2026
Single-cell epigenetic and transcriptomic states across the continuum of monoclonal B cell lymphocytosis to chronic lymphocytic leukemia.
Rathgeber, Anja C. 
ORCID: https://orcid.org/0000-0003-3264-1040, Fernandes, Stacey M., Nagler, Adi, Li, Shuqiang, Dorfman, David M., Bullinger, Lars ORCID: https://orcid.org/0000-0002-5890-5510, Davids, Matthew S., Brown, Jennifer R., Livak, Kenneth J., Ludwig, Leif S. ORCID: https://orcid.org/0000-0002-2916-2164, Wu, Catherine J. and Penter, Livius ORCID: https://orcid.org/0000-0002-9060-0207
Genome Biology 27
(1): 175.
21 May 2026
Endogenous retroviral elements LTR8B and MER65 rewire PSG9 regulation to control trophoblast syncytialization and pre-eclampsia risk.
Singh, Manvendra ORCID: https://orcid.org/0000-0002-8626-5418, Qu, Yuliang ORCID: https://orcid.org/0000-0002-6203-0032, Pande, Amit ORCID: https://orcid.org/0009-0008-0826-973X, Zadora, Julianna ORCID: https://orcid.org/0000-0002-6906-7815, Herse, Florian ORCID: https://orcid.org/0000-0002-9305-8134, Gauster, Martin, Kong, Xuhui, Zheng, Rongyan, Anwar, Rabia, Stevanovic, Katarina, Dechend, Ralf ORCID: https://orcid.org/0000-0001-6636-3080, Cohen, Marie, Molvarec, Attila, Wang, Jichang ORCID: https://orcid.org/0000-0002-7027-0298, Konkel, Miriam K., Zhang, Bin ORCID: https://orcid.org/0000-0001-8835-8370, Feschotte, Cedric, Dveksler, Gabriela, Blois, Sandra M., Hurst, Laurence D. and Izsvak, Zsuzsanna ORCID: https://orcid.org/0000-0002-2053-2384
Genome Biology 27
(1): 73.
9 March 2026
2025
AP1 is a pioneer transcription factor that programmes cell fate through MADS-domain protein tetramerisation.
Xu, Xiaocai ORCID: https://orcid.org/0000-0002-2972-4251, Neumann, Manuel ORCID: https://orcid.org/0000-0002-7883-0843, Carew, Frederic ORCID: https://orcid.org/0009-0003-8387-7149, Chen, Peilin ORCID: https://orcid.org/0000-0002-0498-8349, Braeuning, Caroline ORCID: https://orcid.org/0009-0007-1439-9920, Zubieta, Chloe ORCID: https://orcid.org/0000-0003-4558-9333, Muino, Jose M. ORCID: https://orcid.org/0000-0002-6403-7262, Smaczniak, Cezary ORCID: https://orcid.org/0000-0002-4663-8275 and Kaufmann, Kerstin ORCID: https://orcid.org/0000-0001-7960-6256
Genome Biology 26
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9 December 2025
ERV3-MLT1 provides cis-regulatory elements for human placental functioning and are commonly dysregulated in human-specific preeclampsia.
Anwar, Rabia, Pandey, Amit ORCID: https://orcid.org/0000-0002-8886-1694, Singh, Manvendra ORCID: https://orcid.org/0000-0002-8626-5418, Huang, Zhi ORCID: https://orcid.org/0000-0002-8993-4912, Hallett, Eve ORCID: https://orcid.org/0009-0002-8268-8074, Xie, Yiran, Gellhaus, Alexandra, Herse, Florian ORCID: https://orcid.org/0000-0002-9305-8134, Nonn, Olivia ORCID: https://orcid.org/0000-0001-6385-2866, Gauster, Martin, Raskó, Tamás, Selbach, Matthias ORCID: https://orcid.org/0000-0003-2454-8751, Verlohren, Stefan ORCID: https://orcid.org/0000-0003-3507-8636, Staff, Anne Cathrine, Dechend, Ralf ORCID: https://orcid.org/0000-0001-6636-3080, Pecks, Ulrich, Blois, Sandra M. ORCID: https://orcid.org/0000-0002-0434-2660, Hurst, Laurence D and Izsvák, Zsuzsanna ORCID: https://orcid.org/0000-0002-2053-2384
Genome Biology 26
(1): 364.
5 November 2025
Insights, opportunities, and challenges provided by large cell atlases.
