Publications

Contributions from Bergman Lab members are underlined in the publication list below. Lists of publications co-authored by Casey Bergman can be found in PubMed or Google Scholar. Although we try to publish in journals that deposit in PubMed Central, sometimes this isn’t always possible because of external collaborations. Please email for a reprint if you are not able to access any of these papers. Datasets from relevant papers can be found on our Resources page.

Preprints

 

2017

Bergman C.M., S. Han, M.G. Nelson, V. Bondarenko, I.A. Kozeretska (2017) Genomic analysis of P elements in natural populations of Drosophila melanogasterPeerJ 5:e3824.

Nelson, M.G., R.S. Linheiro & C.M. Bergman (2017) McClintock: An integrated pipeline for detecting transposable element insertions in whole genome shotgun sequencing data. G3

2016

Barsh G.S., C.M. Bergman, C.D. Brown, N.D. Singh & G.P. Copenhaver. Bringing PLOS Genetics editors to preprint servers. PLOS Genetics 12:e1006448

Gutzwiller, F. (2016) Evolution and gene expression of Wolbachia in D. melanogaster. Ph.D. Thesis, University of Manchester, UK.

Manee, M. (2016) Comparative genomics of noncoding DNA. Ph.D. Thesis, University of Manchester, UK.

Miller D.E., K.R. Cook, N. Yeganeh Kazemi, C.B. Smith, A.J. Cockrell, R.S. Hawley & C.M. Bergman. (2016) Rare recombination events generate sequence diversity among balancer chromosomes in Drosophila melanogaster. Proc Natl Acad Sci U S A 113:E1352-61.

2015

Rahman, R, G. Chirn, A. Kanodia, Y.A. Sytnikova, B. Brembs, C.M. Bergman & N.C. Lau (2015) Unique transposon landscapes are pervasive across Drosophila melanogaster genomes. Nucl. Acids Res. 43: 10655-10672.

Nelson, M.G. (2015) Bioinformatic approaches to detect transposable element insertions in high throughput sequence data from Saccharomyces and Drosophila. Ph.D. Thesis, University of Manchester, UK.

Gutzwiller F., C.R. Carmo, D.E. Miller, D.W. Rice, I.L. Newton, L. Teixeira & C.M. Bergman (2015) Dynamics of Wolbachia pipientis gene expression across the Drosophila melanogaster life cycle. G3 5:2843-56.

Dudzic, J.P., S. Kondo, R. Ueda, C.M. Bergman & B. Lemaitre (2015) Drosophila innate immunity: regional and functional specialization of prophenoloxidases. BMC Biology 13:81.

Bergman, C.M. & P.R. Haddrill (2015) Strain-specific and pooled genome sequences for populations of Drosophila melanogaster from three continents. F1000Research 4:31.

Mateo J.L., D.L. van den Berg, M. Haeussler, D. Drechsel, ZB Gaber, DS Castro, P Robson, GE Crawford, P Flicek, L Ettwiller, J Wittbrodt, F Guillemot, B Martynoga. Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multi-functional regulator of self-renewal. Genome Research. 25:41-56.

2014

Kim, K., P. Peluso, P. Baybayan, P.J. Yeadon, C. Yu, W. Fisher, C.-S. Chin, N.A. Rapicavoli, D.R. Rank, J. Li, D. Catcheside, S.E. Celniker, A.M. Phillippy, C.M. Bergman & J.M. Landolin (2014) Long-read, whole genome shotgun sequence data for five model organisms. Scientific Data. 1: 140045.

Blumenstiel, J.P., X. Chen, M. He & C.M. Bergman (2014) An age-of-allele test of neutrality for transposable element insertions. Genetics 196: 523-538.

2013

Prokop, A. & C.M. Bergman (2013) Photogenic Flies – A review of Chyb and Gompel’s Atlas of Drosophila Morphology: Wild-type and Classical Mutants. Frontiers in Genetics 4:147.

Oliveres-Chauvet, P. (2013) Multi-scale analysis of chromosome and nuclear architecture. Ph.D. Thesis, University of Manchester, UK.

