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Multiomic and longitudinal dissection of immune dynamics associated with Parkinsonism after ciltacabtagene autoleucel therapy.
Kadel, Sofie-Katrin, Scheller, Lukas, Leipold, Alexander M., Krammer, Tobias, Raskó, Tamás, Alb, Miriam, Weis, Philipp, Leberzammer, Maria, Schmitt, Friederike, Stetter, Clara, Tamamushi, Yoko, Köck, Alicia, Köberle, Philipp, Reich, Martin, Musacchio, Thomas, Doppler, Kathrin, Sommer, Claudia, Cebulla, Nadine, McFleder, Rhonda, Ip, Chi Wang, Volkmann, Jens, Kallius, Matthias, Serfling, Sebastian E., Hartrampf, Philipp E., Buck, Andreas K., Pande, Amit ORCID: https://orcid.org/0009-0008-0826-973X, Löffler, Dennis, Gernert, Michael, Duell, Johannes, Topp, Max S., Mersi, Julia, Waldschmidt, Johannes, Einsele, Hermann, Hudecek, Michael, Saliba, Antoine-Emmanuel, Rasche, Leo and Kortüm, K. Martin
Blood Cancer Discovery 7 (4): 544-557. 1 July 2026

Multiplexed biomarkers dynamically detect heterogeneous residual neuroblastoma cell clone activity in the bone marrow niche.
Schroeer, Anna M., Winkler, Annika, Fillies, Marion, Kranig, Charleen, Karaman, Eliz, von Stetten, Felix, Zengerle, Roland, Lehnert, Michael, Blume, Alexander ORCID: https://orcid.org/0000-0003-3045-8234, Hollander, Jan F., Lodrini, Marco, Eggert, Angelika, Akalin, Altuna ORCID: https://orcid.org/0000-0002-0468-0117, Astrahantseff, Kathy, Eckert, Cornelia, Deubzer, Hedwig E. ORCID: https://orcid.org/0000-0002-6115-4893 and Szymansky, Annabell ORCID: https://orcid.org/0000-0003-4797-4526
Cancer Letters 645 : 218352. 1 May 2026

Altered cholesterol immunometabolism activates the macrophage NLRP3-inflammasome in lung fibrosis.
Vaso, Mariza, Dukic, Matija, Pennitz, Peter, Manukyan, Artür ORCID: https://orcid.org/0000-0002-0441-9517, Collum, Scott, Lin, Wanchang, Winder, Catherine L, Dunn, Warwick B, Schupp, Jonas C., Braubach, Peter, Wygrecka, Malgorzata, Ren, Dewei, Suarez, Erik E, Huang, Howard J, Hussain, Rahat, Patel, Bela, Karmouty-Quintana, Harry, Akalin, Altuna ORCID: https://orcid.org/0000-0002-0468-0117, Landthaler, Markus ORCID: https://orcid.org/0000-0002-1075-8734, Nouailles, Geraldine, Ochs, Matthias, Lopez-Rodriguez, Elena and Giambelluca, Sonia
American Journal of Respiratory Cell and Molecular Biology 21 February 2026 (In Press)

Flexynesis: a deep learning toolkit for bulk multi-omics data integration for precision oncology and beyond.
Uyar, Bora ORCID: https://orcid.org/0000-0002-3170-4890, Savchyn, Taras, Naghsh Nilchi, Amirhossein ORCID: https://orcid.org/0000-0003-1329-3044, Sarigun, Ahmet ORCID: https://orcid.org/0009-0003-2715-5344, Wurmus, Ricardo ORCID: https://orcid.org/0009-0003-0140-4189, Shaik, Mohammed Maqsood, Grüning, Björn ORCID: https://orcid.org/0000-0002-3079-6586, Franke, Vedran ORCID: https://orcid.org/0000-0003-3606-6792 and Akalin, Altuna ORCID: https://orcid.org/0000-0002-0468-0117
Nature Communications 16 : 8261. 12 September 2025

Evaluating large language model workflows in clinical decision support for triage and referral and diagnosis.
Gaber, F. ORCID: https://orcid.org/0009-0004-5512-8527, Shaik, M., Allega, F., Bilecz, A.J., Busch, F., Goon, K., Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792 and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
NPJ Digital Medicine 8 (1): 263. 9 May 2025

Enhancing biomarker based oncology trial matching using large language models.
Al Khoury, N., Shaik, M., Wurmus, R. ORCID: https://orcid.org/0009-0003-0140-4189 and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
NPJ Digital Medicine 8 (1): 250. 6 May 2025

Leveraging large language models for data analysis automation.
Jansen, J.A., Manukyan, A. ORCID: https://orcid.org/0000-0002-0441-9517, Al Khoury, N. and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
PLoS ONE 20 (2): e0317084. 21 February 2025

Herpesviruses mimic zygotic genome activation to promote viral replication.
Neugebauer, E., Walter, S., Tan, J., Drayman, N., Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, van Gent, M., Pennisi, S., Veratti, P., Stein, K.S., Welker, I., Tay, S., Verjans, G.M.G.M., Timmers, H.T.M., Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734, Ensser, A., Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806 and Full, F.
Nature Communications 16 (1): 710. 16 January 2025

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. ORCID: https://orcid.org/0000-0002-0468-0117, Horvat, F., Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Widder, J., Georg, D. and Slade, D.
Frontiers in Immunology 15 : 1286942. 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. ORCID: https://orcid.org/0000-0003-3980-6469, Kopp, W. ORCID: https://orcid.org/0000-0003-0376-0032, Lutsik, P. and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
BMC Bioinformatics 25 (1): 257. 6 August 2024

Pathogenic mutations of human phosphorylation sites affect protein–protein interactions.
Rrustemi, T. ORCID: https://orcid.org/0000-0002-9075-103X, Meyer, K. ORCID: https://orcid.org/0000-0002-8244-6887, Roske, Y. ORCID: https://orcid.org/0000-0001-6237-388X, Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Imami, K. ORCID: https://orcid.org/0000-0002-7451-4982, Ishihama, Y., Daumke, O. ORCID: https://orcid.org/0000-0002-6190-1414 and Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751
Nature Communications 15 (1): 3146. 11 April 2024

The SPOC proteins DIDO3 and PHF3 co-regulate gene expression and neuronal differentiation.
Benedum, J. ORCID: https://orcid.org/0000-0003-4475-7577, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Appel, L.M. ORCID: https://orcid.org/0000-0002-6769-0777, Walch, L., Bruno, M. ORCID: https://orcid.org/0000-0002-8401-7744, Schneeweiss, R., Gruber, J., Oberndorfer, H., Frank, E., Strobl, X., Polyansky, A. ORCID: https://orcid.org/0000-0002-1011-2706, Zagrovic, B. ORCID: https://orcid.org/0000-0003-3814-3675, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117 and Slade, D. ORCID: https://orcid.org/0000-0002-0052-5910
Nature Communications 14 (1): 7912. 30 November 2023

