Browse by Journal Title

2023

Dominance is common in mammals and is associated with trans-acting gene expression and alternative splicing.
Cui, L. and Yang, B. and Xiao, S. and Gao, J. and Baud, A. and Graham, D. and McBride, M. and Dominiczak, A. and Schafer, S. and Aumatell, R.L. and Mont, C. and Teruel, A.F. and Hübner, N. and Flint, J. and Mott, R. and Huang, L.
Genome Biology 24 (1): 215. 29 September 2023

Inversion polymorphism in a complete human genome assembly.
Porubsky, D. and Harvey, W.T. and Rozanski, A.N. and Ebler, J. and Höps, W. and Ashraf, H. and Hasenfeld, P. and Paten, B. and Sanders, A.D. and Marschall, T. and Korbel, J.O. and Eichler, E.E.
Genome Biology 24 (1): 100. 30 April 2023

2022

MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution.
Kaufmann, T.L. and Petkovic, M. and Watkins, T.B.K. and Colliver, E.C. and Laskina, S. and Thapa, N. and Minussi, D.C. and Navin, N. and Swanton, C. and Van Loo, P. and Haase, K. and Tarabichi, M. and Schwarz, R.F.
Genome Biology 23 (1): 241. 14 November 2022

Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation.
Poetz, F. and Lebedeva, S. and Schott, J. and Lindner, D. and Ohler, U. and Stoecklin, G.
Genome Biology 23 (1): 193. 12 September 2022

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

RNA modification mapping with JACUSA2.
Piechotta, M. and Naarmann-de Vries, I.S. and Wang, Q. and Altmüller, J. and Dieterich, C.
Genome Biology 23 (1): 115. 16 May 2022

2021

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

A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion.
Witte, F. and Ruiz-Orera, J. and Ciolli Mattioli, C. and Blachut, S. and Adami, E. and Schulz, J.F. and Schneider-Lunitz, V. and Hummel, O. and Patone, G. and Mücke, M.B. and Šilhavý, Jan and Heinig, M. and Bottolo, L. and Sanchis, D. and Vingron, M. and Chekulaeva, M. and Pravenec, M. and Hubner, N. and van Heesch, S.
Genome Biology 22 (1): 191. 28 June 2021

GUNC: detection of chimerism and contamination in prokaryotic genomes.
Orakov, A. and Fullam, A. and Coelho, L.P. and Khedkar, S. and Szklarczyk, D. and Mende, D.R. and Schmidt, T.S.B. and Bork, P.
Genome Biology 22 (1): 178. 13 June 2021

Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.
Wirbel, J. and Zych, K. and Essex, M. and Karcher, N. and Kartal, E. and Salazar, G. and Bork, P. and Sunagawa, S. and Zeller, G.
Genome Biology 22 (1): 93. 30 March 2021

2020

Splicing-accessible coding 3'UTRs control protein stability and interaction networks.
Preussner, M. and Gao, Q. and Morrison, E. and Herdt, O. and Finkernagel, F. and Schumann, M. and Krause, E. and Freund, C. and Chen, W. and Heyd, F.
Genome Biology 21 (1): 186. 29 July 2020

2019

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells.
Wolf, F.A. and Hamey, F.K. and Plass, M. and Solana, J. and Dahlin, J.S. and Göttgens, B. and Rajewsky, N. and Simon, L. and Theis, F.J.
Genome Biology 20 (1): 59. 19 March 2019

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

2018

Ten things you should know about transposable elements.
Bourque, G. and Burns, K.H. and Gehring, M. and Gorbunova, V. and Seluanov, A. and Hammell, M. and Imbeault, M. and Izsvák, Z. and Levin, H.L. and Macfarlan, T.S. and Mager, D.L. and Feschotte, C.
Genome Biology 19 (1): 199. 19 November 2018

omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data.
Drewe-Boss, P. and Wessels, H.H. and Ohler, U.
Genome Biology 19 : 183. 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. and Ferraiuolo, M. and Sacconi, A. and Ganci, F. and Vitale, J. and Colombo, T. and Paci, P. and Strano, S. and Macino, G. and Rajewsky, N. and Blandino, G.
Genome Biology 18 (1): 237. 20 December 2017

