cheong, H.S., Jonsdottir, B., Gislason, D., Park, C.S., Rasmussen, L.M., Porsbjerg, C., Hansen, J.W., Backer, V., Werge, T., Janson, C., Jönsson, U.B., Ng, M.C.Y., Chan, J., So, W.Y., Ma, R., Shah, S.H., Granger, C.B., Quyyumi, A.A., Levey, A.I., Vaccarino, V., Reilly, M.P., Rader, D.J., Williams, M.J.A., van Rij, A.M., Jones, G.T., Trabetti, E., Malerba, G., Pignatti, P.F., Boner, A., Pescollderungg, L., Girelli, D., Olivieri, O., Martinelli, N., Ludviksson, B.R., Ludviksdottir, D., Eyjolfsson, G.I., Arnar, D., Thorgeirsson, G., Deichmann, K., Thompson, P.J., Wjst, M., Hall, I.P., Postma, D.S., Gislason, T., Gulcher, J., Kong, A., Jonsdottir, I., Thorsteinsdottir, U. and Stefansson, K.
Nature Genetics 41 (3): 342-7. March 2009

Phenotypic spectrum of BLM- and RMI1-related Bloom syndrome.
Gönenc, I.I., Elcioglu, N.H., Martinez Grijalva, C., Aras, S., Großmann, N., Praulich, I., Altmüller, J., Kaulfuß, S., Li, Y., Nürnberg, P., Burfeind, P., Yigit, G. and Wollnik, B.
Clinical Genetics 101 (5-6): 559-564. May 2022

Long-term data on two sisters with C3GN due to an identical, homozygous CFH mutation and autoantibodies.
Hackl, A., Erger, F., Skerka, C., Wenzel, A., Tschernoster, N., Ehren, R., Burgmaier, K., Riehmer, V., Licht, C., Kirschfink, M., Weber, L.T., Altmueller, J., Zipfel, P.F. and Habbig, S.
Clinical Nephrology 94 (4): 197-206. October 2020

Ion transporter NKCC1, modulator of neurogenesis in murine olfactory neurons.
Haering, C., Kanageswaran, N., Bouvain, P., Scholz, P., Altmüller, J., Becker, C., Gisselmann, G., Wäring-Bischof, J. and Hatt, H.
Journal of Biological Chemistry 290 (15): 9767-9779. 4 January 2021

Germline mutation status, pathological complete response, and disease-free survival in triple-negative breast cancer: secondary analysis of the GeparSixto randomized clinical trial.
Hahnen, E., Lederer, B., Hauke, J., Loibl, S., Kröber, S., Schneeweiss, A., Denkert, C., Fasching, P.A., Blohmer, J.U., Jackisch, C., Paepke, S., Gerber, B., Kümmel, S., Schem, C., Neidhardt, G., Huober, J., Rhiem, K., Costa, S., Altmüller, J., Hanusch, C., Thiele, H., Müller, V., Nürnberg, P., Karn, T., Nekljudova, V., Untch, M., von Minckwitz, G. and Schmutzler, R.K.
JAMA Oncology 3 (10): 1378-1385. 1 October 2017

A sequence variant on 17q21 is associated with age at onset and severity of asthma.
Halapi, E., Gudbjartsson, D.F., Jonsdottir, G.M., Bjornsdottir, U.S., Thorleifsson, G., Helgadottir, H., Williams, C., Koppelman, G.H., Heinzmann, A., Boezen, H.M., Jonasdottir, A., Blondal, T., Gudjonsson, S.A., Jonasdottir, A., Thorlacius, T., Henry, A.P., Altmueller, J., Krueger, M., Shin, H.D., Uh, S.T., Cheong, H.S., Jonsdottir, B., Ludviksson, B.R., Ludviksdottir, D., Gislason, D., Park, C.S., Deichmann, K., Thompson, P.J., Wjst, M., Hall, I.P., Postma, D.S., Gislason, T., Kong, A., Jonsdottir, I., Thorsteinsdottir, U. and Stefansson, K.
European Journal of Human Genetics 18 (8): 902-8. August 2010

Intronic CRISPR repair in a preclinical model of Noonan syndrome-associated cardiomyopathy.
Hanses, U., Kleinsorge, M., Roos, L., Yigit, G., Li, Y., Barbarics, B., El-Battrawy, I., Lan, H., Tiburcy, M., Hindmarsh, R., Lenz, C., Salinas, G., Diecke, S., Müller, C., Adham, I., Altmüller, J., Nürnberg, P., Paul, T., Zimmermann, W.H., Hasenfuss, G., Wollnik, B. and Cyganek, L.
Circulation 142 (11): 1059-1076. 15 September 2020

NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling.
Hanssen, F., Gabernet, G., Smith, N.H., Mertes, C., Neogi, A.G., Brandhoff, L., Ossowski, A., Altmueller, J., Becker, K., Petzold, A., Sturm, M., Stöcker, T., Sivalingam, S., Brand, F., Schmidt, A., Buness, A., Probst, A.J., Motameny, S. and Köster, J.
F1000Research 12 : 1125. 11 September 2023

Coinheritance of biallelic SLURP1 and SLC39A4 mutations cause a severe genodermatosis with skin peeling and hair loss all over the body.
Harms, F.L., Nampoothiri, S., Kortüm, F., Thomas, J., Panicker, V.V., Alawi, M., Altmüller, J., Yesodharan, D. and Kutsche, K.
British Journal of Dermatology 179 (5): 1192-1194. 1 November 2018

Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus.
Harr, B., Karakoc, E., Neme, R., Teschke, M., Pfeifle, C., Pezer, Ž., Babiker, H., Linnenbrink, M., Montero, I., Scavetta, R., Abai, M.R., Molins, M.P., Schlegel, M., Ulrich, R.G., Altmüller, J., Franitza, M., Büntge, A., Künzel, S. and Tautz, D.
Scientific Data 3 : 160075. 13 September 2016

Tumor suppression in basal keratinocytes via dual non-cell-autonomous functions of a Na,K-ATPase beta subunit.
Hatzold, J., Beleggia, F., Herzig, H., Altmüller, J., Nürnberg, P., Bloch, W., Wollnik, B. and Hammerschmidt, M.
eLife 5 : e14277. 15 July 2016

A novel large in-frame deletion within the CACNA1F gene associates with a cone-rod dystrophy 3-like phenotype.
Hauke, J., Schild, A., Neugebauer, A., Lappa, A., Fricke, J., Fauser, S., Rösler, S., Pannes, A., Zarrinnam, D., Altmüller, J., Motameny, S., Nürnberg, G., Nürnberg, P., Hahnen, E. and Beck, B.B.
PLoS ONE 8 (10): e76414. 4 October 2013

Deleterious somatic variants in 473 consecutive individuals with ovarian cancer: results of the observational AGO-TR1 study (NCT02222883).
Hauke, J., Hahnen, E., Schneider, S., Reuss, A., Richters, L., Kommoss, S., Heimbach, A., Marmé, F., Schmidt, S., Prieske, K., Gevensleben, H., Burges, A., Borde, J., De Gregorio, N., Nürnberg, P., El-Balat, A., Thiele, H., Hilpert, F., Altmüller, J., Meier, W., Dietrich, D., Kimmig, R., Schoemig-Markiefka, B., Kast, K., Braicu, E., Baumann, K., Jackisch, C., Park-Simon, T.W., Ernst, C., Hanker, L., Pfisterer, J., Schnelzer, A., du Bois, A., Schmutzler, R.K. and Harter, P.
Journal of Medical Genetics 56 (9): 574-580. September 2019

Sensitivity and specificity of loss of heterozygosity analysis for the classification of rare germline variants in BRCA1/2: results of the observational AGO-TR1 study (NCT02222883).
Hauke, J., Harter, P., Ernst, C., Burges, A., Schmidt, S., Reuss, A., Borde, J., De Gregorio, N., Dietrich, D., El-Balat, A., Kayali, M., Gevensleben, H., Hilpert, F., Altmüller, J., Heimbach, A., Meier, W., Schoemig-Markiefka, B., Thiele, H., Kimmig, R., Nürnberg, P., Kast, K., Richters, L., Sehouli, J., Schmutzler, R.K. and Hahnen, E.
Journal of Medical Genetics 59 (3): 248-252. March 2022

Gene panel testing of 5589 BRCA1/2-negative index patients with breast cancer in a routine diagnostic setting: results of the German Consortium for Hereditary Breast and Ovarian Cancer.
Hauke, J., Horvath, J., Groß, E., Gehrig, A., Honisch, E., Hackmann, K., Schmidt, G., Arnold, N., Faust, U., Sutter, C., Hentschel, J., Wang-Gohrke, S., Smogavec, M., Weber, B.H.F., Weber-Lassalle, N., Weber-Lassalle, K., Borde, J., Ernst, C., Altmüller, J., Volk, A.E., Thiele, H., Hübbel, V., Nürnberg, P., Keupp, K., Versmold, B., Pohl, E., Kubisch, C., Grill, S., Paul, V., Herold, N., Lichey, N., Rhiem, K., Ditsch, N., Ruckert, C., Wappenschmidt, B., Auber, B., Rump, A., Niederacher, D., Haaf, T., Ramser, J., Dworniczak, B., Engel, C., Meindl, A., Schmutzler, R.K. and Hahnen, E.
Cancer Medicine 7 (4): 1349-1358. April 2018