2012

Kayserili, M.A., D.T. Gerrard, P. Tomancak & A.T. Kalinka (2012) An Excess of gene expression divergence on the X chromosome in Drosophila embryos: implications for the faster-X hypothesis PLOS Genetics 8:e1003200.

Richardson, M.F., L.A. Weinert, J.J. Welch, R.S. Linheiro, M.M. Magwire, F.M. Jiggins & C.M. Bergman (2012) Population genomics of the Wolbachia endosymbiont in Drosophila melanogasterPLOS Genetics 8:e1003129. [See also: web companion].

Carr, M., D. Bensasson & C.M. Bergman (2012) Evolutionary genomics of transposable elements in Saccharomyces cerevisiae. PLOS ONE 7:e50978.

Gerner, M., F. Sarafraz, C.M. Bergman & G. Nenadic. (2012) BioContext: an integrated text mining system for large-scale extraction and contextualisation of biomolecular events. Bioinformatics 28:2154-2161. [See also: web companion & Martin Gerner’s presentation describing this project at the 2011 DBCLS BioHackathon on YouTube’s togoTV channel]

Jamieson, D., M. Gerner, F. Sarafraz, G. Nenadic & D. Roberton. (2012) Towards semi-automated curation: using text mining to recreate the HIV-1, human protein interaction database. Database 2012:bas023.

Gerner, M. (2012) Integrating text-mining approaches to identify entities and extract events from the biomedical literature. Ph.D. Thesis, University of Manchester, UK.

Bergman, C.M. (2012) A proposal for the reference-based annotation of de novo transposable element insertions. Mobile Genetic Elements 2:1-4.

Linheiro, R.S. & C.M. Bergman. Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster. PLoS ONE 7:e30008.

Mackay, T.F.C., S. Richards, E.A. Stone, A. Barbadilla, J.F. Ayroles, D. Zhu, S. Casillas, Y. Han, M.M. Magwire, J.M. Cridland, M.F. Richardson, R.R.H. Anholt, M. Barron, C. Bess, K.P. Blankenburg, M.A. Carbone, D. Castellano, L. Chaboub, L. Duncan, Z. Harris, M. Javaid, J.C. Jayaseelan, S.N. Jhangiani, K.W. Jordan, F. Lara, F. Lawrence, S.L. Lee, P. Librado, R.S. Linheiro, R.F. Lyman, A.J. Mackey, M. Munidasa, D.M. Muzny, L. Nazareth, I. Newsham, L. Perales, L.-L. Pu, C. Qu, M. Ramia, J.G. Reid, S.M. Rollmann, J. Rozas, N. Saada, L. Turlapati, K.C. Worley, Y.-Q. Wu, A. Yamamoto, Y. Zhu, C.M. Bergman, K.R. Thornton, D. Mittelman and R.A. Gibbs (2012). The Drosophila melanogaster Genetic Reference Panel.” Nature 482:173-178. [Research Highlight in Nature Genetics]

2011

Z. Lu, H.Y. Kao, C.H. Wei, M. Huang, J. Liu, C.J. Kuo, C.N. Hsu, R. Tsai, H.J. Dai, N. Okazaki, H.C. Cho, M. Gerner, I. Solt, S. Agarwal, F. Liu, D. Vishnyakova, P. Ruch, M. Romacker, F. Rinaldi, S. Bhattacharya, P. Srinivasan, H. Liu, M. Torii, S. Matos, D. Campos, K. Verspoor, K. Livingston & W.J. Wilbur (2011) The gene normalization task in BioCreative III. BMC Bioinformatics 12(Suppl 8 ):S2.

