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

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

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

Association of the human gut microbiota with vascular stiffness.
Cuadrat, R.R.C. and Goris, T. and Birukov, A. and Eichelmann, F. and Andrade, B.G.N. and Bang, C. and Franke, A. and 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. and Kratzer, A. and Arnal, H.G. and Rathgeber, A.C. and Wreczycka, K. and Blume, A. and Gündüz, I.B. and Ebenal, V. and Mauno, T. and Osberg, B. and Moobed, M. and Hartung, J. and Jakobs, K. and Seppelt, C. and Meteva, D. and Haghikia, A. and Leistner, D.M. and Landmesser, Ulf and Akalin, A.
NAR Genomics and Bioinformatics 5 (2): lqad061. June 2023

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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. and Balzer, F. and Haufe, S. and Giesa, N. and Schiefenhövel, F. and Schmieding, M. and Jurth, C. and Kopp, W. and Akalin, A. and Schaller, S.J. and Weber-Carstens, S. and Spies, C. and von Dincklage, F.
Scientific Reports 11 (1): 13205. 24 June 2021

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

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

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

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

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

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

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

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

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

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

Functional interplay of Epstein-Barr virus oncoproteins in a mouse model of B cell lymphomagenesis.
Sommermann, T. and Yasuda, T. and Ronen, J. and Wirtz, T. and Weber, T. and Sack, U. and Caeser, R. and Zhang, J. and Li, X. and Chu, V.T. and Jauch, A. and Unger, K. and Hodson, D.J. and 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages.
Schroder, K. and Irvine, K.M. and Taylor, M.S. and Bokil, N.J. and Le Cao, K.A. and Masterman, K.A. and Labzin, L.I. and Semple, C.A. and Kapetanovic, R. and Fairbairn, L. and Akalin, A. and Faulkner, G.J. and Baillie, J.K. and Gongora, M. and Daub, C.O. and Kawaji, H. and McLachlan, G.J. and Goldman, N. and Grimmond, S.M. and Carninci, P. and Suzuki, H. and Hayashizaki, Y. and Lenhard, B. and 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

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

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

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

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

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

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

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

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

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

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

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

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

Book

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

Review

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. and Cuadrat, R.R.C. and Tonetti, F.R. and Kitazawa, H. and Villena, J.
Bioscience of Microbiota, Food and Health 41 (3): 94-102. 1 July 2022

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

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

Preprint

The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators.
Appel, L.M. and Grishkovskaya, I. and Benedum, J. and Franke, V. and Polyansky, A. and Neudolt, A. and Wunder, A. and Zagrovic, B. and Akalin, A. and Djinovic-Carugo, K. and Slade, D.
bioRxiv : 2022.02.26.482114. 27 February 2022

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

Cell-type specialization in the brain is encoded by specific long-range chromatin topologies.
Winick-Ng, W. and Kukalev, A. and Harabula, I. and Zea Redondo, L. and Meijer, M. and Serebreni, L. and Bianco, S. and Szabo, D. and Chiariello, A.M. and Irastorza-Azcarate, I. and Fiorillo, L. and Musella, F. and Thieme, C. and Irani, E. and Torlai Triglia, E. and Kolodziejczyk, A.A. and Abentung, A. and Apostolova, G, and Paul, E.J. and Franke, V. and Kempfer, R. and Akalin, A. and Teichmann, S. and Dechant, G. and Ungless, M.A. and Nicodemi, M. and Castelo-Branco, G. and Pombo, A.
bioRxiv : 2020.04.02.020990. 12 May 2021

Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning.
Kopp, W. and Akalin, A. and Ohler, U.
bioRxiv : 2021.05.11.443540. 12 May 2021

The SEQC2 Epigenomics Quality Control (EpiQC) Study: comprehensive characterization of epigenetic methods, reproducibility, and quantification.
Foox, J. and Nordlund, J. and Lalancette, C. and Gong, T. and Lacey, M. and Lent, S. and Langhorst, B.W. and Ponnaluri, V.K.C. and Williams, L. and Padmamabhan, K. and Cavalcante, R. and Lundmark, A. and Butler, D. and Gurvitch, J. and Greally, J.M. and Suzuki, M. and Menor, M. and Nasu, M. and Alonso, A. and Sheridan, C. and Scherer, A. and Bruinsma, S. and Golda, G. and Muszynska, A. and Labaj, P.P. and Campbe, M.A. and Wos, F. and Raine, A. and Liljedahl, U. and Axelsson, T. and Wang, C. and Chen, Z. and Yang, Z. and Li, J. and Yang, X. and Wang, H. and Melnick, A. and Guo, S. and Blume, A. and Franke, V. and Ibanez de Caceres, I. and Rodriguez-Antolin, C. and Rosas, R. and Wade Davis, J. and Ishii, J. and Megherbi, D.B. and Xiao, W. and Liao, W. and Xu, J. and Hong, H. and Ning, B. and Tong, W. and Akalin, A. and Wang, Y. and Wang, Y. and Mason, C.E.
bioRxiv : 2020.12.14.421529. 26 April 2021