Clinical and genetic findings in a family with NMNAT1-associated Leber congenital amaurosis: case report and review of the literature.
Hedergott, A., Volk, A.E., Herkenrath, P., Thiele, H., Fricke, J., Altmüller, J., Nürnberg, P., Kubisch, C. and Neugebauer, A.
Graefes Archive for Clinical and Experimental Ophthalmology 253 (12): 2239-2246. December 2015

Circulating tumor DNA sequencing for biologic classification and individualized risk stratification in patients with Hodgkin Lymphoma.
Heger, J.M., Mammadova, L., Mattlener, J., Sobesky, S., Cirillo, M., Altmüller, J., Kirst, E., Reinke, S., Klapper, W., Bröckelmann, P.J., Ferdinandus, J., Kaul, H., Schneider, G., Schneider, J., Schleifenbaum, J.K., Ullrich, R.T., Freihammer, M., Awerkiew, S., Lohmann, M., Klein, F., Nürnberg, P., Hallek, M., Rossi, D., Mauz-Körholz, C., Gattenlöhner, S., Bräuninger, A., Borchmann, P., von Tresckow, B. and Borchmann, S.
Journal of Clinical Oncology 42 (35): 4218-4230. 10 December 2024

Multiregion human bladder cancer sequencing reveals tumour evolution, bladder cancer phenotypes and implications for targeted therapy.
Heide, T., Maurer, A., Eipel, M., Knoll, K., Geelvink, M., Veeck, J., Knuechel, R., van Essen, J., Stoehr, R., Hartmann, A., Altmueller, J., Graham, T.A. and Gaisa, N.T.
Journal of Pathology 248 (2): 230-242. June 2019

Loss of Msh2 and a single-radiation hit induce common, genome-wide, and persistent epigenetic changes in the intestine.
Herberg, M., Siebert, S., Quaas, M., Thalheim, T., Rother, K., Hussong, M., Altmüller, J., Kerner, C., Galle, J., Schweiger, M.R. and Aust, G.
Clinical Epigenetics 11 (1): 65. 27 April 2019

High-resolution SNP scan of chromosome 6p21 in pooled samples from patients with complex diseases.
Herbon, N., Werner, M., Braig, C., Gohlke, H., Dütsch, G., Illig, T., Altmüller, J., Hampe, J., Lantermann, A., Schreiber, S., Bonifacio, E., Ziegler, A., Schwab, S., Wildenauer, D., van den Boom, D., Braun, A., Knapp, M., Reitmeir, P. and Wjst, M.
Genomics 81 (5): 510-8. May 2003

Clonal dynamics towards the development of venetoclax resistance in chronic lymphocytic leukemia.
Herling, C.D., Abedpour, N., Weiss, J., Schmitt, A., Jachimowicz, R.D., Merkel, O., Cartolano, M., Oberbeck, S., Mayer, P., Berg, V., Thomalla, D., Kutsch, N., Stiefelhagen, M., Cramer, P., Wendtner, C.M., Persigehl, T., Saleh, A., Altmüller, J., Nürnberg, P., Pallasch, C., Achter, V., Lang, U., Eichhorst, B., Castiglione, R., Schäfer, S.C., Büttner, R., Kreuzer, K.A., Reinhardt, H.C., Hallek, M., Frenzel, L.P. and Peifer, M.
Nature Communications 9 (1): 727. 20 February 2018

Complex karyotypes and KRAS and POT1 mutations impact outcome in CLL after chlorambucil-based chemotherapy or chemoimmunotherapy.
Herling, C.D., Klaumünzer, M., Rocha, C.K., Altmüller, J., Thiele, H., Bahlo, J., Kluth, S., Crispatzu, G., Herling, M., Schiller, J., Engelke, A., Tausch, E., Döhner, H., Fischer, K., Goede, V., Nürnberg, P., Reinhardt, H.C., Stilgenbauer, S., Hallek, M. and Kreuzer, K.A.
Blood 128 (3): 395-404. 21 July 2016

RNA-seq based transcriptome analysis of the type I interferon host response upon vaccinia virus infection of mouse cells.
Hernáez, B., Alonso, G., Alonso-Lobo, J.M., Rastrojo, A., Fischer, C., Sauer, S., Aguado, B. and Alcamí, A.
Journal of Immunology Research 2017 : 5157626. 9 February 2017

Viral cGAMP nuclease reveals the essential role of DNA sensing in protection against acute lethal virus infection.
Hernáez, B., Alonso, G., Georgana, I., El-Jesr, M., Martín, R., Shair, K.H.Y., Fischer, C., Sauer, S., Maluquer de Motes, C. and Alcamí, A.
Science Advances 6 (38): eabb4565. 18 September 2020

A virus-encoded type I interferon decoy receptor enables evasion of host immunity through cell-surface binding.
Hernáez, B., Alonso-Lobo, J.M., Montanuy, I., Fischer, C., Sauer, S., Sigal, L., Sevilla, N. and Alcamí, A.
Nature Communications 9 (1): 5440. 21 December 2018