Hemberg, Martin, Marini, Federico, Ghazanfar, Shila, Al Ajami, Ahmad, Abassi, Najla, Anchang, Benedict, Benayoun, Bérénice A., Cao, Yue, Chen, Ken, Cuesta-Astroz, Yesid, DeBruine, Zachary, Dendrou, Calliope A., De Vlaminck, Iwijn, Imkeller, Katharina, Korsunsky, Ilya, Lederer, Alex R., Li, Jessica Jingyi, Meysman, Pieter, Miller, Clint L, Mullan, Kerry A., Ohler, Uwe ORCID: https://orcid.org/0000-0002-0881-3116, Panwar, Pratibha, Patikas, Nikolaos, Schuck, Jonas, Siu, Jacqueline H.Y., Triche, Timothy J., Tsankov, Alex, van der Laan, Sander W., Yajima, Masanao, Yang, Jean, Zanini, Fabio and Jelic, Ivana
Genome Biology 26
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20 October 2025
2024
Mapping lineage-traced cells across time points with moslin.
Lange, M., Piran, Z., Klein, M., Spanjaard, B. ORCID: https://orcid.org/0000-0003-1309-8839, Klein, D., Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, Theis, F.J. and Nitzan, M. ORCID: https://orcid.org/0000-0003-0074-9196
Genome Biology 25
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21 October 2024
A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies.
Wirbel, J., Essex, M. ORCID: https://orcid.org/0000-0001-8758-7497, Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Zeller, G. ORCID: https://orcid.org/0000-0003-1429-7485
Genome Biology 25
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25 September 2024
2023
Dominance is common in mammals and is associated with trans-acting gene expression and alternative splicing.
Cui, L., Yang, B., Xiao, S., Gao, J., Baud, A., Graham, D., McBride, M., Dominiczak, A., Schafer, S., Aumatell, R.L., Mont, C., Teruel, A.F., Hübner, N. ORCID: https://orcid.org/0000-0002-1218-6223, Flint, J., Mott, R. ORCID: https://orcid.org/0000-0002-1022-9330 and Huang, L.
Genome Biology 24
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29 September 2023
Inversion polymorphism in a complete human genome assembly.
Porubsky, D., Harvey, W.T., Rozanski, A.N., Ebler, J., Höps, W., Ashraf, H., Hasenfeld, P., Paten, B., Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Marschall, T., Korbel, J.O. and Eichler, E.E. ORCID: https://orcid.org/0000-0002-8246-4014
Genome Biology 24
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30 April 2023
2022
MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution.
Kaufmann, T.L. ORCID: https://orcid.org/0000-0003-4374-1338, Petkovic, M. ORCID: https://orcid.org/0000-0003-2875-216X, Watkins, T.B.K. ORCID: https://orcid.org/0000-0001-7414-737X, Colliver, E.C. ORCID: https://orcid.org/0000-0002-1497-0740, Laskina, S., Thapa, N., Minussi, D.C. ORCID: https://orcid.org/0000-0001-8856-4625, Navin, N. ORCID: https://orcid.org/0000-0002-2106-8624, Swanton, C. ORCID: https://orcid.org/0000-0002-4299-3018, Van Loo, P. ORCID: https://orcid.org/0000-0003-0292-1949, Haase, K. ORCID: https://orcid.org/0000-0002-0944-5618, Tarabichi, M. ORCID: https://orcid.org/0000-0002-1635-2348 and Schwarz, R.F. ORCID: https://orcid.org/0000-0001-9155-4268
Genome Biology 23
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14 November 2022
Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation.
Poetz, F., Lebedeva, S. ORCID: https://orcid.org/0000-0003-0857-8256, Schott, J., Lindner, D., Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116 and Stoecklin, G. ORCID: https://orcid.org/0000-0001-9284-9834
Genome Biology 23
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12 September 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
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30 May 2022
RNA modification mapping with JACUSA2.
Piechotta, M., Naarmann-de Vries, I.S., Wang, Q., Altmüller, J. ORCID: https://orcid.org/0000-0003-4372-1521 and Dieterich, C. ORCID: https://orcid.org/0000-0001-9468-6311
Genome Biology 23
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16 May 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. 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
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6 December 2021
A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion.
