2024
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
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20 September 2024
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
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6 August 2024
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
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11 April 2024
2023
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
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
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
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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
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
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1 February 2023
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
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
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January 2023
2022
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
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
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15 November 2022
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
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
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
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
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26 April 2022
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
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
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
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
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
2021
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
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
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
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
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
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
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
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
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
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
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
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
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
2020
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
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
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
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
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
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
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
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
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April 2020
Computational genomics with R.
Akalin, A.
Chapman and Hall/CRC Computational Biology Series
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CRC Press LLC, Milton.
ISBN 9781498781855
2020
2019
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
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
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
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
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
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
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
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28 March 2019
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 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
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
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
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
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
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
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
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
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., Pimpinella, S., Hackel, P., Akalin, A., Jessell, T.M. and Zampieri, N.
Cell Reports 22
(7): 1681-1694.
13 February 2018
2017
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
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
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
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
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
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
Degrons in cancer.
Meszaros, B., Kumar, M., Gibson, T.J., Uyar, B. and Dosztanyi, Z.
Science Signaling 10
(470): eaak9982.
14 March 2017
2016
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.
Nucleic Acids Research 44
(D1): D27-D37.
4 January 2016
2015
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
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
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
Reproducible and user-controlled software environments in HPC with Guix.
Courtes, L. and Wurmus, R.
Lecture Notes in Computer Science 9523
: 579-591.
2015
2014
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
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
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
2013
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
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
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
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
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
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
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
2011
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
2010
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
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
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
2009
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
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
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
2008
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
2007
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
2006
Predicting the binding affinity of MHC class II peptides.
Altiparmak, F., Akalin, A. and Ferhatosmanoglu, H.
Computational Systems Bioinformatics 2006
: 331-334.
August 2006
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
This list was generated on Mon Oct 14 20:00:12 2024 UTC.