Inflammation and convergent placenta gene co-option contributed to a novel reproductive tissue.
Hilgers, L., Roth, O., Nolte, A.W., Schüller, A., Spanke, T., Flury, J.M., Utama, I.V., Altmüller, J., Wowor, D., Misof, B., Herder, F., Böhne, A. and Schwarzer, J.
Current Biology 32 (3): 715-724. 7 February 2022

Tracheal brush cells release acetylcholine in response to bitter tastants for paracrine and autocrine signaling.
Hollenhorst, M.I., Jurastow, I., Nandigama, R., Appenzeller, S., Li, L., Vogel, J., Wiederhold, S., Althaus, M., Empting, M., Altmüller, J., Hirsch, A.K.H., Flockerzi, V., Canning, B.J., Saliba, A.E. and Krasteva-Christ, G.
FASEB Journal 34 (1): 316-332. January 2020

Multimodal profiling of peripheral blood identifies proliferating circulating effector CD4(+) T cells as predictors for response to integrin α4β7-blocking therapy in inflammatory bowel disease.
Horn, V., Cancino, C.A., Steinheuer, L.M., Obermayer, B., Fritz, K., Nguyen, A.L., Juhran, K.S., Plattner, C., Bösel, D., Oldenburg, L., Burns, M., Schulz, A.R., Saliutina, M., Mantzivi, E., Lissner, D., Conrad, T., Mashreghi, M.F., Zundler, S., Sonnenberg, E., Schumann, M., Haag, L.M., Beule, D., Flatz, L., Trjanoski, Z., D'Haens, G., Weidinger, C., Mei, H.E., Siegmund, B., Thurley, K. and Hegazy, A.N.
Gastroenterology 28 September 2024 (In Press)

Exome sequencing characterizes the somatic mutation spectrum of early serrated lesions in a patient with serrated polyposis syndrome (SPS).
Horpaopan, S., Kirfel, J., Peters, S., Kloth, M., Hüneburg, R., Altmüller, J., Drichel, D., Odenthal, M., Kristiansen, G., Strassburg, C., Nattermann, J., Hoffmann, P., Nürnberg, P., Büttner, R., Thiele, H., Kahl, P., Spier, I. and Aretz, S.
Hereditary Cancer in Clinical Practice 15 : 22. 29 November 2017

Genome-wide CNV analysis in 221 unrelated patients and targeted high-throughput sequencing reveal novel causative candidate genes for colorectal adenomatous polyposis.
Horpaopan, S., Spier, I., Zink, A.M., Altmüller, J., Holzapfel, S., Laner, A., Vogt, S., Uhlhaas, S., Heilmann, S., Stienen, D., Pasternack, S.M., Keppler, K., Adam, R., Kayser, K., Moebus, S., Draaken, M., Degenhardt, F., Engels, H., Hofmann, A., Nöthen, M.M., Steinke, V., Perez-Bouza, A., Herms, S., Holinski-Feder, E., Fröhlich, H., Thiele, H., Hoffmann, P. and Aretz, S.
International Journal of Cancer 136 (6): E578–E589. 15 March 2015

Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021.
Houwaart, Torsten, Belhaj, S., Tawalbeh, E., Nagels, D., Fröhlich, Y., Finzer, P., Ciruela, P., Sabrià, A., Herrero, M., Andrés, C., Antón, A., Benmoumene, A., Asskali, D., Haidar, H., von Dahlen, J., Nicolai, J., Stiller, M., Blum, J., Lange, C., Adelmann, C., Schroer, B., Osmers, U., Grice, C., Kirfel, P.P., Jomaa, H., Strelow, D., Hülse, L., Pigulla, M., Kreuzer, P., Tyshaieva, A., Weber, J., Wienemann, T., Kohns Vasconcelos, M., Hoffmann, K., Lübke, N., Hauka, S., Andree, M., Scholz, C.J., Jazmati, N., Göbels, K., Zotz, R., Pfeffer, K., Timm, J., Ehlkes, L., Walker, A. and Dilthey, A.T.
Eurosurveillance 27 (43): 2101089. 27 October 2022

Nonsense mutations in SMPX, encoding a protein responsive to physical force, result in X-chromosomal hearing loss.
Huebner, A.K., Gandia, M., Frommolt, P., Maak, A., Wicklein, E.M., Thiele, H., Altmüller, J., Wagner, F., Viñuela, A., Aguirre, L.A., Moreno, F., Maier, H., Rau, I., Giesselmann, S., Nürnberg, G., Gal, A., Nürnberg, P., Hübner, C.A., del Castillo, I. and Kurth, I.
American Journal of Human Genetics 88 (5): 621-7. 13 May 2011