Transcriptional reprogramming by mutated IRF4 in lymphoma.
Schleussner, N. ORCID: https://orcid.org/0009-0001-3549-5600, Cauchy, P. ORCID: https://orcid.org/0000-0002-0659-0799, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Giefing, M., Fornes, O. ORCID: https://orcid.org/0000-0002-5969-3054, Vankadari, N. ORCID: https://orcid.org/0000-0001-9363-080X, Assi, S.A., Costanza, M. ORCID: https://orcid.org/0000-0002-8959-1083, Weniger, M.A., Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Anagnostopoulos, I. ORCID: https://orcid.org/0000-0002-5043-6043, Bukur, T., Casarotto, M.G. ORCID: https://orcid.org/0000-0002-0571-7671, Damm, F. ORCID: https://orcid.org/0000-0001-5553-1173, Daumke, O. ORCID: https://orcid.org/0000-0002-6190-1414, Edginton-White, B., Gebhardt, J.C.M. ORCID: https://orcid.org/0000-0003-1900-600X, Grau, M., Grunwald, S. ORCID: https://orcid.org/0000-0003-3978-6277, Hansmann, M.L., Hartmann, S. ORCID: https://orcid.org/0000-0003-3424-1091, Huber, L., Kärgel, E., Lusatis, S., Noerenberg, D., Obier, N., Pannicke, U. ORCID: https://orcid.org/0000-0002-0929-1794, Fischer, A. ORCID: https://orcid.org/0000-0002-7145-2544, Reisser, A., Rosenwald, A., Schwarz, K. ORCID: https://orcid.org/0000-0003-3178-5990, Sundararaj, S., Weilemann, A. ORCID: https://orcid.org/0009-0001-1340-6486, Winkler, W. ORCID: https://orcid.org/0000-0001-8807-9259, Xu, W., Lenz, G. ORCID: https://orcid.org/0000-0002-4728-1693, Rajewsky, K. ORCID: https://orcid.org/0000-0002-6633-6370, Wasserman, W.W. ORCID: https://orcid.org/0000-0001-6098-6412, Cockerill, P.N. ORCID: https://orcid.org/0000-0002-4410-8174, Scheidereit, C. ORCID: https://orcid.org/0000-0002-0446-6129, Siebert, R., Küppers, R., Grosschedl, R. ORCID: https://orcid.org/0000-0002-0058-1250, Janz, M. ORCID: https://orcid.org/0000-0002-1127-0044, Bonifer, C. ORCID: https://orcid.org/0000-0002-4267-0825 and Mathas, S. ORCID: https://orcid.org/0000-0001-9626-1413
Nature Communications 14 (1): 6947. 7 November 2023

Association of the human gut microbiota with vascular stiffness.
Cuadrat, R.R.C. ORCID: https://orcid.org/0000-0001-8289-2599, 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. ORCID: https://orcid.org/0000-0001-8289-2599, Kratzer, A. ORCID: https://orcid.org/0000-0002-6151-5097, Arnal, H.G. ORCID: https://orcid.org/0000-0002-5763-9388, Rathgeber, A.C. ORCID: https://orcid.org/0000-0003-3264-1040, Wreczycka, K. ORCID: https://orcid.org/0000-0002-5994-4802, Blume, A. ORCID: https://orcid.org/0000-0003-3045-8234, Gündüz, I.B. ORCID: https://orcid.org/0000-0003-2641-0916, Ebenal, V., Mauno, T., Osberg, B. ORCID: https://orcid.org/0000-0002-9854-9901, Moobed, M., Hartung, J., Jakobs, K., Seppelt, C. ORCID: https://orcid.org/0000-0003-4892-6809, Meteva, D. ORCID: https://orcid.org/0000-0003-4741-924X, Haghikia, A. ORCID: https://orcid.org/0000-0001-5568-8808, Leistner, D.M., Landmesser, Ulf ORCID: https://orcid.org/0000-0002-0214-3203 and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
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. ORCID: https://orcid.org/0000-0001-8810-0492, Sundaravinayagam, D. ORCID: https://orcid.org/0000-0003-0717-7530, Blume, A. ORCID: https://orcid.org/0000-0003-3045-8234, Marg, A. ORCID: https://orcid.org/0000-0003-3673-4244, Grunwald, S. ORCID: https://orcid.org/0000-0002-3899-5424, Metzler, E. ORCID: https://orcid.org/0000-0003-1735-6364, Escobar, H. ORCID: https://orcid.org/0000-0002-8128-7845, Müthel, S. ORCID: https://orcid.org/0000-0002-3525-8859, Wang, H. ORCID: https://orcid.org/0000-0003-3720-3859, Wollersheim, T. ORCID: https://orcid.org/0000-0002-3170-0996, Weber-Carstens, S., Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Di Virgilio, M. ORCID: https://orcid.org/0000-0001-5189-0793, Tursun, B. ORCID: https://orcid.org/0000-0001-7293-8629 and Spuler, S. ORCID: https://orcid.org/0000-0002-0155-1117
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. ORCID: https://orcid.org/0000-0002-6769-0777, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Benedum, J. ORCID: https://orcid.org/0000-0003-4475-7577, Grishkovskaya, I. ORCID: https://orcid.org/0000-0003-0164-9373, Strobl, X., Polyansky, A. ORCID: https://orcid.org/0000-0002-1011-2706, Ammann, G. ORCID: https://orcid.org/0000-0003-2135-058X, Platzer, S. ORCID: https://orcid.org/0000-0002-2518-6273, Neudolt, A. ORCID: https://orcid.org/0000-0002-5298-1205, Wunder, A., Walch, L., Kaiser, S., Zagrovic, B. ORCID: https://orcid.org/0000-0003-3814-3675, Djinovic-Carugo, K. ORCID: https://orcid.org/0000-0003-0252-2972, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117 and Slade, D. ORCID: https://orcid.org/0000-0002-0052-5910
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. ORCID: https://orcid.org/0009-0001-3549-5600, 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. ORCID: https://orcid.org/0000-0002-0468-0117, 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. ORCID: https://orcid.org/0000-0002-8959-1083, Cui, C., Daumke, O. ORCID: https://orcid.org/0000-0002-6190-1414, Del Bel, K.L., Eibel, H., Feng, X., Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Gebhardt, J.C.M., Götz, A., Grunwald, S. ORCID: https://orcid.org/0000-0003-3978-6277, Hoareau, B., Hughes, T.R., Jacobsen, E.M., Janz, M. ORCID: https://orcid.org/0000-0002-1127-0044, 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. ORCID: https://orcid.org/0000-0001-8807-9259, 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. ORCID: https://orcid.org/0000-0001-9626-1413, Rosenzweig, S.D., Schwarz, K., 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. ORCID: https://orcid.org/0000-0003-0227-7428, de Castro Cuadrat, R.R. ORCID: https://orcid.org/0000-0001-8289-2599, Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806, Wurmus, R. ORCID: https://orcid.org/0009-0003-0140-4189, Deter, A., Quedenau, C. ORCID: https://orcid.org/0000-0002-6846-4915, Dohmen, J. ORCID: https://orcid.org/0000-0002-7826-3025, Faxel, M. ORCID: https://orcid.org/0009-0007-4891-1734, Borodina, T. ORCID: https://orcid.org/0000-0002-6978-016X, Blume, A. ORCID: https://orcid.org/0000-0003-3045-8234, Freimuth, J. ORCID: https://orcid.org/0000-0002-9259-3696, Meixner, M., Grau, J.H., Liere, K., Hackenbeck, T., Zietzschmann, F., Gnirss, R., Böckelmann, U., Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Barke, N. ORCID: https://orcid.org/0009-0004-5862-6628, Altmüller, J. ORCID: https://orcid.org/0000-0003-4372-1521, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734 and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
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. ORCID: https://orcid.org/0000-0001-7217-3881, Gündüz, I.B. ORCID: https://orcid.org/0000-0003-2641-0916, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890 and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
Cancers 14 (22): 5604. 15 November 2022