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

McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes.
Hafez, D. and Karabacak, A. and Krueger, S. and Hwang, Y.C. and Wang, L.S. and Zinzen, R.P. and Ohler, U.
Genome Biology 18 (1): 199. 26 October 2017

Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy.
Heinig, M. and Adriaens, M.E. and Schafer, S. and van Deutekom, H.W.M. and Lodder, E.M. and Ware, J.S. and Schneider, V. and Felkin, L.E. and Creemers, E.E. and Meder, B. and Katus, H.A. and Rühle, F. and Stoll, M. and Cambien, F. and Villard, E. and Charron, P. and Varro, A. and Bishopric, N.H. and George, A.L. and Dos Remedios, C. and Moreno-Moral, A. and Pesce, F. and Bauerfeind, A. and Rüschendorf, F. and Rintisch, C. and Petretto, E. and Barton, P.J. and Cook, S.A. and Pinto, Y.M. and Bezzina, C.R. and Hubner, N.
Genome Biology 18 (1): 170. 14 September 2017

2016

Spatiotemporal variation of mammalian protein complex stoichiometries.
Ori, A. and Iskar, M. and Buczak, K. and Kastritis, P. and Parca, L. and Andres-Pons, A. and Singer, S. and Bork, P. and Beck, M.
Genome Biology 17 (1): 47. 14 March 2016

2015

Pop in, pop out: a novel gene-targeting strategy for use with CRISPR-Cas9.
Kühn, R. and Chu, V.T.
Genome Biology 16 (1): 244. 10 November 2015

Extensive identification and analysis of conserved small ORFs in animals.
Mackowiak, S.D. and Zauber, H. and Bielow, C. and Thiel, D. and Kutz, K. and Calviello, L. and Mastrobuoni, G. and Rajewsky, N. and Kempa, S. and Selbach, M. and Obermayer, B.
Genome Biology 16 : 179. 14 September 2015

Temporal and technical variability of human gut metagenomes.
Voigt, A.Y. and Costea, P.I. and Kultima, J.R. and Li, S.S. and Zeller, G. and Sunagawa, S. and Bork, P.
Genome Biology 16 (1): 73. 8 April 2015

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

2014

Differential protein occupancy profiling of the mRNA transcriptome.
Schueler, M. and Munschauer, M. and Gregersen, L.H. and Finzel, A. and Loewer, A. and Chen, W. and Landthaler, M. and Dieterich, C.
Genome Biology 15 (1): R15. 13 January 2014

Global target mRNA specification and regulation by the RNA-binding protein ZFP36.
Mukherjee, N. and Jacobs, N.C. and Hafner, M. and Kennington, E.A. and Nusbaum, J.D. and Tuschl, T. and Blackshear, P.J. and Ohler, U.
Genome Biology 15 (1): R12. 8 January 2014

2013

Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.
Megraw, M. and Mukherjee, S. and Ohler, U.
Genome Biology 14 (8): R85. 23 August 2013

A blood based 12-miRNA signature of Alzheimer disease patients.
Leidinger, P. and Backes, C. and Deutscher, S. and Schmitt, K. and Mueller, S.C. and Frese, K. and Haas, J. and Ruprecht, K. and Paul, F. and Stähler, C. and Lang, C.J.G. and Meder, B. and Bartfai, T. and Meese, E. and Keller, A.
Genome Biology 14 (7): R78. 29 July 2013

2012

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

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity.
Tewari, A.K. and Yardimci, G.G. and Shibata, Y. and Sheffield, N.C. and Song, L. and Taylor, B.S. and Georgiev, S.G. and Coetzee, GA. and Ohler, U. and Furey, T.S. and Crawford, G.E. and Febbo, P.G.
Genome Biology 13 (10): R88. 3 October 2012

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions.
Sugimoto, Y. and König, J. and Hussain, S. and Zupan, B. and Curk, T. and Frye, M. and Ule, J.
Genome Biology 13 (8): R67. 3 August 2012

2011

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data.
Corcoran, D.L. and Georgiev, S. and Mukherjee, N. and Gottwein, E. and Skalsky, R.L. and Keene, J.D. and Ohler, U.
Genome Biology 12 (8): R79. 18 August 2011

2010

Mapping the complexity of transcription control in higher eukaryotes.
Tomancak, P. and Ohler, U.
Genome Biology 11 (4): 115. 30 April 2010