Baran, J., M. Hauessler, M. Gerner, G. Nenadic & C.M. Bergman. (2011) pubmed2ensembl: a resource for mining the biological literature on genes. PLoS ONE 6:e24716. [See also: web companion]

Hakenberg, J., M. Gerner, M. Haeussler, C. Plake, M. Schroeder, G. Gonzalez, G. Nenadic & C.M. Bergman (2011) The GNAT library for online and offline gene mention normalization. Bioinformatics 27:2769-2771. [See also: web companion]

Sherwood A.M., C. Desmarais, R.J. Livingston, J. Andriesen, M. Haussler, C.S. Carlson & H. Robins (2011) Deep sequencing of the human TCRγ and TCRβ repertoires suggests that TCRβ rearranges after αβ and γδ T cell commitment. Science Translational Medicine 3:90ra61.

Linheiro, R.S. (2011) Computational analysis of transposable element target site preferences in Drosophila melanogaster. Ph.D. Thesis, University of Manchester, UK.

Haeussler, M., M. Gerner & C.M. Bergman (2011) Annotating genes and genomes with DNA sequences extracted from biomedical articles. Bioinformatics 27:980-6. [See also: web companion] [Nature News] [SPARC Article] [Guardian Article] [NRC Handelsblad Article (in Dutch, requires subscription)].

Mendez-Lago, M., C.M. Bergman, B. de Pablos, A. Tracey, S.L. Whitehead, and A. Villasante. (2011) A large palindrome with interchromosomal duplications in the pericentromeric region of the D. melanogaster Y chromosome. Mol. Biol. Evol. 28:1967-71.

Gallo, S.M, D.T. Gerrard, M. Simich, B. Dessoye, C.M. Bergman & M.S. Halfon (2011) REDfly v3.0: Towards a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Research 39: D118-D123. [See also: web companion]

2010

Kalinka, A.T., K. Varga, D.T. Gerrard, S. Preibisch, D. Corcoran, J. Jarrells, U. Ohler, C.M. Bergman & P. Tomancak. (2010) Gene expression divergence recapitulates the developmental hourglass model. Nature 468:811-814. [See also Pavel Tomancak’s round-up of media coverage on this article] [News and Views in Nature] [Listen also to Henry Gee discuss this work on the Nature podcast.]

Solt, I., M. Gerner, P. Thomas, G. Nenadic, C.M. Bergman, U. Leser & J. Hakenberg (2010) Gene mention normalization in full texts using GNAT and LINNAEUS. Proceedings of the BioCreative III Workshop pp 134-139.

Barton M., D. Delneri, S.G. Oliver, M. Rattray & C.M. Bergman. (2010) Evolutionary systems biology of amino acid biosynthetic cost in yeast. PLoS ONE 5:e11935.

Gerner M., G. Nenadic & C.M. Bergman. (2010) An exploration of mining gene expression mentions and their anatomical locations from biomedical text. Proceedings of the 2010 Workshop on Biomedical Natural Language Processing pp.72-80. [See also: web companion]

Rogers, H. C.M. Bergman & S. Griffiths-Jones. (2010) Evolution of tRNA genes in Drosophila. Genome Biology and Evolution 2:467-477.

Gerner M., G. Nenadic & C.M. Bergman. (2010) LINNAEUS: a species name identification system for biomedical literature. BMC Bioinformatics 11:85. [See also: web companion] [Highly Accessed Article]

2009

Sackton T.B., R.J. Kulathinal, C.M. Bergman, A.R. Quinlan, E.B. Dopman, M. Carneiro, G.T. Marth, D.L. Hartl & A.G. Clark (2009) Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome Biology and Evolution 1:439-455. [See also: Andy Clark’s NISC 10th Anniversary Symposium presentation on YouTube’s GenomeTV channel].

Barton, M.D. (2009) Evolutionary systems biology of amino acid cost and gene importance in Saccharomyces cerevisiae. Ph.D. Thesis, University of Manchester, UK.

Yang H., J. Keane, C.M. Bergman, G. Nenadic. (2009) Assigning roles to protein mentions: the case of transcription factors. Journal of Biomedical Informatics 42:887-894.