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.
Baranasic, D. ORCID: https://orcid.org/0000-0001-5948-0932, Hörtenhuber, M. ORCID: https://orcid.org/0000-0002-5599-5565, Balwierz, P.J. ORCID: https://orcid.org/0000-0002-1548-4605, Zehnder, T. ORCID: https://orcid.org/0000-0002-4127-2673, Mukarram, A.K., Nepal, C., Várnai, C. ORCID: https://orcid.org/0000-0003-0048-9507, Hadzhiev, Y. ORCID: https://orcid.org/0000-0002-1134-4904, Jimenez-Gonzalez, A. ORCID: https://orcid.org/0000-0001-7702-6135, Li, N. ORCID: https://orcid.org/0000-0002-8919-2357, Wragg, J., D'Orazio, F.M., Relic, D. ORCID: https://orcid.org/0000-0001-6237-3345, Pachkov, M. ORCID: https://orcid.org/0000-0001-7616-6435, Díaz, N. ORCID: https://orcid.org/0000-0002-0319-3448, Hernández-Rodríguez, B. ORCID: https://orcid.org/0000-0002-5118-8715, Chen, Z. ORCID: https://orcid.org/0000-0002-8376-7367, Stoiber, M., Dong, M. ORCID: https://orcid.org/0000-0003-4084-3099, Stevens, I. ORCID: https://orcid.org/0000-0003-3823-1499, Ross, S.E., Eagle, A., Martin, R., Obasaju, O. ORCID: https://orcid.org/0000-0001-5952-3103, Rastegar, S. ORCID: https://orcid.org/0000-0003-4411-5646, McGarvey, A.C. ORCID: https://orcid.org/0000-0003-3838-1139, Kopp, W. ORCID: https://orcid.org/0000-0003-0376-0032, Chambers, E. ORCID: https://orcid.org/0000-0003-1252-8059, Wang, D. ORCID: https://orcid.org/0000-0003-0068-1005, Kim, H.R., Acemel, R.D. ORCID: https://orcid.org/0000-0003-4120-0140, Naranjo, S. ORCID: https://orcid.org/0000-0002-4529-3332, Łapiński, M. ORCID: https://orcid.org/0000-0003-4892-976X, Chong, V. ORCID: https://orcid.org/0000-0002-2547-3694, Mathavan, S., Peers, B., Sauka-Spengler, T. ORCID: https://orcid.org/0000-0001-9289-0263, Vingron, M. ORCID: https://orcid.org/0000-0002-1765-4241, Carninci, P. ORCID: https://orcid.org/0000-0001-7202-7243, Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116, Lacadie, S.A. ORCID: https://orcid.org/0000-0002-0893-5340, Burgess, S.M. ORCID: https://orcid.org/0000-0003-1147-0596, Winata, C. ORCID: https://orcid.org/0000-0002-7718-5248, van Eeden, F. ORCID: https://orcid.org/0000-0003-3483-8269, Vaquerizas, J.M. ORCID: https://orcid.org/0000-0002-6583-6541, Gómez-Skarmeta, J.L. ORCID: https://orcid.org/0000-0001-5125-4332, Onichtchouk, D. ORCID: https://orcid.org/0000-0001-6497-1445, Brown, B.J. ORCID: https://orcid.org/0000-0002-5898-5848, Bogdanovic, O. ORCID: https://orcid.org/0000-0001-5680-0056, van Nimwegen, E. ORCID: https://orcid.org/0000-0001-6338-1312, Westerfield, M. ORCID: https://orcid.org/0000-0003-1187-7839, Wardle, F.C ORCID: https://orcid.org/0000-0001-5444-1889, Daub, C.O. ORCID: https://orcid.org/0000-0002-3295-8729, Lenhard, B. ORCID: https://orcid.org/0000-0002-1114-1509 and Müller, F. ORCID: https://orcid.org/0000-0002-0996-774X
Nature Genetics 54 (7): 1037-1050. July 2022

Identifying tumor cells at the single-cell level using machine learning.
Dohmen, J. ORCID: https://orcid.org/0000-0002-7826-3025, Baranovskii, A. ORCID: https://orcid.org/0000-0001-7217-3881, Ronen, J. ORCID: https://orcid.org/0000-0003-3980-6469, Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792 and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
Genome Biology 23 (1): 123. 30 May 2022

Rapid inflammasome activation is attenuated in post-myocardial infarction monocytes.
Giral, H., Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, 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. ORCID: https://orcid.org/0000-0002-0468-0117, 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. ORCID: https://orcid.org/0000-0003-0376-0032, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117 and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
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. ORCID: https://orcid.org/0000-0003-3838-1139, Kopp, W. ORCID: https://orcid.org/0000-0003-0376-0032, Vučićević, D. ORCID: https://orcid.org/0000-0002-1162-6709, Mattonet, K. ORCID: https://orcid.org/0000-0002-9705-8086, Kempfer, R. ORCID: https://orcid.org/0000-0002-8588-8576, Hirsekorn, A., Bilić, I. ORCID: https://orcid.org/0000-0002-2730-1634, Gil, M. ORCID: https://orcid.org/0000-0002-3885-7806, Trinks, A. ORCID: https://orcid.org/0000-0001-9983-1506, Merks, A.M. ORCID: https://orcid.org/0000-0001-5677-7204, Panáková, D. ORCID: https://orcid.org/0000-0002-8739-6225, Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, Stainier, D.Y.R. ORCID: https://orcid.org/0000-0002-0382-0026, Garfield, D. ORCID: https://orcid.org/0000-0002-8790-797X, Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116 and Lacadie, S.A. ORCID: https://orcid.org/0000-0002-0893-5340
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. ORCID: https://orcid.org/0000-0002-4399-5250, Egan, P.J., Nagler, J., Ronen, J. ORCID: https://orcid.org/0000-0003-3980-6469 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. ORCID: https://orcid.org/0000-0001-7702-5749, Morao, A.K. ORCID: https://orcid.org/0000-0003-2194-8071, Kim, J. ORCID: https://orcid.org/0000-0001-9473-3093, Jimenez, D.S. ORCID: https://orcid.org/0000-0003-0943-9063, Maryn, N. ORCID: https://orcid.org/0000-0002-0975-3354, Bikkasani, K. ORCID: https://orcid.org/0000-0002-4000-1863, Carrozza, M.J., Albritton, S.E. ORCID: https://orcid.org/0000-0001-6093-9560, Kramer, M. ORCID: https://orcid.org/0000-0002-1643-0756, Street, L.A. ORCID: https://orcid.org/0000-0002-5473-6713, Cerimi, K. ORCID: https://orcid.org/0000-0003-0775-3032, Schumann, V.F. ORCID: https://orcid.org/0000-0003-0227-7428, Bahry, E. ORCID: https://orcid.org/0000-0002-6358-2576, Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Woehler, A. ORCID: https://orcid.org/0000-0001-5157-9313 and Ercan, S. ORCID: https://orcid.org/0000-0001-7297-1648
Journal of Cell Science 135 (2): jcs258818. January 2022

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. ORCID: https://orcid.org/0000-0003-3045-8234, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, 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. ORCID: https://orcid.org/0000-0002-0468-0117, Wang, Y., Deng, Y. and Mason, C.E. ORCID: https://orcid.org/0000-0002-1850-1642
Genome Biology 22 (1): 332. 6 December 2021

Cell-type specialization is encoded by specific chromatin topologies.
Winick-Ng, W. ORCID: https://orcid.org/0000-0002-8716-5558, Kukalev, A. ORCID: https://orcid.org/0000-0001-5847-3773, Harabula, I. ORCID: https://orcid.org/0000-0002-9094-0519, Zea-Redondo, L. ORCID: https://orcid.org/0000-0001-9064-9126, Szabó, D. ORCID: https://orcid.org/0000-0001-8109-5088, Meijer, M. ORCID: https://orcid.org/0000-0003-3314-1224, Serebreni, L. ORCID: https://orcid.org/0000-0003-3831-9722, Zhang, Y., Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Irastorza-Azcarate, I. ORCID: https://orcid.org/0000-0001-5245-2322, Thieme, C.J. ORCID: https://orcid.org/0000-0002-1566-0971, Sparks, T.M. ORCID: https://orcid.org/0000-0002-9455-8309, Carvalho, S. ORCID: https://orcid.org/0000-0001-6436-205X, Fiorillo, L., Musella, F., Irani, E. ORCID: https://orcid.org/0000-0002-8194-960X, Triglia, E.T. ORCID: https://orcid.org/0000-0002-6059-0116, Kolodziejczyk, A.A., Abentung, A., Apostolova, G., Paul, E.J., Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Kempfer, R. ORCID: https://orcid.org/0000-0002-8588-8576, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Teichmann, S.A., Dechant, G., Ungless, M.A., Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416, Welch, L., Castelo-Branco, G. and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
Nature 599 (7886): 684-691. 25 November 2021

Lymphocyte access to lymphoma is impaired by high endothelial venule regression.
Menzel, L. ORCID: https://orcid.org/0000-0002-3816-6255, Zschummel, M. ORCID: https://orcid.org/0000-0002-4778-8742, Crowley, T. ORCID: https://orcid.org/0000-0002-1404-6005, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Grau, M., Ulbricht, C. ORCID: https://orcid.org/0000-0003-2983-6242, Hauser, A., Siffrin, V. ORCID: https://orcid.org/0000-0002-1532-2868, Bajénoff, M., Acton, S.E., Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Lenz, G., Willimsky, G. ORCID: https://orcid.org/0000-0002-9693-948X, Höpken, U.E. ORCID: https://orcid.org/0000-0002-0776-4893 and Rehm, A. ORCID: https://orcid.org/0000-0001-7490-1950
Cell Reports 37 (4): 109878. 26 October 2021

PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC.
Appel, L.M. ORCID: https://orcid.org/0000-0002-6769-0777, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Bruno, M. ORCID: https://orcid.org/0000-0002-8401-7744, Grishkovskaya, I., Kasiliauskaite, A., Kaufmann, T. ORCID: https://orcid.org/0000-0002-9734-260X, Schoeberl, U.E., Puchinger, M.G., Kostrhon, S., Ebenwaldner, C., Sebesta, M., Beltzung, E., Mechtler, K. ORCID: https://orcid.org/0000-0002-3392-9946, Lin, G., Vlasova, A., Leeb, M. ORCID: https://orcid.org/0000-0001-5114-4782, Pavri, R., Stark, A. ORCID: https://orcid.org/0000-0003-2611-0841, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Stefl, R., Bernecky, C. ORCID: https://orcid.org/0000-0003-0893-7036, Djinovic-Carugo, K. ORCID: https://orcid.org/0000-0003-0252-2972 and Slade, D. ORCID: https://orcid.org/0000-0002-0052-5910
Nature Communications 12 (1): 6078. 19 October 2021

Immunobiotic Lactobacilli improve resistance of respiratory epithelial cells to SARS-CoV-2 infection.
Islam, M.A. ORCID: https://orcid.org/0000-0003-1979-9652, Albarracin, L., Tomokiyo, M., Valdez, J.C., Sacur, J. ORCID: https://orcid.org/0000-0002-0514-5087, Vizoso-Pinto, M.G., Andrade, B.G.N., Cuadrat, R.C. ORCID: https://orcid.org/0000-0001-8289-2599, Kitazawa, H. ORCID: https://orcid.org/0000-0003-4586-5553 and Villena, J. ORCID: https://orcid.org/0000-0003-4941-4960
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. ORCID: https://orcid.org/0000-0001-8289-2599
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. ORCID: https://orcid.org/0000-0003-0376-0032, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, 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. ORCID: https://orcid.org/0000-0003-1979-9652, Albarracin, L. ORCID: https://orcid.org/0000-0001-8216-2190, Melnikov, V. ORCID: https://orcid.org/0000-0002-0825-7930, Andrade, B.G.N. ORCID: https://orcid.org/0000-0003-2481-401X, Cuadrat, R.R.C. ORCID: https://orcid.org/0000-0001-8289-2599, Kitazawa, H. ORCID: https://orcid.org/0000-0003-4586-5553 and Villena, J. ORCID: https://orcid.org/0000-0003-4941-4960
Pathogens 10 (6): 634. 21 May 2021

Parallel genetics of regulatory sequences using scalable genome editing in vivo.
Froehlich, J.J. ORCID: https://orcid.org/0000-0002-9176-4633, Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890, Herzog, M., Theil, K. ORCID: https://orcid.org/0000-0002-7205-6308, Glažar, P. ORCID: https://orcid.org/0000-0003-0842-0088, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
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. ORCID: https://orcid.org/0000-0003-1033-0954, Schaff, J., Duda, M., Pataki, B.Á., Sun, M., Snyder, P. ORCID: https://orcid.org/0000-0002-6967-2185, 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. ORCID: https://orcid.org/0000-0001-5648-4532, Espino, C., Glaab, E. ORCID: https://orcid.org/0000-0003-3977-7469, Goan, E., Golabchi, F.N., Görmez, Y., Jaakkola, M.K., Jonnagaddala, J. ORCID: https://orcid.org/0000-0002-9912-2344, Klén, R., Li, D., McDaniel, C., Perrin, D. ORCID: https://orcid.org/0000-0002-4007-5256, Perumal, T.M., Rad, N.M., Rainaldi, E. ORCID: https://orcid.org/0000-0003-1082-7055, Sapienza, S., Schwab, P., Shokhirev, N., Venäläinen, M.S. ORCID: https://orcid.org/0000-0003-1777-4259, Vergara-Diaz, G., Zhang, Y. ORCID: https://orcid.org/0000-0002-7538-872X, Wang, Y., Guan, Y. ORCID: https://orcid.org/0000-0001-8275-2852, Brunner, D., Bonato, P. ORCID: https://orcid.org/0000-0002-1818-1714, Mangravite, L.M. ORCID: https://orcid.org/0000-0001-7841-3612 and Omberg, L. ORCID: https://orcid.org/0000-0002-4719-9120
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. ORCID: https://orcid.org/0000-0002-9884-1806, Mösbauer, K., Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Diag, A., Gottula, L.T., Arsiè, R. ORCID: https://orcid.org/0000-0002-7869-7624, Klironomos, F., Koppstein, D. ORCID: https://orcid.org/0000-0002-8618-7237, Hönzke, K., Ayoub, S. ORCID: https://orcid.org/0000-0001-5043-8922, Buccitelli, C. ORCID: https://orcid.org/0000-0002-2637-2131, Hoffmann, K., Richter, A., Legnini, I. ORCID: https://orcid.org/0000-0002-8984-5215, Ivanov, A. ORCID: https://orcid.org/0000-0002-4824-1925, Mari, T. ORCID: https://orcid.org/0000-0001-6011-9386, Del Giudice, S. ORCID: https://orcid.org/0000-0003-0194-3767, Papies, J., Praktiknjo, S. ORCID: https://orcid.org/0000-0002-0186-5271, Meyer, T.F., Müller, M.A., Niemeyer, D. ORCID: https://orcid.org/0000-0002-1897-6365, Hocke, A., Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Drosten, C. and Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734
iScience 24 (3): 102151. 19 March 2021

Transcriptional repression of NFKBIA triggers constitutive IKK- and proteasome-independent p65/RelA activation in senescence.
Kolesnichenko, M. ORCID: https://orcid.org/0000-0001-7366-9061, Mikuda, N., Höpken, U.E. ORCID: https://orcid.org/0000-0002-0776-4893, Kärgel, E., Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890, Tufan, A.B. ORCID: https://orcid.org/0000-0002-8734-9736, Milanovic, M. ORCID: https://orcid.org/0000-0003-1860-6003, Sun, W. ORCID: https://orcid.org/0000-0001-9607-1361, Krahn, I., Schleich, K., von Hoff, L., Hinz, M. ORCID: https://orcid.org/0000-0003-2611-4121, Willenbrock, M., Jungmann, S., Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Lee, S. ORCID: https://orcid.org/0000-0002-4614-2931, Schmidt-Ullrich, R. ORCID: https://orcid.org/0000-0002-2472-6530, Schmitt, C.A. ORCID: https://orcid.org/0000-0002-4731-2226 and Scheidereit, C. ORCID: https://orcid.org/0000-0002-0446-6129
EMBO Journal 40 (6): e104296. 15 March 2021

Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells.
Kim, M. ORCID: https://orcid.org/0000-0002-6863-841X, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Brandt, B., Lowenstein, E.D. ORCID: https://orcid.org/0000-0003-3755-0818, Schöwel, V. ORCID: https://orcid.org/0000-0002-5924-3088, Spuler, S. ORCID: https://orcid.org/0000-0002-0155-1117, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117 and Birchmeier, C. ORCID: https://orcid.org/0000-0002-2041-8872
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. ORCID: https://orcid.org/0000-0002-0077-1935, Berruezo-Llacuna, M., Altwasser, R. ORCID: https://orcid.org/0009-0002-6216-6068, Winkler, W. ORCID: https://orcid.org/0000-0001-8807-9259, Sundaravinayagam, D. ORCID: https://orcid.org/0000-0003-0717-7530, Balasubramanian, S. ORCID: https://orcid.org/0000-0003-1830-5737, Caganova, M. ORCID: https://orcid.org/0000-0002-4576-6574, Graf, R. ORCID: https://orcid.org/0000-0002-5400-9938, Rahjouei, A. ORCID: https://orcid.org/0000-0003-3973-6333, Henke, M.T. ORCID: https://orcid.org/0000-0001-6572-1667, Driesner, M., Keller, L., Prigione, A. ORCID: https://orcid.org/0000-0001-9457-1952, Janz, M. ORCID: https://orcid.org/0000-0002-1127-0044, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117 and Di Virgilio, M. ORCID: https://orcid.org/0000-0001-5189-0793
Journal of Experimental Medicine 217 (10): e20200137. 5 October 2020