High-resolution transcription atlas of the mitotic cell cycle in budding yeast.
Granovskaia, M.V. and Jensen, L.J. and Ritchie, M.E. and Toedling, J. and Ning, Y. and Bork, P. and Huber, W. and Steinmetz, L.M.
Genome Biology 11 (3): R24. 1 March 2010

Evidence-ranked motif identification.
Georgiev, S. and Boyle, A.P. and Jayasurya, K. and Ding, X. and Mukherjee, S. and Ohler, U.
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. and Yuan, H.Y. and Majoros, W.H. and Tomancak, P. and Ohler, U.
Genome Biology 10 (7): R73. 9 July 2009

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

Genomic parasites and genome evolution.
Ivics, Z.
Genome Biology 10 (4): 306. 15 April 2009

Sequence-based feature prediction and annotation of proteins.
Juncker, A.S. and Jensen, L.J. and Pierleoni, A. and Bernsel, A. and Tress, M.L. and Bork, P. and von Heijne, G. and Valencia, A. and Ouzounis, C.A. and 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. and Tomancak, P. and Lopez-Marti, J. and Suyama, M. and Bork, P. and Milan, M. and 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. and Furlong, E.E.
Genome Biology 9 (11): 240. 4 November 2008

Circular reasoning rather than cyclic expression.
Jensen, L.J. and de Lichtenberg, U. and Jensen, T.S. and Brunak, S. and Bork, P.
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. and Schulz, H. and Hummel, O. and Huebner, N. and Hatzopoulos, A. and Kretsovali, A.
Genome Biology 9 (4): R65. 4 April 2008

2007

An idea whose time has come.
Banci, L. and Baumeister, W. and Heinemann, U. and Schneider, G. and Silman, I. and 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. and Izsvak, Z. and Ivics, Z.
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. and Nevins, J.R. and Ohler, U.
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. and Chen, S. and Winkler, J. and Hippler-Altenburg, R. and Odenthal, M. and Wickenhauser, C. and Balaraman, S. and Schulz, H. and Hummel, O. and Huebner, N. and Ghosh-Choudhury, N. and Sotiriadou, I. and 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. and Winkler, J. and Chen, S. and Hippler-Altenburg, R. and Sotiriadou, I. and Halbach, M. and Pfannkuche, K. and Liang, H. and Schulz, H. and Hummel, O. and Huebner, N. and Rottscheidt, R. and Hescheler, J. and Sachinidis, A.
Genome Biology 8 (4): R56. 11 April 2007

Prediction of effective genome size in metagenomic samples.
Raes, J. and Korbel, J.O. and Lercher, M.J. and von Mering, C. and Bork, P.
Genome Biology 8 (1): R10. 15 January 2007

2006

Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.
Bajic, V.B. and Brent, M.R. and Brown, R.H. and Frankish, A. and Harrow, J. and Ohler, U. and 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. and Ansel, K.M. and Xiao, C. and Socci, N.D. and Krichevsky, A.M. and Thai, T.H. and Rajewsky, N. and Marks, D.S. and Sander, C. and Rajewsky, K. and 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.
Genome Biology 6 (13): 365. 2005

2003

From linear genome sequence to three-dimensional organization of the cell nucleus.
Politz, J. and van Driel, R. and Sauer, M. and Pombo, A.
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. and Forslund, K. and Holland, B. 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. and Ciccarelli, F.D. and Perez-Iratxeta, C. and Bork, P.
Genome Biology 3 (9): research0047. 15 August 2002

Identification of attenuation and antitermination regulation in prokaryotes.
Lathe, W.C. and Suyama, M. and Bork, P.
Genome Biology 3 : preprint0003.1. 30 April 2002

Computational analysis of core promoters in the Drosophila genome.
Ohler, U. and Liao, G.C. and Niemann, H. and Rubin, G.M.
Genome Biology 3 (12): RESEARCH0087. 2002

2001

Genome sequences and great expectations.
Iliopoulos, I. and Tsoka, S. and Andrade, M.A. and Janssen, P. and Audit, B. and Tramontano, A. and Valencia, A. and Leroy, C. and 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. and Aravind, L. and Bork, P. and Hofmann, K. and Mushegian, A.R. and Zhulin, I.B. and Koonin, E.V.
Genome Biology 2 (12): RESEARCH0051. 2001