Activating de novo mutations in NFE2L2 encoding NRF2 cause a multisystem disorder.
Huppke, P., Weissbach, S., Church, J.A., Schnur, R., Krusen, M., Dreha-Kulaczewski, S., Kühn-Velten, W.N., Wolf, A., Huppke, B., Millan, F., Begtrup, A., Almusafri, F., Thiele, H., Altmüller, J., Nürnberg, P., Müller, M. and Gärtner, J.
Nature Communications 8 (1): 818. 10 October 2017

A truncating mutation of CEP135 causes primary microcephaly and disturbed centrosomal function.
Hussain, M.S., Baig, S.M., Neumann, S., Nürnberg, G., Farooq, M., Ahmad, I., Alef, T., Hennies, H.C., Technau, M., Altmüller, J., Frommolt, P., Thiele, H., Noegel, A.A. and Nürnberg, P.
American Journal of Human Genetics 90 (5): 871-8. 4 May 2012

CDK6 associates with the centrosome during mitosis and is mutated in a large Pakistani family with primary microcephaly.
Hussain, M.S., Baig, S.M., Neumann, S., Peche, V.S., Szczepanski, S., Nürnberg, G., Tariq, M., Jameel, M., Khan, T.N., Fatima, A., Malik, N.A., Ahmad, I., Altmüller, J., Frommolt, P., Thiele, H., Höhne, W., Yigit, G., Wollnik, B., Neubauer, B.A., Nürnberg, P. and Noegel, A.A.
Human Molecular Genetics 22 (25): 5199-5214. 20 December 2013

Mutations in CKAP2L, the human homolog of the mouse Radmis gene, cause Filippi syndrome.
Hussain, M.S., Battaglia, A., Szczepanski, S., Kaygusuz, E., Toliat, M.R., Sakakibara, S., Altmüller, J., Thiele, H., Nürnberg, G., Moosa, S., Yigit, G., Beleggia, F., Tinschert, S., Clayton-Smith, J., Vasudevan, P., Urquhart, J.E., Donnai, D., Fryer, A., Percin, F., Brancati, F., Dobbie, A., Smigiel, R., Gillessen-Kaesbach, G., Wollnik, B., Noegel, A.A., Newman, W.G. and Nürnberg, P.
American Journal of Human Genetics 95 (5): 622-632. 6 November 2014

De novo FUS mutations are the most frequent genetic cause in early-onset German ALS patients.
Hübers, A., Just, W., Rosenbohm, A., Müller, K., Marroquin, N., Goebel, I., Högel, J., Thiele, H., Altmüller, J., Nürnberg, P., Weishaupt, J.H., Kubisch, C., Ludolph, A.C. and Volk, A.E.
Neurobiology of Aging 36 (11): 3117.e1-3117.e6. November 2015

Diagnosing recipient- vs. donor-derived posttransplant myelodysplastic neoplasm via targeted single-cell mutational profiling.
Ihlow, J., Penter, L., Vuong, L.G., Bischoff, P., Obermayer, B., Trinks, A., Blau, O., Behnke, A., Conrad, T., Morkel, M., Wu, C.J., Westermann, J., Bullinger, L., von Brünneck, A.C., Blüthgen, N., Horst, D. and Praktiknjo, S.D.
Med 6 December 2024 (In Press)

Genome-wide association study of lung function decline in adults with and without asthma.
Imboden, M., Bouzigon, E., Curjuric, I., Ramasamy, A., Kumar, A., Hancock, D.B., Wilk, J.B., Vonk, J.M., Thun, G.A., Siroux, V., Nadif, R., Monier, F., Gonzalez, J.R., Wjst, M., Heinrich, J., Loehr, L.R., Franceschini, N., North, K.E., Altmüller, J., Koppelman, G.H., Guerra, S., Kronenberg, F., Lathrop, M., Moffatt, M.F., O'Connor, G.T., Strachan, D.P., Postma, D.S., London, S.J., Schindler, C., Kogevinas, M., Kauffmann, Fr., Jarvis, D.L., Demenais, F. and Probst-Hensch, N.M.
Journal of Allergy and Clinical Immunology 129 (5): 1218-28. May 2012

Biallelic variants in PCDHGC4 cause a novel neurodevelopmental syndrome with progressive microcephaly, seizures, and joint anomalies.
Iqbal, M., Maroofian, R., Çavdarlı, B., Riccardi, F., Field, M., Banka, S., Bubshait, D.K., Li, Y., Hertecant, J., Baig, S.M., Dyment, D., Efthymiou, S., Abdullah, U., Makhdoom, E.U.H., Ali, Z., Scherf de Almeida, T, Molinari, F., Mignon-Ravix, C., Chabrol, B., Antony, J., Ades, L., Pagnamenta, A.T., Jackson, A., Douzgou, S., Beetz, C., Karageorgou, V., Vona, B., Rad, A., Baig, J.M., Sultan, T., Alvi, J.R., Maqbool, S., Rahman, F., Toosi, M.B., Ashrafzadeh, F., Imannezhad, S., Karimiani, E.G., Sarwar, Y., Khan, S., Jameel, M., Noegel, A.A., Budde, B., Altmüller, J., Motameny, S., Höhne, W., Houlden, H., Nürnberg, P., Wollnik, B., Villard, L., Alkuraya, F.S., Osmond, M., Hussain, M.S. and Yigit, G.
Genetics in Medicine 23 (11): 2138-2149. November 2021