Liti, G.,D.M. Carter, A.M. Moses, J. Warringer, L. Parts, S.A. James, R.P. Davey, I.N. Roberts, A. Burt, V. Koufopanou, I.J. Tsai, C.M. Bergman, D. Bensasson, M.J.T. O’Kelly, A. van Oudenaarden, D.B.H. Barton, E. Bailes, A.N. Nguyen, M. Jones, M.A. Quail, I. Goodhead, S. Sims, F. Smith, A. Blomberg, R. Durbin & E.J. Louis (2009) Population genomics of domestic and wild yeasts. Nature 458:337-341. [See also: web companion] [Editor’s Note in Nature] [Commentary in Planet Earth]

2008

Linheiro, R.S. & C.M. Bergman. (2008) Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element. Nucleic Acids Research 36:6199-6208.

Altman, R. C.M. Bergman, J. Blake, C. Blaschke, A. Cohen, F. Gannon, L. Grivell, U. Hahn, W. Hersh, L. Hirschman, L.J. Jensen, M. Krallinger, B. Mons, S.I. O’Donoghue, M. Peitsch, D. Rebholz-Schumann, H. Shatkay & A. Valencia. (2008) Text Mining for Biology: The Way Forward. Genome Biology 9:S7.

Aerts, S., M. Haeussler, O.L. Griffith, S. van Vooren, S.J.M. Jones, S. Montgomery, C.M. Bergman & The Open Regulatory Annotation Consortium. (2008) Text-mining assisted regulatory annotation. Genome Biology 9:R31. [Highly Accessed Article]

Halfon, M., S. Gallo & C.M. Bergman. (2008) REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. Nucleic Acids Research 36: D594-D598. [See also: web companion]

Griffith O.L., S.B. Montgomery, B. Bernier, B. Chu, S. Aerts, M.C. Sleumer, M. Bilenky, M. Haeussler, M. Griffith, S.M. Gallo, B. Giardine, S. Mahony, B. Hooghe, P. Van Loo, E. Blanco, A. Ticoll, S. Lithwick, E. Portales-Casamar, I.J. Donaldson, G. Robertson, C. Wadelius, P. De Bleser, D. Vlieghe, M.S. Halfon, W. Wasserman, R. Hardison, C.M. Bergman, S.J.M. Jones & The Open Regulatory Annotation Consortium. (2008) ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Research 36: D107-D113. [See also: web companion]

2007

Bergman, C.M. & H. Quesneville. (2007) Discovering and detecting transposable elements in genome sequences. Briefings in Bioinformatics 8:382-392. [See also: web companion]

Drosophila 12 Genomes Consortium. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218. [News and Views in Nature] [Commentary in BMC] [Commentary in Cell] [Commentary in Heredity] [Commentary in Science] [See also: Andy Clark’s NISC 10th Anniversary Symposium presentation on YouTube’s GenomeTV channel] [Listen also: to segment on Radio 4’s Today Programme or Nature’s podcast.]

Casillas, S., R. Egea, N. Petit, C.M. Bergman & A. Barbadilla. (2007) Drosophila Polymorphism Database (DPDB): a portal for nucleotide polymorphism in Drosophila. Fly 1:4, e1-e7. [See also: web companion]

Casillas, S., A. Barbadilla & C.M. Bergman. (2007) Purifying selection maintains highly conserved noncoding sequences in Drosophila. Molecular Biology and Evolution 24:2222-2234.

Bergman, C.M. & D. Bensasson. (2007) Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster. Proceedings of the National Acadademy of Sciences 104:11340-11345.

Ranz, J.M., D. Maurin, Y.S. Chan, M. von Grotthuss, L.W. Hillier, J. Roote, M. Ashburner & C.M. Bergman. (2007) Principles of genome evolution in the Drosophila melanogaster species group. PLoS Biology 5:e152. [See also: commentary in Heredity]

Down, T.A., C.M. Bergman, J. Su & T.J.P. Hubbard. (2007) Large scale discovery of promoter motifs in Drosophila melanogaster. PLoS Computational Biology 3:e7 [See also: web companion]

2006

Bergman, C.M., H. Quesneville, D. Anxolabéhère & M. Ashburner. (2006) Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome. Genome Biology 7:R112.

Pierstorff, N., C.M. Bergman & T. Wiehe. (2006) Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA. Bioinformatics 22:2858-2864.