Witte, F., Ruiz-Orera, J. ORCID: https://orcid.org/0000-0002-8317-0034, Ciolli Mattioli, C. ORCID: https://orcid.org/0000-0002-8499-1387, Blachut, S. ORCID: https://orcid.org/0009-0007-0102-9867, Adami, E. ORCID: https://orcid.org/0000-0002-1813-6681, Schulz, J.F. ORCID: https://orcid.org/0000-0002-8157-2224, Schneider-Lunitz, V. ORCID: https://orcid.org/0000-0002-3980-3789, Hummel, O. ORCID: https://orcid.org/0009-0000-9986-8333, Patone, G. ORCID: https://orcid.org/0000-0002-7242-0341, Mücke, M.B. ORCID: https://orcid.org/0000-0002-4957-3307, Šilhavý, Jan, Heinig, M. ORCID: https://orcid.org/0000-0002-5612-1720, Bottolo, L., Sanchis, D., Vingron, M., Chekulaeva, M. ORCID: https://orcid.org/0000-0002-6868-7887, Pravenec, M. ORCID: https://orcid.org/0000-0001-9197-5871, Hubner, N. ORCID: https://orcid.org/0000-0002-1218-6223 and van Heesch, S. ORCID: https://orcid.org/0000-0001-9593-1980
Genome Biology 22
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28 June 2021
GUNC: detection of chimerism and contamination in prokaryotic genomes.
Orakov, A. ORCID: https://orcid.org/0000-0001-6823-5269, Fullam, A., Coelho, L.P., Khedkar, S., Szklarczyk, D., Mende, D.R., Schmidt, T.S.B. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Genome Biology 22
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13 June 2021
Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.
Wirbel, J. ORCID: https://orcid.org/0000-0002-4073-3562, Zych, K. ORCID: https://orcid.org/0000-0001-7426-0516, Essex, M. ORCID: https://orcid.org/0000-0001-8758-7497, Karcher, N. ORCID: https://orcid.org/0000-0001-7894-8182, Kartal, E. ORCID: https://orcid.org/0000-0002-7720-455X, Salazar, G. ORCID: https://orcid.org/0000-0002-9786-1493, Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, Sunagawa, S. ORCID: https://orcid.org/0000-0003-3065-0314 and Zeller, G. ORCID: https://orcid.org/0000-0003-1429-7485
Genome Biology 22
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30 March 2021
2020
Splicing-accessible coding 3'UTRs control protein stability and interaction networks.
Preussner, M., Gao, Q. ORCID: https://orcid.org/0000-0002-9930-8499, Morrison, E., Herdt, O., Finkernagel, F., Schumann, M., Krause, E., Freund, C., Chen, W. ORCID: https://orcid.org/0000-0003-3263-1627 and Heyd, F. ORCID: https://orcid.org/0000-0001-9377-9882
Genome Biology 21
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29 July 2020
2019
PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells.
Wolf, F.A. ORCID: https://orcid.org/0000-0002-8760-7838, Hamey, F.K., Plass, M. ORCID: https://orcid.org/0000-0002-9891-2723, Solana, J. ORCID: https://orcid.org/0000-0002-6770-3929, Dahlin, J.S., Göttgens, B., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Simon, L. and Theis, F.J.
Genome Biology 20
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19 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
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21 February 2019
2018
Ten things you should know about transposable elements.
Bourque, G. ORCID: https://orcid.org/0000-0002-3933-9656, Burns, K.H., Gehring, M., Gorbunova, V., Seluanov, A., Hammell, M., Imbeault, M., Izsvák, Z. ORCID: https://orcid.org/0000-0002-2053-2384, Levin, H.L., Macfarlan, T.S., Mager, D.L. and Feschotte, C.
Genome Biology 19
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19 November 2018
omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data.
Drewe-Boss, P. ORCID: https://orcid.org/0000-0002-5459-9771, Wessels, H.H. ORCID: https://orcid.org/0000-0001-5551-404X and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
Genome Biology 19
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1 November 2018
2017
The oncogenic role of circPVT1 in head and neck squamous cell carcinoma is mediated through the mutant p53/YAP/TEAD transcription-competent complex.
Verduci, L., Ferraiuolo, M., Sacconi, A., Ganci, F., Vitale, J., Colombo, T. ORCID: https://orcid.org/0000-0003-2415-7507, Paci, P., Strano, S., Macino, G., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Blandino, G.
Genome Biology 18
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20 December 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
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31 October 2017
McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes.
Hafez, D., Karabacak, A. ORCID: https://orcid.org/0000-0002-4740-7938, Krueger, S., Hwang, Y.C., Wang, L.S., Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102 and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
Genome Biology 18
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26 October 2017
Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy.