Mechanism suppressing H3K9 trimethylation in pluripotent stem cells and its demise by polyQ-expanded huntingtin mutations.
Irmak, D., Fatima, A., Gutiérrez-Garcia, R., Rinschen, M.M., Wagle, P., Altmüller, J., Arrigoni, L., Hummel, B., Klein, C., Frese, C.K., Sawarkar, R., Rada-Iglesias, A. and Vilchez, D.
Human Molecular Genetics 27 (23): 4117-4134. 1 December 2018

Rare gene deletions in genetic generalized and Rolandic epilepsies.
Jabbari, K., Bobbili, D.R., Lal, D., Reinthaler, E.M., Schubert, J., Wolking, S., Sinha, V., Motameny, S., Thiele, H., Kawalia, A., Altmüller, J., Toliat, M.R., Kraaij, R., van Rooij, J., Uitterlinden, A.G., Ikram, M.A., Zara, F., Lehesjoki, A.E., Krause, R., Zimprich, F., Sander, T., Neubauer, B.A., May, P., Lerche, H. and Nürnberg, P.
PLoS ONE 13 (8): e0202022. 27 August 2018

The role of microRNAs in defining LSECs cellular identity and in regulating F8 gene expression.
Jamil, M. A., Al-Rifai, R., Nuesgen, N., Altmüller, J., Oldenburg, J. and El-Maarri, O.
Frontiers in Genetics 15 : 1302685. 19 February 2024

MCH neurons regulate permeability of the median eminence barrier.
Jiang, H., Gallet, S., Klemm, P., Scholl, P., Folz-Donahue, K., Altmüller, J., Alber, J., Heilinger, C., Kukat, C., Loyens, A., Müller-Fielitz, H., Sundaram, S., Schwaninger, M., Prevot, V. and Brüning, J.C.
Neuron 107 (2): 306-319. 22 July 2020

Oncogenic role and target properties of the lysine-specific demethylase KDM1A in chronic lymphocytic leukemia.
Jiang, Q., Stachelscheid, J., Bloehdorn, J., Pacholewska, A., Aszyk, C.M., Grotenhuijs, F., Müller, T.A., Onder, O., Wagle, P., Herling, C.D., Kleppe, M., Wang, Z., Coombes, K.R., Robrecht, S., Dalvi, P.S., Plosnita, B., Mayer, P., Abruzzo, L.V., Altmüller, J., Gathof, B.S., Persigehl, T., Fischer, K., Jebaraj, B.M.C., Rienhoff, H.Y., Ecker, R.C., Zhao, Y., Bruns, C.J., Stilgenbauer, S., Elenitoba-Johnson, K.S.J., Hallek, M., Schweiger, M.R., Odenthal, M., Vasyutina, E. and Herling, M.
Blood 142 (1): 44-61. 6 July 2023

The integrated RNA landscape of renal preconditioning against ischemia-reperfusion injury.
Johnsen, M., Kubacki, T., Yeroslaviz, A., Späth, M.R., Mörsdorf, J., Göbel, H., Bohl, K., Ignarski, M., Meharg, C., Habermann, B., Altmüller, J., Beyer, A., Benzing, T., Schermer, B., Burst, V. and Müller, R.U.
Journal of the American Society of Nephrology 31 (4): 716-730. April 2020

SSBP1 mutations in dominant optic atrophy with variable retinal degeneration.
Jurkute, N., Leu, C., Pogoda, H.M., Arno, G., Robson, A.G., Nürnberg, G., Altmüller, J., Thiele, H., Motameny, S., Toliat, M.R., Powell, K., Höhne, W., Michaelides, M., Webster, A.R., Moore, A.T., Hammerschmidt, M., Nürnberg, P., Yu-Wai-Man, P. and Votruba, M.
Annals of Neurology 86 (3): 368-383. September 2019

STIL mutation causes autosomal recessive microcephalic lobar holoprosencephaly.
Kakar, N., Ahmad, J., Morris-Rosendahl, D.J., Altmüller, J., Friedrich, K., Barbi, G., Nürnberg, P., Kubisch, C., Dobyns, W.B. and Borck, G.
Human Genetics 134 (1): 45-51. January 2015

Novel PNKP mutations causing defective DNA strand break repair and PARP1 hyperactivity in MCSZ.
Kalasova, I., Hanzlikova, H., Gupta, N., Li, Y., Altmüller, J., Reynolds, J.J., Stewart, G.S., Wollnik, B., Yigit, G. and Caldecott, K.W.
Neurology Genetics 5 (2): e320. April 2019