Single-molecule analysis reveals agonist-specific dimer formation of µ-opioid receptors.
Möller, J. ORCID: https://orcid.org/0000-0001-8429-3784, Isbilir, A. ORCID: https://orcid.org/0000-0002-9629-1150, Sungkaworn, T., Osberg, B. ORCID: https://orcid.org/0000-0002-9854-9901, Karathanasis, C., Sunkara, V., Grushevskyi, E.O. ORCID: https://orcid.org/0000-0003-1779-8306, Bock, A. ORCID: https://orcid.org/0000-0002-6344-6494, Annibale, P. ORCID: https://orcid.org/0000-0003-3208-5347, Heilemann, M. ORCID: https://orcid.org/0000-0002-9821-3578, Schütte, C. and Lohse, M.J. ORCID: https://orcid.org/0000-0002-0599-3510
Nature Chemical Biology 16 (9): 946-954. September 2020

Deep learning for genomics using Janggu.
Kopp, W. ORCID: https://orcid.org/0000-0003-0376-0032, Monti, R. ORCID: https://orcid.org/0000-0002-6354-8319, Tamburrini, A., Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116 and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
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. ORCID: https://orcid.org/0000-0002-0468-0117, 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. ORCID: https://orcid.org/0000-0003-0555-6561, 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. ORCID: https://orcid.org/0000-0003-2899-0256, Yasuda, T. ORCID: https://orcid.org/0000-0001-9997-6852, Ronen, J. ORCID: https://orcid.org/0000-0003-3980-6469, Wirtz, T. ORCID: https://orcid.org/0009-0005-5677-9804, Weber, T. ORCID: https://orcid.org/0000-0003-2079-842X, Sack, U., Caeser, R., Zhang, J., Li, X. ORCID: https://orcid.org/0000-0002-1173-1066, Chu, V.T. ORCID: https://orcid.org/0000-0003-1327-8696, Jauch, A., Unger, K., Hodson, D.J. ORCID: https://orcid.org/0000-0001-6225-2033, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117 and Rajewsky, K. ORCID: https://orcid.org/0000-0002-6633-6370
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. ORCID: https://orcid.org/0000-0003-3083-6880, Pribisalić, A., Patarčić, I. ORCID: https://orcid.org/0000-0003-0527-6252, Hayward, C., Polašek, O. and Kolčić, I. ORCID: https://orcid.org/0000-0001-7918-6052
Nutrients 12 (4): 1164. April 2020

Evaluation of colorectal cancer subtypes and cell lines using deep learning.
Ronen, J. ORCID: https://orcid.org/0000-0003-3980-6469, Hayat, S. and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
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. ORCID: https://orcid.org/0000-0002-3525-8859, Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890, He, M., Krause, A. ORCID: https://orcid.org/0000-0001-9515-2477, Vitrinel, B. ORCID: https://orcid.org/0000-0002-5049-6572, Bulut, S., Vasiljevic, D., Marchal, I., Kempa, S. ORCID: https://orcid.org/0000-0002-0696-9299, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117 and Tursun, B. ORCID: https://orcid.org/0000-0001-7293-8629
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. ORCID: https://orcid.org/0000-0002-9884-1806, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Menegatti, J., Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Praktiknjo, S. ORCID: https://orcid.org/0000-0002-0186-5271, Walch-Rückheim, B., Bosse, J. ORCID: https://orcid.org/0000-0001-7252-5541, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Grässer, F., Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117 and Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734
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. ORCID: https://orcid.org/0000-0003-3980-6469 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. ORCID: https://orcid.org/0000-0002-5994-4802, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890, Wurmus, R. ORCID: https://orcid.org/0009-0003-0140-4189, Bulut, S., Tursun, B. ORCID: https://orcid.org/0000-0001-7293-8629 and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
Nucleic Acids Research : gkz460. 20 June 2019

Global identification of functional microRNA-mRNA interactions in Drosophila.
Wessels, H.H. ORCID: https://orcid.org/0000-0001-5551-404X, Lebedeva, S. ORCID: https://orcid.org/0000-0003-0857-8256, Hirsekorn, A., Wurmus, R. ORCID: https://orcid.org/0009-0003-0140-4189, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Mukherjee, N. ORCID: https://orcid.org/0000-0003-0017-1400 and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
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. ORCID: https://orcid.org/0000-0003-3606-6792, McShane, E. ORCID: https://orcid.org/0000-0002-7806-2063, Schulz-Beiss, K.W., Patone, G. ORCID: https://orcid.org/0000-0002-7242-0341, Schleussner, N. ORCID: https://orcid.org/0009-0001-3549-5600, Kolesnichenko, M. ORCID: https://orcid.org/0000-0001-7366-9061, Hübner, N. ORCID: https://orcid.org/0000-0002-1218-6223, Daumke, O. ORCID: https://orcid.org/0000-0002-6190-1414, Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Mathas, S. ORCID: https://orcid.org/0000-0001-9626-1413 and Scheidereit, C. ORCID: https://orcid.org/0000-0002-0446-6129
Blood 133 (13): 1489-1494. 28 March 2019

Alternative 3' UTRs direct localization of functionally diverse protein isoforms in neuronal compartments.
Ciolli Mattioli, C. ORCID: https://orcid.org/0000-0002-8499-1387, Rom, A., Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Imami, K. ORCID: https://orcid.org/0000-0002-7451-4982, Arrey, G., Terne, M., Woehler, A. ORCID: https://orcid.org/0000-0001-5157-9313, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Ulitsky, I. ORCID: https://orcid.org/0000-0003-0555-6561 and Chekulaeva, M. ORCID: https://orcid.org/0000-0002-6868-7887
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. ORCID: https://orcid.org/0000-0002-4740-7938, Hirsekorn, A., Wurmus, R. ORCID: https://orcid.org/0009-0003-0140-4189, Yusuf, D. ORCID: https://orcid.org/0000-0001-8683-7845 and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
Genome Biology 20 (1): 42. 21 February 2019

Deciphering human ribonucleoprotein regulatory networks.
Mukherjee, N. ORCID: https://orcid.org/0000-0003-0017-1400, Wessels, H.H. ORCID: https://orcid.org/0000-0001-5551-404X, Lebedeva, S. ORCID: https://orcid.org/0000-0003-0857-8256, Sajek, M., Ghanbari, M. ORCID: https://orcid.org/0000-0002-6015-2968, Garzia, A., Munteanu, A. ORCID: https://orcid.org/0000-0002-6328-3947, Yusuf, D. ORCID: https://orcid.org/0000-0001-8683-7845, Farazi, T., Hoell, J.I., Akat, K.M., Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Tuschl, T. and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
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. ORCID: https://orcid.org/0000-0001-6098-2761, 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. ORCID: https://orcid.org/0000-0002-0468-0117 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. ORCID: https://orcid.org/0009-0003-0140-4189, 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 IκB kinase complex is a regulator of mRNA stability.
Mikuda, N., Kolesnichenko, M. ORCID: https://orcid.org/0000-0001-7366-9061, Beaudette, P., Popp, O. ORCID: https://orcid.org/0000-0001-6240-4666, Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890, Sun, W. ORCID: https://orcid.org/0000-0001-9607-1361, Tufan, A.B. ORCID: https://orcid.org/0000-0002-8734-9736, Perder, B., Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Chen, W. ORCID: https://orcid.org/0000-0003-3263-1627, Mertins, P. ORCID: https://orcid.org/0000-0002-2245-528X, Dittmar, G. ORCID: https://orcid.org/0000-0003-3647-8623, Hinz, M. ORCID: https://orcid.org/0000-0003-2611-4121 and Scheidereit, C. ORCID: https://orcid.org/0000-0002-0446-6129
EMBO Journal 37 (24): e98658. 14 December 2018