Heinig, M. ORCID: https://orcid.org/0000-0002-5612-1720, Adriaens, M.E., Schafer, S., van Deutekom, H.W.M., Lodder, E.M., Ware, J.S., Schneider, V. ORCID: https://orcid.org/0000-0002-3980-3789, Felkin, L.E., Creemers, E.E., Meder, B., Katus, H.A., Rühle, F., Stoll, M., Cambien, F., Villard, E., Charron, P., Varro, A., Bishopric, N.H., George, A.L., Dos Remedios, C., Moreno-Moral, A., Pesce, F., Bauerfeind, A., Rüschendorf, F. ORCID: https://orcid.org/0000-0001-5640-810X, Rintisch, C., Petretto, E., Barton, P.J., Cook, S.A., Pinto, Y.M., Bezzina, C.R. and Hubner, N. ORCID: https://orcid.org/0000-0002-1218-6223
Genome Biology 18
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14 September 2017
2016
Spatiotemporal variation of mammalian protein complex stoichiometries.
Ori, A., Iskar, M., Buczak, K., Kastritis, P., Parca, L., Andres-Pons, A., Singer, S., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X and Beck, M.
Genome Biology 17
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14 March 2016
2015
Pop in, pop out: a novel gene-targeting strategy for use with CRISPR-Cas9.
Kühn, R. ORCID: https://orcid.org/0000-0003-1694-9803 and Chu, V.T. ORCID: https://orcid.org/0000-0003-1327-8696
Genome Biology 16
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10 November 2015
Extensive identification and analysis of conserved small ORFs in animals.
Mackowiak, S.D., Zauber, H. ORCID: https://orcid.org/0000-0003-2595-1147, Bielow, C. ORCID: https://orcid.org/0000-0001-5756-3988, Thiel, D., Kutz, K., Calviello, L. ORCID: https://orcid.org/0000-0002-5600-0988, Mastrobuoni, G. ORCID: https://orcid.org/0000-0003-4509-1295, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Kempa, S. ORCID: https://orcid.org/0000-0002-0696-9299, Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751 and Obermayer, B. ORCID: https://orcid.org/0000-0002-9116-630X
Genome Biology 16
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14 September 2015
Temporal and technical variability of human gut metagenomes.
Voigt, A.Y., Costea, P.I., Kultima, J.R., Li, S.S., Zeller, G., Sunagawa, S. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Genome Biology 16
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8 April 2015
Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data.
Fernandez-Cuesta, L., Sun, R., Menon, R., George, J., Lorenz, S., Meza-Zepeda, L.A., Peifer, M., Plenker, D., Heuckmann, J.M., Leenders, F., Zander, T., Dahmen, I., Koker, M., Schöttle, J., Ullrich, R.T., Altmüller, J. ORCID: https://orcid.org/0000-0003-4372-1521, Becker, C., Nürnberg, P., Seidel, H., Böhm, D., Göke, F., Ansén, S., Russell, P.A., Wright, G.M., Wainer, Z., Solomon, B., Petersen, I., Clement, J.H., Sänger, J., Brustugun, O.T., Helland, Å., Solberg, S., Lund-Iversen, M., Buettner, R., Wolf, J., Brambilla, E., Vingron, M., Perner, S., Haas, S.A. and Thomas, R.K.
Genome Biology 16
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5 January 2015
2014
Differential protein occupancy profiling of the mRNA transcriptome.
Schueler, M., Munschauer, M. ORCID: https://orcid.org/0000-0001-6143-4548, Gregersen, L.H. ORCID: https://orcid.org/0000-0002-1205-604X, Finzel, A., Loewer, A., Chen, W. ORCID: https://orcid.org/0000-0003-3263-1627, Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734 and Dieterich, C. ORCID: https://orcid.org/0000-0001-9468-6311
Genome Biology 15
(1): R15.
13 January 2014
Global target mRNA specification and regulation by the RNA-binding protein ZFP36.
Mukherjee, N. ORCID: https://orcid.org/0000-0003-0017-1400, Jacobs, N.C. ORCID: https://orcid.org/0000-0002-2617-6173, Hafner, M., Kennington, E.A., Nusbaum, J.D., Tuschl, T., Blackshear, P.J. and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
Genome Biology 15
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8 January 2014
2013
Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.
Megraw, M., Mukherjee, S. and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
Genome Biology 14
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23 August 2013
A blood based 12-miRNA signature of Alzheimer disease patients.