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

Parallel genetics of regulatory sequences in vivo.
Froehlich, J. and Uyar, B. and Herzog, M. and Theil, K. and Glažar, P. and Akalin, A. and Rajewsky, N.
bioRxiv : 2020.07.28.224998. 29 July 2020

Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in wildtype and cloche/npas4l mutant zebrafish embryos.
McGarvey, A.C. and Kopp, W. and Vučićević, D. and Kempfer, R. and Mattonet, K. and Hirsekorn, A. and Bilić, I. and Trinks, A. and Merks, A.M. and Panáková, D. and Pombo, A. and Akalin, A. and Junker, J.P. and Stainier, D.Y.R. and Garfield, D. and Ohler, U. and Lacadie, S.A.
bioRxiv : 2020.06.26.173377. 26 June 2020

Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention.
Wyler, E. and Mösbauer, K. and Franke, V. and Diag, A. and Gottula, L.T. and Arsie, R. and Klironomos, F. and Koppstein, D. and Ayoub, S. and Buccitelli, C. and Richter, A. and Legnini, I. and Ivanov, A. and Mari, T. and Del Giudice, S. and Papies, J.P. and Müller, M.A. and Niemeyer, D. and Selbach, M. and Akalin, A. and Rajewsky, N. and Drosten, C. and Landthaler, M.
bioRxiv : 2020.05.05.079194. 5 May 2020

Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells.
Kim, M. and Franke, V. and Brandt, B. and Spuler, S. and Akalin, A. and Birchmeier, C.
bioRxiv : 2020.04.14.041665. 15 April 2020

PHF3 regulates neuronal gene expression through the new Pol II CTD reader domain SPOC.
Appel, L.M. and Franke, V. and Bruno, M. and Grishkovskaya, I. and Kasiliauskaite, A. and Schoeberl, U.E. and Puchinger, M.G. and Kostrhon, S. and Beltzung, E. and Mechtler, K. and Lin, G. and Vlasova, A. and Leeb, M. and Pavri, R. and Stark, A. and Akalin, A. and Stefl, R. and Bernecky, C. and Djinovic-Carugo, K. and Slade, D.
bioRxiv : 2020.02.11.943159. 12 February 2020

Pdap1 protects mature B lymphocytes from stress-induced cell death and promotes antibody gene diversification.
Delgado-Benito, V. and Berruezo-Llacuna, M. and Altwasser, R. and Winkler, W. and Balasubramanian, S. and Sundaravinayagam, D. and Graf, R. and Rahjouei, A. and Driesner, M. and Keller, L. and Janz, M. and Akalin, A. and Di Virgilio, M.
bioRxiv : 2020.01.30.917062. 31 January 2020

A novel IKK- and proteasome-independent mechanism of RelA activation triggers senescence associated secretome via transcriptional repression of NFKBIA.
Kolesnichenko, M. and Mikuda, N. and Höpken, U.E. and Milanovic, M. and Tufan, A.B. and Uyar, B. and Sun, W. and Schleich, K. and von Hoff, L. and Willenbrock, M. and Krahn, I. and Jungmann, S. and Hinz, M. and Akalin, A. and Lee, S. and Schmidt-Ullrich, R. and Schmitt, C.A. and Scheidereit, C.
bioRxiv : 2019.12.19.882225. 20 December 2019

Functional annotation of human long non-coding RNAs via molecular phenotyping.
Ramilowski, J. and Yip, C.W. and Agrawal, S. and Chang, J.C. and Ciani, Y. and Kulakovskiy, I.V. and Mendez, M. and Ooi, J.L.C. and Ouyang, J.F. and Parkinson, N. and Petri, A. and Roos, L. and Severin, J. and Yasuzawa, K. and Abugessaisa, I. and Akalin, A. and Antonov, I. and Arner, E. and Bonetti, A. and Bono, H. and Borsari, B. and Brombacher, F. and Cannistraci, C.V. and Cameron, C.J.F. and Cardenas, R. and Cardon, M. and Chang, H. and Dostie, J. and Ducoli, L. and Favorov, A. and Fort, A. and Garrido, D. and Gil, N. and Gimenez, J. and Guler, R. and Handoko, L. and Harshbarger, J. and Hasegawa, A. and Hasegawa, Y. and Hashimoto, K. and Hayatsu, N. and Heutink, P. and Hirose, T. and Imada, E.L. and Itoh, M. and Kaczkowski, B. and Kanhere, A. and Kawabata, E. and Kawaji, H. and Kawashima, T. and Kelly, T. and Kojima, M. and Kondo, N. and Koseki, H. and Kouno, T. and Kratz, A. and Kurowska-Stolarska, M. and Kwon, A.T.J. and Leek, J. and Lennartsson, A. and Lizio, M. and Lopez, F. and Luginbühl, J. and Maeda, S. and Makeev, V. and Marchionni, L. and Medvedeva, Y.A. and Minoda, A. and Müller, F. and Aguirre, M.M. and Murata, M. and Nishiyori, H. and Nitta, K. and Noguchi, S. and Noro, Y. and Nurtdinov, R. and Okazaki, Y. and Orlando, V. and Paquette, D. and Parr, C. and Rackham, O.J.L. and Rizzu, P. and Sanchez, D.F. and Sandelin, A. and Sanjana, P. and Semple, C.A.M. and Sharma, H. and Shibayama, Y. and Sivaraman, D. and Suzuki, T. and Szumowski, S. and Tagami, M. and Taylor, M.S. and Terao, C. and Thodberg, M. and Thongjuea, S. and Tripathi, V. and Ulitsky, I. and Verardo, R. and Vorontsov, I. and Yamamoto, C. and Young, R.S. and Baillie, J.K. and Forrest, A.R.R. and Guigó, R. and Hoffman, M.M. and Hon, C.C. and Kasukawa, T. and Kauppinen, S. and Kere, J. and Lenhard, B. and Schneider, C. and Suzuki, H. and Yagi, K. and de Hoon, M. and Shin, J.W. and Carninci, P.
bioRxiv : 700864. 18 July 2019

