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Twenty years with Genome Biology

Genome Biology is celebrating 20 years of publication this year! We’ve put together a list of some of our most accessed and interesting articles over the last two decades. While this list is by no means exhaustive, we hope you enjoy looking back at how far the field of genomics has come.


  1. Bulk chromatin motion has not been analyzed at high resolution. We present Hi-D, a method to quantitatively map dynamics of chromatin and abundant nuclear proteins for every pixel simultaneously over the entir...

    Authors: Haitham A. Shaban, Roman Barth, Ludmila Recoules and Kerstin Bystricky

    Citation: Genome Biology 2020 21:95

    Content type: Method

    Published on:

  2. Somatic mutations in healthy tissues contribute to aging, neurodegeneration, and cancer initiation, yet they remain largely uncharacterized.

    Authors: Pablo E. García-Nieto, Ashby J. Morrison and Hunter B. Fraser

    Citation: Genome Biology 2019 20:298

    Content type: Research

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  3. Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing,...

    Authors: F. Alexander Wolf, Philipp Angerer and Fabian J. Theis

    Citation: Genome Biology 2018 19:15

    Content type: Software

    Published on:

  4. Conditional knockout mice and transgenic mice expressing recombinases, reporters, and inducible transcriptional activators are key for many genetic studies and comprise over 90% of mouse models created. Condit...

    Authors: Rolen M. Quadros, Hiromi Miura, Donald W. Harms, Hisako Akatsuka, Takehito Sato, Tomomi Aida, Ronald Redder, Guy P. Richardson, Yutaka Inagaki, Daisuke Sakai, Shannon M. Buckley, Parthasarathy Seshacharyulu, Surinder K. Batra, Mark A. Behlke, Sarah A. Zeiner, Ashley M. Jacobi…

    Citation: Genome Biology 2017 18:92

    Content type: Research

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    The Related Article to this article has been published in Nature Protocols 2017 13:BFnprot2017153

  5. RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, ...

    Authors: Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang and Ali Mortazavi

    Citation: Genome Biology 2016 17:13

    Content type: Review

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    The Erratum to this article has been published in Genome Biology 2016 17:181

  6. DNA methylation levels change with age. Recent studies have identified biomarkers of chronological age based on DNA methylation levels. It is not yet known whether DNA methylation age captures aspects of biolo...

    Authors: Riccardo E Marioni, Sonia Shah, Allan F McRae, Brian H Chen, Elena Colicino, Sarah E Harris, Jude Gibson, Anjali K Henders, Paul Redmond, Simon R Cox, Alison Pattie, Janie Corley, Lee Murphy, Nicholas G Martin, Grant W Montgomery, Andrew P Feinberg…

    Citation: Genome Biology 2015 16:25

    Content type: Research

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  7. Recent data from genome-wide chromosome conformation capture analysis indicate that the human genome is divided into conserved megabase-sized self-interacting regions called topological domains. These topologi...

    Authors: Jonas Ibn-Salem, Sebastian Köhler, Michael I Love, Ho-Ryun Chung, Ni Huang, Matthew E Hurles, Melissa Haendel, Nicole L Washington, Damian Smedley, Christopher J Mungall, Suzanna E Lewis, Claus-Eric Ott, Sebastian Bauer, Paul N Schofield, Stefan Mundlos, Malte Spielmann…

    Citation: Genome Biology 2014 15:423

    Content type: Research

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  8. TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat. TopHat2 can align reads of various le...

    Authors: Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley and Steven L Salzberg

    Citation: Genome Biology 2013 14:R36

    Content type: Method

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  9. Cannabis sativa has been cultivated throughout human history as a source of fiber, oil and food, and for its medicinal and intoxicating properties. Selective breeding has produced cannabis plants for specific use...

    Authors: Harm van Bakel, Jake M Stout, Atina G Cote, Carling M Tallon, Andrew G Sharpe, Timothy R Hughes and Jonathan E Page

    Citation: Genome Biology 2011 12:R102

    Content type: Research

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  10. We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced...

    Authors: Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay, Thomas Heider, Katherine Belov, Willem Rens, Paul D Waters, Elizabeth A Pharo, Geoff Shaw, Emily SW Wong, Christophe M Lefèvre, Kevin R Nicholas, Yoko Kuroki, Matthew J Wakefield, Kyall R Zenger…

    Citation: Genome Biology 2011 12:R81

    Content type: Research

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    The Erratum to this article has been published in Genome Biology 2011 12:414

  11. High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer differential signal in such data correctly and with good statis...

    Authors: Simon Anders and Wolfgang Huber

    Citation: Genome Biology 2010 11:R106

    Content type: Method

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  12. The genome of the domestic cow, Bos taurus, was sequenced using a mixture of hierarchical and whole-genome shotgun sequencing methods.

    Authors: Aleksey V Zimin, Arthur L Delcher, Liliana Florea, David R Kelley, Michael C Schatz, Daniela Puiu, Finnian Hanrahan, Geo Pertea, Curtis P Van Tassell, Tad S Sonstegard, Guillaume Marçais, Michael Roberts, Poorani Subramanian, James A Yorke and Steven L Salzberg

    Citation: Genome Biology 2009 10:R42

    Content type: Research

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  13. We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and use...

    Authors: Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li and X Shirley Liu

    Citation: Genome Biology 2008 9:R137

    Content type: Method

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  14. The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative developme...

    Authors: Robert C Gentleman, Vincent J Carey, Douglas M Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch…

    Citation: Genome Biology 2004 5:R80

    Content type: Method

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  15. The recent discoveries of microRNA (miRNA) genes and characterization of the first few target genes regulated by miRNAs in Caenorhabditis elegans and Drosophila melanogaster have set the stage for elucidation of ...

    Authors: Anton J Enright, Bino John, Ulrike Gaul, Thomas Tuschl, Chris Sander and Debora S Marks

    Citation: Genome Biology 2003 5:R1

    Content type: Research

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  16. The distributed nature of biological knowledge poses a major challenge to the interpretation of genome-scale datasets, including those derived from microarray and proteomic studies. This report describes DAVID...

    Authors: Glynn Dennis Jr, Brad T Sherman, Douglas A Hosack, Jun Yang, Wei Gao, H Clifford Lane and Richard A Lempicki

    Citation: Genome Biology 2003 4:R60

    Content type: Software

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  17. Gene-expression analysis is increasingly important in biological research, with real-time reverse transcription PCR (RT-PCR) becoming the method of choice for high-throughput and accurate expression profiling ...

    Authors: Jo Vandesompele, Katleen De Preter, Filip Pattyn, Bruce Poppe, Nadine Van Roy, Anne De Paepe and Frank Speleman

    Citation: Genome Biology 2002 3:research0034.1

    Content type: Research

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