Leidinger, P., Backes, C., Deutscher, S., Schmitt, K., Mueller, S.C., Frese, K., Haas, J., Ruprecht, K., Paul, F. ORCID: https://orcid.org/0000-0002-6378-0070, Stähler, C., Lang, C.J.G., Meder, B., Bartfai, T., Meese, E. and Keller, A.
Genome Biology 14
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29 July 2013
2012
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
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3 October 2012
Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity.
Tewari, A.K., Yardimci, G.G., Shibata, Y., Sheffield, N.C., Song, L., Taylor, B.S., Georgiev, S.G., Coetzee, GA., Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116, Furey, T.S., Crawford, G.E. and Febbo, P.G.
Genome Biology 13
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3 October 2012
Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions.
Sugimoto, Y. ORCID: https://orcid.org/0000-0003-1646-7679, König, J., Hussain, S., Zupan, B., Curk, T., Frye, M. and Ule, J.
Genome Biology 13
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3 August 2012
2011
PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data.
Corcoran, D.L., Georgiev, S., Mukherjee, N., Gottwein, E., Skalsky, R.L., Keene, J.D. and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
Genome Biology 12
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18 August 2011
2010
Mapping the complexity of transcription control in higher eukaryotes.
Tomancak, P. and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
Genome Biology 11
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30 April 2010
High-resolution transcription atlas of the mitotic cell cycle in budding yeast.
Granovskaia, M.V., Jensen, L.J. ORCID: https://orcid.org/0000-0001-7885-715X, Ritchie, M.E., Toedling, J. ORCID: https://orcid.org/0000-0003-1471-1295, Ning, Y., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, Huber, W. and Steinmetz, L.M.
Genome Biology 11
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1 March 2010
Evidence-ranked motif identification.
Georgiev, S., Boyle, A.P., Jayasurya, K., Ding, X., Mukherjee, S. and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
Genome Biology 11
(2): R19.
15 February 2010
2009
Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome.
Rach, E.A., Yuan, H.Y., Majoros, W.H., Tomancak, P. and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
Genome Biology 10
(7): R73.
9 July 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
Genomic parasites and genome evolution.
Ivics, Z. ORCID: https://orcid.org/0000-0002-7803-6658
Genome Biology 10
(4): 306.
15 April 2009
Sequence-based feature prediction and annotation of proteins.
Juncker, A.S., Jensen, L.J. ORCID: https://orcid.org/0000-0001-7885-715X, Pierleoni, A., Bernsel, A., Tress, M.L., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, von Heijne, G., Valencia, A., Ouzounis, C.A., Casadio, R. and Brunak, S.
Genome Biology 10
(2): 206.
2 February 2009
2008
Selective maintenance of Drosophila tandemly-arranged duplicated genes during evolution.
Quijano, C., Tomancak, P., Lopez-Marti, J., Suyama, M., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, Milan, M., Torrents, D. and Manzanares, M.
Genome Biology 9
(12): R176.
16 December 2008
Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis.
Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102 and Furlong, E.E.
Genome Biology 9
(11): 240.
4 November 2008
Circular reasoning rather than cyclic expression.
Jensen, L.J. ORCID: https://orcid.org/0000-0001-7885-715X, de Lichtenberg, U., Jensen, T.S., Brunak, S. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Genome Biology 9
(6): 403.
23 June 2008
Histone deacetylase inhibition accelerates the early events of stem cell differentiation: transcriptomic and epigenetic analysis.
Karantzali, E., Schulz, H. ORCID: https://orcid.org/0000-0002-0226-964X, Hummel, O. ORCID: https://orcid.org/0009-0000-9986-8333, Huebner, N. ORCID: https://orcid.org/0000-0002-1218-6223, Hatzopoulos, A. and Kretsovali, A.
Genome Biology 9
(4): R65.
4 April 2008
2007
An idea whose time has come.
Banci, L., Baumeister, W., Heinemann, U. ORCID: https://orcid.org/0000-0002-8191-3850, Schneider, G., Silman, I., Stuart, D.I. and Sussman, J.L.
Genome Biology 8
(11): 408.
7 November 2007
Technology transfer from worms and flies to vertebrates: transposition-based genome manipulations and their future perspectives.
Mates, L. ORCID: https://orcid.org/0000-0002-0058-470X, Izsvak, Z. ORCID: https://orcid.org/0000-0002-2053-2384 and Ivics, Z. ORCID: https://orcid.org/0000-0002-7803-6658
Genome Biology 8 Suppl 1
: S1.