Janggu: deep learning for genomics.
Kopp, W. and Monti, R. and Tamburrini, A. and Ohler, U. and Akalin, A.
bioRxiv : 700450. 16 July 2019

Single-cell RNA-sequencing of Herpes simplex virus 1-infected cells identifies NRF2 activation as an antiviral program.
Wyler, E. and Franke, V. and Menegatti, J. and Kocks, C. and Boltengagen, A. and Praktiknjo, S. and Walch-Rückheim, B. and Rajewsky, N. and Grässer, F. and Akalin, A. and Landthaler, M.
bioRxiv : 566992. 4 March 2019

The conserved histone chaperone LIN-53 links lifespan and healthspan regulation in C. elegans.
Müthel, S. and Uyar, B. and He, M. and Krause, A. and Vitrinel, B. and Bulut, S. and Vasiljevic, D. and Akalin, A. and Kempa, S. and Tursun, B.
bioRxiv : 539015. 2 February 2019

Evaluation of colorectal cancer subtypes and cell lines using deep learning.
Ronen, J. and Hayat, S. and Akalin, A.
bioRxiv : 464743. 12 November 2018

Long non-coding RNAs defining major subtypes of B cell precursor acute lymphoblastic leukemia.
Rani James, A. and Schroeder, M.P. and Neumann, M. and Bastian, L. and Eckert, C. and Gökbuget, N. and Tanchez, J.O. and Schlee, C. and Isaakidis, K. and Schwartz, S. and Burmeister, T. and von Stackelberg, A. and Rieger, M.A. and Göllner, S. and Horstman, M. and Schrappe, M. and Kirschner-Schwabe, R. and Brüggemann, M. and Müller-Tidow, C. and Serve, H. and Akalin, A. and Baldus, C.D.
bioRxiv : 365429. 9 July 2018

Reproducible genomics analysis pipelines with GNU Guix.
Wurmus, R. and Uyar, B. and Osberg, B. and Franke, V. and Gosdschan, A. and Wreczycka, K. and Ronen, J. and Akalin, A.
bioRxiv : 298653. 21 April 2018

Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets via protocol-specific bias modeling.
Karabacak Calviello, A. and Hirsekorn, A. and Wurmus, R. and Yusuf, D. and Ohler, U.
bioRxiv : 284364. 19 March 2018

netSmooth: Network-smoothing based imputation for single cell RNA-seq.
Ronen, J. and Akalin, A.
bioRxiv : 234021. 13 December 2017

FACT sets a barrier for cell fate reprogramming in C. elegans and human.
Kolundzic, E. and Ofenbauer, A. and Uyar, B. and Sommermeier, A. and Seelk, S. and He, M. and Baytek, G. and Akalin, A. and Diecke, S. and Lacadie, S.A. and Tursun, B.
bioRxiv : 185116. 6 September 2017

Strategies for analyzing bisulfite sequencing data.
Wreczycka, K. and Gosdschan, A. and Yusuf, D. and Gruening, B. and Assenov, Y. and Akalin, A.
bioRxiv : 109512. 9 August 2017

HOT or not: Examining the basis of high-occupancy target regions.
Wreczycka, K. and Franke, V. and Uyar, B. and Wurmus, R. and Akalin, A.
bioRxiv : 107680. 31 July 2017

Mutations in disordered regions cause disease by creating endocytosis motifs.
Meyer, K. and Uyar, B. and Kirchner, M. and Cheng, J. and Akalin, A. and Selbach, M.
bioRxiv : 141622. 24 May 2017