OR2H2 regulates the differentiation of human myoblast cells by its ligand aldehyde 13-13.
Kalbe, B., Osterloh, M., Schulz, V.M., Altmüller, J., Becker, C., Osterloh, S. and Hatt, H.
Archives of Biochemistry and Biophysics 645 : 72-80. 1 May 2018

SORCS2 activity in pancreatic α-cells safeguards insulin granule formation and release from glucose-stressed β-cells.
Kalnytska, O., Qvist, P., Kunz, S., Conrad, T., Willnow, T.E. and Schmidt, V.
iScience 27 (1): 108725. 19 January 2024

Deep sequencing of the murine olfactory receptor neuron transcriptome.
Kanageswaran, N., Demond, M., Nagel, M., Schreiner, B.S.P., Baumgart, S., Scholz, P., Altmüller, J., Becker, C., Doerner, J.F., Conrad, H., Oberland, S., Wetzel, C.H., Neuhaus, E.M., Hatt, H. and Gisselmann, G.
PLoS ONE 10 (1): e0113170. 2015

(RB1)-negative retinal organoids display proliferation of cone photoreceptors and loss of retinal differentiation.
Kanber, D., Woestefeld, J., Döpper, H., Bozet, M., Brenzel, A., Altmüller, J., Kilpert, F., Lohmann, D., Pommerenke, C. and Steenpass, L.
Cancers 14 (9): 2166. 26 April 2022

Biallelic variant in AGTPBP1 causes infantile lower motor neuron degeneration and cerebellar atrophy.
Karakaya, M., Paketci, C., Altmueller, J., Thiele, H., Hoelker, I., Yis, U. and Wirth, B.
American Journal of Medical Genetics Part A 179 (8): 1580-1584. August 2019

Targeted sequencing with expanded gene profile enables high diagnostic yield in non-5q-spinal muscular atrophies.
Karakaya, M., Storbeck, M., Strathmann, E.A., Delle Vedove, A., Hölker, I., Altmueller, J., Naghiyeva, L., Schmitz-Steinkrüger, L., Vezyroglou, K., Motameny, S., Alawbathani, S., Thiele, H., Polat, A.I., Okur, D., Boostani, R., Karimiani, E.G., Wunderlich, G., Ardicli, D., Topaloglu, H., Kirschner, J., Schrank, B., Maroofian, R., Magnusson, O., Yis, U., Nürnberg, P., Heller, R. and Wirth, B.
Human Mutation 39 (9): 1284-1298. September 2018

Overarching control of autophagy and DNA damage response by CHD6 revealed by modeling a rare human pathology.
Kargapolova, Y., Rehimi, R., Kayserili, H., Brühl, J., Sofiadis, K., Zirkel, A., Palikyras, S., Mizi, A., Li, Y., Yigit, G., Hoischen, A., Frank, S., Russ, N., Trautwein, J., van Bon, B., Gilissen, C., Laugsch, M., Gusmao, E.G., Josipovic, N., Altmüller, J., Nürnberg, P., Längst, G., Kaiser, F.J., Watrin, E., Brunner, H., Rada-Iglesias, A., Kurian, L., Wollnik, B., Bouazoune, K. and Papantonis, A.
Nature Communications 12 (1): 3014. 21 May 2021

Whole exome sequencing identifies a mutation in EYA1 and GLI3 in a patient with branchio‑otic syndrome and esophageal atresia: Coincidence or a digenic mode of inheritance?
Kause, F., Reutter, H., Marsch, F., Thiele, H., Altmüller, J., Ludwig, M. and Zhang, R.
Molecular Medicine Reports 17 (2): 3200-3205. February 2018

HSPA6: s new autosomal recessive candidate gene for the VATER/VACTERL malformation spectrum.
Kause, F., Zhang, R., Ludwig, M., Schmiedeke, E., Rissmann, A., Thiele, H., Altmueller, J., Herms, S., Hilger, A.C., Hildebrandt, F. and Reutter, H.
Birth Defects Research 111 (10): 591-597. 1 June 2019

Single cell RNA-sequencing-based analysis of CD4(+) T-cell subset-specific susceptibility to transcriptional modulation by HIV-1 latency-reversing agents.
Kazmierski, J., Postmus, D., Wyler, E., Fischer, C., Jansen, J., Meixenberger, K., Vitcetz, S.N., Sohn, M., Sauer, S., Bannert, N., Landthaler, M. and Goffinet, C.
bioRxiv : 2020.05.04.075119. 5 May 2020

Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA.
Keil, P., Wulf, A., Kachariya, N., Reuscher, S., Hühn, K., Silbern, I., Altmüller, J., Keller, M., Stehle, R., Zarnack, K., Sattler, M., Urlaub, H. and Sträßer, K.
Nucleic Acids Research 51 (2): 831-851. 25 January 2023