PiGx: reproducible genomics analysis pipelines with GNU Guix.
Wurmus, R. ORCID: https://orcid.org/0009-0003-0140-4189, Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890, Osberg, B. ORCID: https://orcid.org/0000-0002-9854-9901, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Gosdschan, A. ORCID: https://orcid.org/0000-0003-3045-8234, Wreczycka, K. ORCID: https://orcid.org/0000-0002-5994-4802, Ronen, J. ORCID: https://orcid.org/0000-0003-3980-6469 and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
GigaScience 7 (12): giy123. 1 December 2018

Mutations in disordered regions can cause disease by creating dileucine motifs.
Meyer, K. ORCID: https://orcid.org/0000-0002-8244-6887, Kirchner, M. ORCID: https://orcid.org/0000-0002-7049-534X, Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890, Cheng, J.Y. ORCID: https://orcid.org/0000-0001-8942-0607, Russo, G., Hernandez-Miranda, L.R. ORCID: https://orcid.org/0000-0002-0498-708X, Szymborska, A. ORCID: https://orcid.org/0000-0003-1741-4106, Zauber, H. ORCID: https://orcid.org/0000-0003-2595-1147, Rudolph, I.M. ORCID: https://orcid.org/0000-0002-3903-0755, Willnow, T.E. ORCID: https://orcid.org/0000-0001-9515-7921, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Haucke, V. ORCID: https://orcid.org/0000-0003-3119-6993, Gerhardt, H. ORCID: https://orcid.org/0000-0002-3030-0384, Birchmeier, C. ORCID: https://orcid.org/0000-0002-2041-8872, Kühn, R. ORCID: https://orcid.org/0000-0003-1694-9803, Krauss, M., Diecke, S. ORCID: https://orcid.org/0000-0002-5219-5992, Pascual, J.M. and Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751
Cell 175 (1): 239-253. 20 September 2018

FACT sets a barrier for cell fate reprogramming in Caenorhabditis elegans and human cells.
Kolundzic, E. ORCID: https://orcid.org/0000-0002-7811-3174, Ofenbauer, A. ORCID: https://orcid.org/0000-0003-0379-9105, Bulut, S.I., Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890, Baytek, G. ORCID: https://orcid.org/0000-0001-9731-9461, Sommermeier, A., Seelk, S. ORCID: https://orcid.org/0000-0002-3525-8859, He, M., Hirsekorn, A., Vucicevic, D. ORCID: https://orcid.org/0000-0002-1162-6709, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Diecke, S. ORCID: https://orcid.org/0000-0002-5219-5992, Lacadie, S.A. ORCID: https://orcid.org/0000-0002-0893-5340 and Tursun, B. ORCID: https://orcid.org/0000-0001-7293-8629
Developmental Cell 46 (5): 611-626. 10 September 2018

netSmooth: network-smoothing based imputation for single cell RNA-seq.
Ronen, J. ORCID: https://orcid.org/0000-0003-3980-6469 and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
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. ORCID: https://orcid.org/0000-0003-3093-3138, Pimpinella, S., Hackel, P., Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Jessell, T.M. and Zampieri, N. ORCID: https://orcid.org/0000-0002-2228-9453
Cell Reports 22 (7): 1681-1694. 13 February 2018

Strategies for analyzing bisulfite sequencing data.
Wreczycka, K. ORCID: https://orcid.org/0000-0002-5994-4802, Gosdschan, A. ORCID: https://orcid.org/0000-0003-3045-8234, Yusuf, D., Grüning, B., Assenov, Y. and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
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. ORCID: https://orcid.org/0000-0002-9884-1806, Menegatti, J., Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Hennig, T., Theil, K. ORCID: https://orcid.org/0000-0002-7205-6308, Rutkowski, A., Ferrai, C. ORCID: https://orcid.org/0000-0002-8088-2757, Baer, L., Kermas, L., Friedel, C. ORCID: https://orcid.org/0000-0003-3569-4877, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Dölken, L., Grässer, F. and Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734
Genome Biology 18 (1): 209. 31 October 2017

RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation.
Ferrai, C. ORCID: https://orcid.org/0000-0002-8088-2757, Torlai Triglia, E. ORCID: https://orcid.org/0000-0002-6059-0116, Risner-Janiczek, J.R., Rito, T., Rackham, O.J.L. ORCID: https://orcid.org/0000-0002-4390-0872, De Santiago, I., Kukalev, A. ORCID: https://orcid.org/0000-0001-5847-3773, Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Li, M., Ungless, M.A. ORCID: https://orcid.org/0000-0002-1730-3353 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
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. ORCID: https://orcid.org/0000-0002-8499-1387, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Imami, K. ORCID: https://orcid.org/0000-0002-7451-4982, McShane, E. ORCID: https://orcid.org/0000-0002-7806-2063, Moreno-Estelles, M., Calviello, L. ORCID: https://orcid.org/0000-0002-5600-0988, Filipchyk, A. ORCID: https://orcid.org/0000-0002-2029-8460, Peguero-Sanchez, E. ORCID: https://orcid.org/0000-0002-8317-5572, Müller, T. ORCID: https://orcid.org/0000-0001-8096-1853, Woehler, A. ORCID: https://orcid.org/0000-0001-5157-9313, Birchmeier, C. ORCID: https://orcid.org/0000-0002-2041-8872, Merino, E., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116, Mazzoni, E.O., Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117 and Chekulaeva, M. ORCID: https://orcid.org/0000-0002-6868-7887
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. ORCID: https://orcid.org/0000-0001-8683-7845, 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. ORCID: https://orcid.org/0000-0002-0468-0117, Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116, 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. ORCID: https://orcid.org/0000-0002-3170-4890, Yusuf, D. ORCID: https://orcid.org/0000-0001-8683-7845, Wurmus, R. ORCID: https://orcid.org/0009-0003-0140-4189, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116 and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
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., Colombo, D.F., Wirbelauer, C., Schmidt, J., Burger, L., Krebs, A.R., Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0135 and Schübeler, D.
Nature 520 (7546): 243-247. 9 April 2015

genomation: a toolkit to summarize, annotate and visualize genomic intervals.
Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0118, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, 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. ORCID: https://orcid.org/0000-0001-9468-6311, Wurmus, R. ORCID: https://orcid.org/0009-0003-0140-4189, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734 and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
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. ORCID: https://orcid.org/0009-0003-0140-4189
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., Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0132, 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. ORCID: https://orcid.org/0000-0002-0468-0119, 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. ORCID: https://orcid.org/0000-0002-0468-0120, 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

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. ORCID: https://orcid.org/0000-0002-0468-0121, 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. ORCID: https://orcid.org/0000-0002-0468-0122, 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. ORCID: https://orcid.org/0000-0002-0468-0123, 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

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles.
Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0136, 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. ORCID: https://orcid.org/0000-0002-0468-0125, 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. ORCID: https://orcid.org/0000-0002-0468-0124, 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. ORCID: https://orcid.org/0000-0002-0468-0138, 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

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. ORCID: https://orcid.org/0000-0002-0468-0126, Lenhard, B., 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., Herrmann, C., Pascual-Anaya, J., D'Aniello, S., Garcia-Fernandez, J., Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0127, 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. ORCID: https://orcid.org/0000-0002-0468-0133, 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. ORCID: https://orcid.org/0000-0002-0468-0128, 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., Tena, J.J., de la Calle-Mustienes, E., Fernandez-Minan, A., Naranjo, S., Fernandez, A., Montoliu, L., Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0139, 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. ORCID: https://orcid.org/0000-0002-0468-0134, 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. ORCID: https://orcid.org/0000-0002-0468-0129, 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

Differential evolution of the 13 Atlantic salmon Hox clusters.
Mungpakdee, S., Seo, H.C., Angotzi, A.R., Dong, X., Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0140 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., Laplante, M., Navratilova, P., Komisarczuk, A.Z., Engstroem, P.G., Fredman, D., Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0130, 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

Predicting the binding affinity of MHC class II peptides.
Altiparmak, F., Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0137 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. ORCID: https://orcid.org/0000-0002-0468-0131, 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

Book Section

Genome-wide analysis of DNA methylation patterns by high-throughput sequencing.
Baubec, T. and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
In: Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing. Springer International Publishing, Cham, 197-221. ISBN 978-3-319-31348-1 9 June 2016