31 October 2007
Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools.
Huang, W., Nevins, J.R. and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
Genome Biology 8
(10): R225.
24 October 2007
Transcriptomic and phenotypic analysis of murine embryonic stem cell derived BMP2+ lineage cells: an insight into mesodermal patterning.
Doss, M.X., Chen, S., Winkler, J., Hippler-Altenburg, R., Odenthal, M., Wickenhauser, C., Balaraman, S., Schulz, H. ORCID: https://orcid.org/0000-0002-0226-964X, Hummel, O. ORCID: https://orcid.org/0009-0000-9986-8333, Huebner, N. ORCID: https://orcid.org/0000-0002-1218-6223, Ghosh-Choudhury, N., Sotiriadou, I., Hescheler, J. and Sachinidis, A.
Genome Biology 8
(9): R184.
4 September 2007
Global transcriptome analysis of murine embryonic stem cell-derived cardiomyocytes.
Doss, M.X., Winkler, J., Chen, S., Hippler-Altenburg, R., Sotiriadou, I., Halbach, M., Pfannkuche, K., Liang, H., Schulz, H. ORCID: https://orcid.org/0000-0002-0226-964X, Hummel, O. ORCID: https://orcid.org/0009-0000-9986-8333, Huebner, N. ORCID: https://orcid.org/0000-0002-1218-6223, Rottscheidt, R., Hescheler, J. and Sachinidis, A.
Genome Biology 8
(4): R56.
11 April 2007
Prediction of effective genome size in metagenomic samples.
Raes, J., Korbel, J.O., Lercher, M.J., von Mering, C. ORCID: https://orcid.org/0000-0001-7734-9102 and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Genome Biology 8
(1): R10.
15 January 2007
2006
Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.
Bajic, V.B., Brent, M.R., Brown, R.H., Frankish, A., Harrow, J., Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116, Solovyev, V.V. and Tan, S.L.
Genome Biology 7 Suppl 1
: S3.1-13.
2006
2005
MicroRNA profiling of the murine hematopoietic system.
Monticelli, S., Ansel, K.M., Xiao, C., Socci, N.D., Krichevsky, A.M., Thai, T.H., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Marks, D.S., Sander, C., Rajewsky, K. ORCID: https://orcid.org/0000-0002-6633-6370, Rao, A. and Kosik, K.S.
Genome Biology 6
(8): R71.
2005
A full menu for stem-cell research.
Spagnoli, F.M. and Brivanlou, A.H.
Genome Biology 6
(3): 311.
2005
From single cells to whole organisms.
Sperling, S. ORCID: https://orcid.org/0000-0002-7135-3298
Genome Biology 6
(13): 365.
2005
2003
From linear genome sequence to three-dimensional organization of the cell nucleus.
Politz, J., van Driel, R., Sauer, M. and Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288
In: Jackson Laboratory 'Advances in nanostructural genomics II' meeting, 3-6 Oct 2002, Bar Harbor, USA.
28 February 2003
A novel exploratory method for visual recombination detection.
Strimmer, K. ORCID: https://orcid.org/0000-0001-7917-2056, Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, Holland, B. ORCID: https://orcid.org/0000-0002-4628-7938 and Moulton, V.
Genome Biology 4
(5): R33.
2003
2002
NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria.
Andrade, M.A. ORCID: https://orcid.org/0000-0001-6650-1711, Ciccarelli, F.D., Perez-Iratxeta, C. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Genome Biology 3
(9): research0047.
15 August 2002
Identification of attenuation and antitermination regulation in prokaryotes.
Lathe, W.C., Suyama, M. and Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X
Genome Biology 3
: preprint0003.1.
30 April 2002
Computational analysis of core promoters in the Drosophila genome.
Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116, Liao, G.C., Niemann, H. and Rubin, G.M.
Genome Biology 3
(12): RESEARCH0087.
2002
2001
Genome sequences and great expectations.
Iliopoulos, I., Tsoka, S., Andrade, M.A. ORCID: https://orcid.org/0000-0001-6650-1711, Janssen, P., Audit, B., Tramontano, A., Valencia, A., Leroy, C., Sander, C. and Ouzounis, C.A.
Genome Biology 2
(1): Interactions0001.1-Interactions0001.3.
1 January 2001
Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences.
Iyer, L.M., Aravind, L., Bork, P., Hofmann, K., Mushegian, A.R., Zhulin, I.B. and Koonin, E.V.
Genome Biology 2
(12): RESEARCH0051.
2001
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