Genomic variants causing mitochondrial dysfunction are common in hereditary lower motor neuron disease.
Keller, N., Paketci, C., Altmueller, J., Fuhrmann, N., Wunderlich, G., Schrank, B., Unver, O., Yilmaz, S., Boostani, R., Karimiani, E.G., Motameny, S., Thiele, H., Nürnberg, P., Maroofian, R., Yis, U., Wirth, Br. and Karakaya, M.
Human Mutation 42 (4): 460-472. April 2021

Neonatal diabetes mellitus with hypergalactosemia.
Kentrup, H., Altmüller, J., Pfäffle, R. and Heimann, G.
European Journal of Endocrinology 141 (4): 379-81. October 1999

iPSC-derived reactive astrocytes from patients with multiple-sclerosis protect cocultured neurons in inflammatory conditions.
Kerkering, J., Muinjonov, B., Rosiewicz, K.S., Diecke, S., Biese, C., Schiweck, J., Chien, C., Zocholl, D., Conrad, T., Paul, F., Alisch, M. and Siffrin, V.
Journal of Clinical Investigation 133 (13): e164637. 3 July 2023

A deep intronic CLRN1 (USH3A) founder mutation generates an aberrant exon and underlies severe Usher syndrome on the Arabian Peninsula.
Khan, A.O., Becirovic, E., Betz, C., Neuhaus, C., Altmüller, J., Maria Riedmayr, L., Motameny, S., Nürnberg, G., Nürnberg, P. and Bolz, H.J.
Scientific Reports 7 (1): 1411. 3 May 2017

A missense mutation in the PISA domain of HsSAS-6 causes autosomal recessive primary microcephaly in a large consanguineous Pakistani family.
Khan, M.A., Rupp, V.M., Orpinell, M., Hussain, M.S., Altmüller, J., Steinmetz, M.O., Enzinger, C., Thiele, H., Höhne, W., Nürnberg, G., Baig, S.M., Ansar, M., Nürnberg, P., Vincent, J.B., Speicher, M.R., Gönczy, P. and Windpassinger, C.
Human Molecular Genetics 23 (22): 5940-5949. 15 November 2014

MFSD2A-associated primary microcephaly - expanding the clinical and mutational spectrum of this ultra-rare disease.
Khuller, K., Yigit, G., Martínez Grijalva, C., Altmüller, J., Thiele, H., Nürnberg, P., Elcioglu, N.H., Yeter, B., Hehr, U., Stein, A., Della Marina, A., Köninger, A., Depienne, C., Kaiser, F.J., Wollnik, B. and Kuechler, A.
European Journal of Medical Genetics 64 (10): 104310. October 2021

Heat stress causes chromatin accessibility and related gene expression changes in crown tissues of barley (Hordeum vulgare).
Kiełbowicz-Matuk, A., Smaczniak, C., Mikołajczak, K., Kuczyńska, A., Xu, X., Braeuning, C. and Krajewski, P.
Plant Molecular Biology 114 (6): 115. 22 October 2024

ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIF–containing protein that controls root growth angle in barley and wheat.
Kirschner, G.K., Rosignoli, S., Guo, L., Vardanega, I., Imani, J., Altmüller, J., Milner, S.G., Balzano, R:, Nagel, K.A., Pflugfelder, D., Forestan, C., Bovina, R., Koller, R., Stöcker, T.G., Mascher, M., Simmonds, J., Uauy, C., Schoof, H., Tuberosa, R., Salvi, S. and Hochholdinger, F.
Proceedings of the National Academy of Sciences of the United States of America 118 (35): e2101526118. 31 August 2021

A protocol for laser microdissection (LMD) followed by transcriptome analysis of plant reproductive tissue in phylogenetically distant angiosperms.
Kivivirta, K., Herbert, D., Lange, M., Beuerlein, K., Altmüller, J. and Becker, A.
Plant Methods 15 : 151. 16 December 2019

ANK3 related neurodevelopmental disorders: expanding the spectrum of heterozygous loss-of-function variants.
Kloth, K., Lozic, B., Tagoe, J., Hoffer, M.J.V., Van der Ven, A., Thiele, H., Altmüller, J., Kubisch, C., Au, P.Y.B., Denecke, J., Bijlsma, E.K. and Lessel, D.
Neurogenetics 22 (4): 263-269. October 2021

m(6)A-mRNA methylation regulates cardiac gene expression and cellular growth.
Kmietczyk, V., Riechert, E., Kalinski, L., Boileau, E., Malovrh, E., Malone, B., Gorska, A., Hofmann, C., Varma, E., Jürgensen, L., Kamuf-Schenk, V., Altmüller, J., Tappu, R., Busch, M., Most, P., Katus, H.A., Dieterich, C. and Völkers, M.
Life Science Alliance 2 (2): e201800233. April 2019