Montgomery, S.B., O.L. Griffith, M.C. Sleumer, C.M. Bergman, M. Bilenky, E.D. Pleasance, Y. Prychyna, X. Zhang & S.J.M. Jones. (2006) ORegAnno: An open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics 22:637-640.

2005

Ashburner, M. & C.M. Bergman. (2005) Drosophila melanogaster: A case study of a genomic sequence and its consequences. Genome Research 15:1661-1667.

Lipatov, M., K.D. Lenkov, D.A. Petrov & C.M. Bergman. (2005) Paucity of chimeric gene-transposable element transcripts in the Drosophila melanagaster genome. BMC Biology 3:24. [BMC Research Highlight] [Highlighted in July 2006 Genetics Society News].

Quesneville, H., C.M. Bergman, O. Andrieu, D. Autard, D. Nouaud, M. Ashburner & D. Anxolabéhère. (2005) Combined evidence annotation of transposable elements in genome sequences. PLoS Computational Biology 1:e22.

Russell, S. & C.M. Bergman. (2005) The Drosophila genome(s). Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics.

Bergman, C.M., J.W. Carlson and S.E. Celniker. (2005) Drosophila DNase I footprint database: A systematic genome annotation of transcription factor binding sites in the fruitfly, D. melanogaster. Bioinformatics 21:1747-1749. [See also: web companion.]

Ludwig, M.Z., A. Palsson, E. Alekseeva, C.M. Bergman, J. Nathan & M. Kreitman. (2005) Functional evolution of a cis-regulatory module. PLoS Biology 3:e93. [Commentary in PLoS Biology.]

2004

Pollard, D.A., C.M. Bergman, J. Stoye, S.E. Celniker & M.B. Eisen. (2004) Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 5:6. [See also: web companion.] [Note: correction.] [Highly Accessed Article] [Selected by Thomson-ISI as a Essential Science Indicator (ESI) “New Hot Paper.”]

Bergman, C.M. & N.H. Patel. (2004) Identifying changes in cis-regulatory evolution: approaches and implications. In: Evolution: From Molecules to Ecosystems pp. 48-58 (ISBN: 0-19-851542-1). Moya, A. and E. Font, eds. Oxford University Press, Oxford, UK.

2003

Johnson, A.N., C.M. Bergman, M. Kreitman & S.J. Newfeld. (2003) Embryonic enhancers in the dpp disk region regulate a second round of Dpp signaling from the dorsal ectoderm to the mesoderm that represses Zfh-1 expression in a subset of pericardial cells. Developmental Biology 262:137-51.

Dermitzakis, E.T., C.M. Bergman & A.G. Clark. (2003) Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites. Molecular Biology and Evolution 20:703-714.

2002

Bergman, C.M., B.D. Pfeiffer, D.E. Rincon-Limas, R.A. Hoskins, A. Gnirke, C.J. Mungall, A.M. Wang, B. Kronmiller, J. Pacleb, S. Park, M. Stapleton, K. Wan, R. George, P.J. de Jong, J. Botas, G.M Rubin & S.E. Celniker. (2002) Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. Genome Biology 3:RESEARCH0086. [See also: web companion.] [Highly Accessed Article]

Kaminker, J.S., C.M. Bergman, B. Kronmiller, J. Carlson, R. Svirskas, S. Patel, E. Frise, D.A. Wheeler, S. Lewis, G.M. Rubin, M. Ashburner & S.E. Celniker. (2002) The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biology 3:RESEARCH0084. [See also: web companion.] [Highly Accessed Article]

2001

Bergman, C.M. & M. Kreitman. (2001) Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences. Genome Research 11:1335-45. [Commentary in Genome Research.]

Bergman, C.M. (2001) Evolutionary analyses of transcriptional control sequences in Drosophila. Ph.D. Thesis, University of Chicago, USA.

2000

Ludwig, M.Z., C. Bergman, N.H. Patel & M. Kreitman. (2000) Evidence for stabilizing selection in a eukaryotic cis-regulatory element. Nature 403:564-566.

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