Browse by Journal Title

2024

Mapping lineage-traced cells across time points with moslin.
Lange, M., Piran, Z., Klein, M., Spanjaard, B., Klein, D., Junker, J.P., Theis, F.J. and Nitzan, M.
Genome Biology 25 (1): 277. 21 October 2024

A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies.
Wirbel, J., Essex, M., Forslund, S.K. and Zeller, G.
Genome Biology 25 (1): 247. 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., Flint, J., Mott, R. and Huang, L.
Genome Biology 24 (1): 215. 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., Marschall, T., 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., Petkovic, M., Watkins, T.B.K., Colliver, E.C., Laskina, S., Thapa, N., Minussi, D.C., Navin, N., Swanton, C., Van Loo, P., Haase, K., 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., Lebedeva, S., Schott, J., Lindner, D., 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., Baranovskii, A., Ronen, J., Uyar, B., Franke, V. and Akalin, A.
Genome Biology 23 (1): 123. 30 May 2022

RNA modification mapping with JACUSA2.
Piechotta, M., Naarmann-de Vries, I.S., Wang, Q., Altmüller, J. and Dieterich, C.
Genome Biology 23 (1): 115. 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., Franke, V., Ibanez de Caceres, I., Rodriguez-Antolin, C., Rosas, R., Davis, J.W., Ishii, J., Megherbi, D.B., Xiao, W., Liao, W., Xu, J., Hong, H., Ning, B., Tong, W., Akalin, A., Wang, Y., Deng, Y. and Mason, C.E.
Genome Biology 22 (1): 332. 6 December 2021

A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion.
Witte, F., Ruiz-Orera, J., Ciolli Mattioli, C., Blachut, S., Adami, E., Schulz, J.F., Schneider-Lunitz, V., Hummel, O., Patone, G., Mücke, M.B., Šilhavý, Jan, Heinig, M., Bottolo, L., Sanchis, D., Vingron, M., Chekulaeva, M., Pravenec, M., 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., Fullam, A., Coelho, L.P., Khedkar, S., Szklarczyk, D., Mende, D.R., 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., Zych, K., Essex, M., Karcher, N., Kartal, E., Salazar, G., Bork, P., 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., Gao, Q., Morrison, E., Herdt, O., Finkernagel, F., Schumann, M., Krause, E., Freund, C., 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., Hamey, F.K., Plass, M., Solana, J., Dahlin, J.S., Göttgens, B., Rajewsky, N., 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., Hirsekorn, A., Wurmus, R., Yusuf, D. and Ohler, U.
Genome Biology 20 (1): 42. 21 February 2019

2018

Ten things you should know about transposable elements.
Bourque, G., Burns, K.H., Gehring, M., Gorbunova, V., Seluanov, A., Hammell, M., Imbeault, M., Izsvák, Z., Levin, H.L., Macfarlan, T.S., 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., 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., Ferraiuolo, M., Sacconi, A., Ganci, F., Vitale, J., Colombo, T., Paci, P., Strano, S., Macino, G., 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., Menegatti, J., Franke, V., Kocks, C., Boltengagen, A., Hennig, T., Theil, K., Rutkowski, A., Ferrai, C., Baer, L., Kermas, L., Friedel, C., Rajewsky, N., Akalin, A., Dölken, L., Grässer, F. and Landthaler, M.
Genome Biology 18 (1): 209. 31 October 2017

McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes.
Hafez, D., Karabacak, A., Krueger, S., Hwang, Y.C., Wang, L.S., 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., Adriaens, M.E., Schafer, S., van Deutekom, H.W.M., Lodder, E.M., Ware, J.S., Schneider, V., 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., Rintisch, C., Petretto, E., Barton, P.J., Cook, S.A., Pinto, Y.M., Bezzina, C.R. and Hubner, N.
Genome Biology 18 (1): 170. 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. 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., Zauber, H., Bielow, C., Thiel, D., Kutz, K., Calviello, L., Mastrobuoni, G., Rajewsky, N., Kempa, S., Selbach, M. and Obermayer, B.
Genome Biology 16 : 179. 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.
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., 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., 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 : 7. 5 January 2015

2014

Differential protein occupancy profiling of the mRNA transcriptome.
Schueler, M., Munschauer, M., Gregersen, L.H., Finzel, A., Loewer, A., Chen, W., 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., Jacobs, N.C., Hafner, M., Kennington, E.A., Nusbaum, J.D., Tuschl, T., 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., 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., Backes, C., Deutscher, S., Schmitt, K., Mueller, S.C., Frese, K., Haas, J., Ruprecht, K., Paul, F., Stähler, C., Lang, C.J.G., Meder, B., Bartfai, T., 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., 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

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., Furey, T.S., 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., König, J., Hussain, S., Zupan, B., Curk, T., 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., Georgiev, S., Mukherjee, N., Gottwein, E., Skalsky, R.L., 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., Jensen, L.J., Ritchie, M.E., Toedling, J., Ning, Y., Bork, P., Huber, W. and Steinmetz, L.M.
Genome Biology 11 (3): R24. 1 March 2010

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

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

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., Jensen, L.J., Pierleoni, A., Bernsel, A., Tress, M.L., Bork, P., 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., 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. and Furlong, E.E.
Genome Biology 9 (11): 240. 4 November 2008

Circular reasoning rather than cyclic expression.
Jensen, L.J., de Lichtenberg, U., Jensen, T.S., 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., Schulz, H., Hummel, O., Huebner, N., 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., 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., 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., 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., Chen, S., Winkler, J., Hippler-Altenburg, R., Odenthal, M., Wickenhauser, C., Balaraman, S., Schulz, H., Hummel, O., Huebner, N., 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., Hummel, O., Huebner, N., 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. 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., Brent, M.R., Brown, R.H., Frankish, A., Harrow, J., Ohler, U., 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., Marks, D.S., Sander, C., Rajewsky, K., 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., van Driel, R., 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., Forslund, K., 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., Ciccarelli, F.D., 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., Suyama, M. and Bork, P.
Genome Biology 3 : preprint0003.1. 30 April 2002

Computational analysis of core promoters in the Drosophila genome.
Ohler, U., 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., 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