Book

Computational genomics with R.
Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
Chapman and Hall/CRC Computational Biology Series . CRC Press LLC, Milton. ISBN 9781498781855 2020

Review

Deep learning-based analysis of gene expression data and gene-related information in pediatric surgical oncology: a scoping review.
Berhe, Simon, Fuchs, Steffen E., Akalin, Altuna ORCID: https://orcid.org/0000-0002-0468-0117, van der Steeg, Alida F.W., Warmann, Steven W., Buser, Myrthe A.D. ORCID: https://orcid.org/0000-0003-0640-6434 and Markel, Moritz
Cancer Medicine 15 (5): e71976. May 2026

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. ORCID: https://orcid.org/0000-0001-8289-2599, Tonetti, F.R., 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. ORCID: https://orcid.org/0000-0002-3170-4890, Palmer, D., Kowald, A., Escobar, H.M., Barrantes, I., Möller, S., Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117 and Fuellen, G.
Ageing Research Reviews 64 : 101156. December 2020

Degrons in cancer.
Meszaros, B., Kumar, M., Gibson, T.J. ORCID: https://orcid.org/0000-0003-0657-5166, Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890 and Dosztanyi, Z. ORCID: https://orcid.org/0000-0002-3624-5937
Science Signaling 10 (470): eaak9982. 14 March 2017

Preprint

2nd SpatialData hackathon: frameworks, formats and interoperability.
Manukyan, Artür ORCID: https://orcid.org/0000-0002-0441-9517, Marconato, Luca ORCID: https://orcid.org/0000-0003-3198-1326, Albert, Marvin ORCID: https://orcid.org/0000-0003-2536-2545, Barnes, Chris ORCID: https://orcid.org/0000-0002-1296-7310, Blume, Alexander ORCID: https://orcid.org/0000-0003-3045-8234, Cerrone, Lorenzo ORCID: https://orcid.org/0000-0001-7337-2313, Crowell, Helena L. ORCID: https://orcid.org/0000-0002-4801-1767, Drummer, Francesca ORCID: https://orcid.org/0009-0002-7156-9125, Gruson, Hugo ORCID: https://orcid.org/0000-0002-4094-1476, Hess, Max ORCID: https://orcid.org/0000-0001-9528-4445, Hu, Taobo ORCID: https://orcid.org/0009-0009-2596-7588, Kedziora, Katarzyna ORCID: https://orcid.org/0000-0001-6524-7731, Kollotzek, Aaron ORCID: https://orcid.org/0009-0009-7142-4015, Macrí, Silvia Maria ORCID: https://orcid.org/0009-0009-2075-8699, Moerth, Eric ORCID: https://orcid.org/0000-0003-1625-0146, Moustafa, Samir ORCID: https://orcid.org/0000-0002-0674-9667, Ozleyen, Selman ORCID: https://orcid.org/0009-0009-2596-7588, Todd, Peter, Sarigün, Ahmet ORCID: https://orcid.org/0009-0003-2715-5344, Stockhaus, Sonja ORCID: https://orcid.org/0009-0005-7712-8154, Varrone, Marco ORCID: https://orcid.org/0000-0002-0538-3464, Vierdag, Wouter Michiel ORCID: https://orcid.org/0000-0003-1666-5421, Zappia, Luke ORCID: https://orcid.org/0000-0001-7744-8565, Zheng, Yimin ORCID: https://orcid.org/0000-0002-0394-9735, Stegle, Oliver ORCID: https://orcid.org/0000-0002-8818-7193 and Akalin, Altuna ORCID: https://orcid.org/0000-0002-0468-0117
BioHackrXiv : s6bph_v2. 29 June 2026

An atlas-scale generative model for unified representation learning of bulk RNA-seq data.
Pande, Amit ORCID: https://orcid.org/0009-0008-0826-973X, Uyar, Bora ORCID: https://orcid.org/0000-0002-3170-4890 and Akalin, Altuna ORCID: https://orcid.org/0000-0002-0468-0117
bioRxiv : 2026.06.18.733198. 24 June 2026

ECG-derived age deviation predicts cardiovascular diseases across lead configurations and cohorts.
Aydogdu, Deniz ORCID: https://orcid.org/0009-0006-9058-8021, Gaber, Farieda ORCID: https://orcid.org/0009-0004-5512-8527, Sorooshmehr, Arash and Akalin, Altuna ORCID: https://orcid.org/0000-0002-0468-0117
medRxiv : 2026.06.05.26354974. 8 June 2026

Unraveling the single-cell spatial landscapes of melanoma brain metastases.
Manukyan, Artür ORCID: https://orcid.org/0000-0002-0441-9517, Peters, Kristin, Radbruch, Helena ORCID: https://orcid.org/0000-0001-6941-3397, Fusco, Federico, Geserick, Felicitas, Rossner, Florian, Lehmann, Annika, Kleo, Karsten ORCID: https://orcid.org/0000-0001-9136-6902, Conrad, Thomas ORCID: https://orcid.org/0000-0001-5618-6295, Altmüller, Janine ORCID: https://orcid.org/0000-0003-4372-1521, Plumbom, Izabela ORCID: https://orcid.org/0009-0006-3720-3700, Akalin, Altuna ORCID: https://orcid.org/0000-0002-0468-0117, Jürchott, Karsten, Wyler, Emanuel ORCID: https://orcid.org/0000-0002-9884-1806, Landthaler, Markus ORCID: https://orcid.org/0000-0002-1075-8734, Delbridge, Claire, Sendler, Matthias, Radke, Josefine ORCID: https://orcid.org/0000-0001-9860-2007 and Redmer, Torben ORCID: https://orcid.org/0000-0002-0050-9478
medRxiv : 2025.08.29.25334740v3. 3 June 2026

Supporting-like cells constitute an alternative steroidogenic lineage conserved in amniotes.
Barberá-Aura, Iván ORCID: https://orcid.org/0009-0007-6058-3796, Chung, Wai-Yee, Dujardin, Emilie ORCID: https://orcid.org/0000-0002-8189-8742, Hurtado, Alicia ORCID: https://orcid.org/0000-0001-6267-704X, Galmiche, Mathieu ORCID: https://orcid.org/0000-0001-5840-4786, Mayère, Chloé ORCID: https://orcid.org/0000-0002-9254-4886, Guy, Maëva ORCID: https://orcid.org/0009-0007-7802-5186, Mandon-Pépin, Béatrice ORCID: https://orcid.org/0000-0002-5424-0822, Franke, Vedran ORCID: https://orcid.org/0000-0003-3606-6792, Jaszczyszyn, Yan ORCID: https://orcid.org/0000-0002-2269-677X, Acemel, Rafael D. ORCID: https://orcid.org/0000-0003-4120-0140, Rudaz, Serge ORCID: https://orcid.org/0000-0002-4180-5417, Mckey, Jennifer ORCID: https://orcid.org/0000-0002-2640-1502, Nef, Serge ORCID: https://orcid.org/0000-0001-5462-0676, Pailhoux, Eric ORCID: https://orcid.org/0000-0001-8012-9143 and Lupiáñez, Darío G. ORCID: https://orcid.org/0000-0002-3165-036X
bioRxiv : 2026.05.25.726204. 28 May 2026

A generative AI framework for disease-specific lung microtissue bioengineering.
Bahry, Ella ORCID: https://orcid.org/0000-0002-6358-2576, Pestoni, Jeanine C., Hirzel, Kai, Savchyn, Taras, Porras-Gonzalez, Diana, Getmanchuk-Zaporoshchenko, Vera, Gregor, Martin, Conlon, Thomas M, Önder Yildirim, Ali, Harrington, Kyle ORCID: https://orcid.org/0000-0002-7237-1973, Schmidt, Deborah ORCID: https://orcid.org/0000-0002-8621-9438, Burgstaller, Gerald and Heymann, Michael
bioRxiv : 2026.04.15.718723. 16 April 2026

Oncogene inactivation-induced senescence facilitates tumor relapse.
Schmitt, P., Hönig, K., Norcia, M.T. ORCID: https://orcid.org/0009-0007-8042-4530, Nogueira, M.F. ORCID: https://orcid.org/0000-0002-7607-4570, Flore, V. ORCID: https://orcid.org/0009-0001-3023-433X, Simó Vesperinas, I. ORCID: https://orcid.org/0000-0001-8965-127X, Villoro-Agud, M., Peng, L., Safyürek, Z. ORCID: https://orcid.org/0009-0004-8412-5069, Tariq, M. ORCID: https://orcid.org/0009-0003-5217-2226, Milojkovic, A. ORCID: https://orcid.org/0009-0001-7621-2283, Anders, K. ORCID: https://orcid.org/0000-0002-0429-200X, Schröck, E., Sauer, S. ORCID: https://orcid.org/0000-0002-4794-3693, Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Willimsky, G. ORCID: https://orcid.org/0000-0002-9693-948X, Haas, S. ORCID: https://orcid.org/0000-0001-9227-2051, Martínez-Reyes, I. ORCID: https://orcid.org/0000-0003-0479-1535 and Blankenstein, T. ORCID: https://orcid.org/0000-0002-3357-4321
bioRxiv : 2024.07.13.603369. 5 March 2026

Stability and individuality of ECG foundation model embeddings in a longitudinal case study.
Akalin, Altuna ORCID: https://orcid.org/0000-0002-0468-0117 and Domanska-Akalin, Anna
Preprints.org : Preprints:202601.2053. 27 January 2026

DNA virus infections shape transposable elements activity in vitro and in vivo.
Tan, J., Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Neugebauer, E., Pennisi, S., Schächtle, M.A., Lagisquet, J., Kuderna, A.K., Walter, S., Welker, I., Ensser, A., Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734, Stamminger, T., Gramberg, T., Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806 and Full, F.
bioRxiv : 2024.04.18.589901v2. 30 June 2025

PocketVina enables scalable and highly accurate physically valid docking through multi-pocket conditioning.
Sarigun, A. ORCID: https://orcid.org/0009-0003-2715-5344, Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792 and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
arXiv : 2506.20043. 24 June 2025

CompassDock: comprehensive accurate assessment approach for deep learning-based molecular docking in inference and fine-tuning.
Sariguen, A. ORCID: https://orcid.org/0009-0003-2715-5344, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890 and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
arXiv : 2406.06841. 1 October 2024

A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons.
Szabó, D. ORCID: https://orcid.org/0000-0001-8109-5088, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Bianco, S. ORCID: https://orcid.org/0000-0001-5819-060X, Batiuk, M.Y. ORCID: https://orcid.org/0000-0001-6681-4048, Paul, E.J. ORCID: https://orcid.org/0000-0003-1183-9285, Kukalev, A. ORCID: https://orcid.org/0000-0001-5847-3773, Pfisterer, U.G. ORCID: https://orcid.org/0000-0002-4613-6427, Irastorza-Azcarate, I. ORCID: https://orcid.org/0000-0001-5245-2322, Chiariello, A.M. ORCID: https://orcid.org/0000-0002-6112-0167, Demharter, S. ORCID: https://orcid.org/0000-0001-7352-3994, Zea-Redondo, L. ORCID: https://orcid.org/0000-0001-9064-9126, Lopez-Atalaya, J.P. ORCID: https://orcid.org/0000-0001-6064-7584, Nicodemi, M. ORCID: https://orcid.org/0000-0002-8416-6416, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Khodosevich, K. ORCID: https://orcid.org/0000-0001-7232-5558, Ungless, M.A. ORCID: https://orcid.org/0000-0002-1730-3353, Winick-Ng, W. ORCID: https://orcid.org/0000-0002-8716-5558 and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
bioRxiv : 2024.05.10.593308. 12 May 2024

VoltRon: a spatial omics analysis platform for multi-resolution and multi-omics integration using image registration.
Manukyan, A. ORCID: https://orcid.org/0000-0002-0441-9517, Bahry, E. ORCID: https://orcid.org/0000-0002-6358-2576, Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806, Becher, E., Pascual-Reguant, Anna, Plumbom, I. ORCID: https://orcid.org/0009-0006-3720-3700, Dikmen, H.O., Elezkurtaj, S., Conrad, T. ORCID: https://orcid.org/0000-0001-5618-6295, Altmüller, J. ORCID: https://orcid.org/0000-0003-4372-1521, Hauser, A.E., Hocke, A., Radbruch, H. ORCID: https://orcid.org/0000-0001-6941-3397, Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734 and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
bioRxiv : 2023.12.15.571667. 15 December 2023

Multi-omics and deep learning provide a multifaceted view of cancer.
Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890, Ronen, J. ORCID: https://orcid.org/0000-0003-3980-6469, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Gargiulo, G. ORCID: https://orcid.org/0000-0001-5414-4251 and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
bioRxiv : 2021.09.29.462364. 1 October 2021

Dataset

Tissue-supervised VAE: training compendium, model weights, and embeddings (118K-sample bulk RNA-seq).
Pande, Amit ORCID: https://orcid.org/0009-0008-0826-973X, Uyar, Bora ORCID: https://orcid.org/0000-0002-3170-4890 and Akalin, Altuna ORCID: https://orcid.org/0000-0002-0468-0117
[Dataset] 12 June 2026

Panchamahabhuta Genomics: Tridosha disease prediction model.
Pande, Amit ORCID: https://orcid.org/0009-0008-0826-973X
[Dataset] 10 February 2026

Datasets and Rscripts for : Multiomic and Longitudinal Dissection of Immune Dynamics Associated with Parkinsonism after Ciltacabtagene Autoleucel Therapy.
Kadel, Sofie-Katrin ORCID: https://orcid.org/0009-0003-8871-5261, Leipold, Alexander M. ORCID: https://orcid.org/0000-0002-9471-3276, Raskó, Tamás and Pande, Amit ORCID: https://orcid.org/0009-0008-0826-973X
[Dataset] 2026

MIMIC-IV-Ext clinical decision support for referral, triage and diagnosis.
Gaber, Farieda ORCID: https://orcid.org/0009-0004-5512-8527 and Akalin, Altuna ORCID: https://orcid.org/0000-0002-0468-0117
[Dataset] 8 October 2025

Extended supplementary data for manuscript: Gene regulatory mechanisms of cellular memory of a single cocaine exposure in VTA dopaminergic neurons.
Zea-Redondo, Luna ORCID: https://orcid.org/0000-0001-9064-9126, Franke, Vedran ORCID: https://orcid.org/0000-0003-3606-6792, Paul, Eleanor J., Kukalev, Alexander ORCID: https://orcid.org/0000-0001-5847-3773, Arguedas Jimenez, Laura ORCID: https://orcid.org/0009-0004-2240-7781, Braeuning, Caroline ORCID: https://orcid.org/0009-0007-1439-9920, Marin, Oscar, Akalin, Altuna ORCID: https://orcid.org/0000-0002-0468-0117, Ungless, Mark A., Winick-Ng, Warren ORCID: https://orcid.org/0000-0002-8716-5558 and Pombo, Ana ORCID: https://orcid.org/0000-0002-7493-6288
[Dataset] 4 September 2025

Flexynesis tutorials input data.
Naghsh Nilchi, Amirhossein ORCID: https://orcid.org/0000-0003-1329-3044 and Uyar, Bora ORCID: https://orcid.org/0000-0002-3170-4890
[Dataset] 21 July 2025

Supplementary datasets for the study "Flexynesis: A deep learning toolkit for bulk multi-omics data integration for precision oncology and beyond".
Uyar, Bora ORCID: https://orcid.org/0000-0002-3170-4890
[Dataset] July 2025

PocketVina enables scalable and highly accurate physically valid docking through multi-pocket conditioning.
Sarigun, Ahmet ORCID: https://orcid.org/0009-0003-2715-5344, Uyar, Bora ORCID: https://orcid.org/0000-0002-3170-4890, Franke, Vedran ORCID: https://orcid.org/0000-0003-3606-6792 and Akalin, Altuna ORCID: https://orcid.org/0000-0002-0468-0117
[Dataset] 24 June 2025

Herpesviral induction of germline transcription factor DUX4 is critical for viral gene expression.
Walter, S., Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Drayman, N., Tay, S., Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806, Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Ensser, A. and Full, F.
[Dataset] 21 May 2021