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!DOCTYPE html>html langen>head>        meta charsetutf-8 />        meta namegenerator contentPelican />        title>About/title>        link relstylesheet href/theme/css/main.css />/head>body idindex classhome>        header idbanner classbody>                h1>a href/>Python - Algorithms - Bioinformatics/a>/h1>                nav>ul>                    li classactive>a href/>About/a>/li>                    li>a href/category/combinatorics>Combinatorics/a>/li>                /ul>/nav>        /header>!-- /#banner -->section idcontent classbody>    h1 classentry-title>About/h1>        p>I am a Robertson Fellow in Biomedical Data Science at thea classreference external hrefhttps://www.bdi.ox.ac.uk/>Big Data Institute/a>, a classreference external hrefhttp://www.ox.ac.uk/>University ofOxford/a>. I develop algorithms and softwareto tackle difficult problems in large-scale genomics, integratingwith the Python data science stack./p>hr classdocutils />div classsection idcontact>h2>Contact/h2>table border1 classdocutils>colgroup>col width33% />col width33% />col width33% />/colgroup>tbody valigntop>tr>td>strong>Email/strong>/td>td>a classreference external hrefmailto:jerome.kelleher@bdi.ox.ac.uk>jerome.kelleher@bdi.ox.ac.uk/a>/td>td rowspan5>blockquote classfirst>em>Me at the BDI/em>/blockquote>p classlast>img altJerome Kelleher src/images/profile-picture.jpg stylewidth: 200px; />/p>/td>/tr>tr>td>strong>GitHub/strong>/td>td>a classreference external hrefhttps://github.com/jeromekelleher>@jeromekelleher/a>/td>/tr>tr>td>strong>Twitter/strong>/td>td>a classreference external hrefhttps://twitter.com/jeromekelleher>@jeromekelleher/a>/td>/tr>tr>td>strong>Orcid/strong>/td>td>a classreference external hrefhttp://orcid.org/0000-0002-7894-5253>orcid.org/0000-0002-7894-5253/a>/td>/tr>tr>td>strong>Google Scholar/strong>/td>td>a classreference external hrefhttps://scholar.google.co.uk/citations?useraYTQa_AAAAAJ&hlen&oiao>profile/a>/td>/tr>/tbody>/table>p>strong>Address:/strong>/p>div classline-block>div classline>Dr Jerome Kelleher/div>div classline>Big Data Institute/div>div classline>Li Ka Shing Centre for Health Information and Discovery/div>div classline>Old Road Campus/div>div classline>Oxford/div>div classline>OX3 7LF/div>div classline>UK/div>/div>/div>hr classdocutils />div classsection idactivities>h2>Activities/h2>ul classsimple>li>I am co-organising Probabilistic Modelling in Genomics 2022 conference.Please see the a classreference external hrefhttps://probgen22.github.io/>ProbGen22 website/a>for more details./li>li>I lead development of a classreference external hrefhttps://tskit.dev/tskit/>tskit/a>, thetree sequence toolkit. Tskit is a Python and C API that allows us towork with genealogical histories at unprecedented scale./li>li>I also lead development of the a classreference external hrefhttps://tskit.dev/msprime>msprime/a> coalescent simulator, which is based ontskit, and can simulate of the exact coalescent with recombination overchromosome-sized regions with hundreds of thousands of samples./li>li>Im a member of the a classreference external hrefhttps://github.com/popsim-consortium>PopSim Consortium/a>and lead development of its first product,a classreference external hrefhttps://popsim-consortium.github.io/stdpopsim-docs/stable/index.html>stdpopsim/a>./li>li>Im part of the a classreference external hrefhttp://ga4gh.org/#>Data Working Group/a> in the a classreference external hrefhttp://genomicsandhealth.org/>GlobalAlliance for Genomics and Health/a> (GA4GH).I am currently participating in the design and a classreference external hrefhttps://github.com/jeromekelleher/htsget>client side implementation/a> of the a classreference external hrefhttp://samtools.github.io/hts-specs/htsget.html>htsget data access protocol/a>./li>li>During my postdoc in theoretical population genetics , I worked primarilyon a new model for populations evolving in a a classreference external hrefhttp://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2010.01019.x/full>spatial continuum/a>.During this time I developed two Python simulation packages: one tosimulate a a classreference external hrefhttps://pypi.python.org/pypi/ercs>general form/a> of the modeland another to simulate a more a classreference external hrefhttps://pypi.python.org/pypi/discsim>specialised form/a> much more efficiently./li>li>I found some bugs in a classreference external hrefhttp://www-cs-faculty.stanford.edu/~uno/taocp.html>TAOCP/a>volume 4A while it was still in beta-test fascicle form. I am therefore aproud saver at the a classreference external hrefhttp://www-cs-faculty.stanford.edu/~uno/boss.html>The Bank of San Serriffe/a>!/li>/ul>/div>hr classdocutils />div classsection idcv-sketch>h2>CV Sketch/h2>dl classdocutils>dt>2019-present/dt>dd>Robertson Fellowship in Biomedical Data Science at thea classreference external hrefhttps://www.bdi.ox.ac.uk/>Big Data Institute/a>,University of Oxford./dd>dt>2014-2019/dt>dd>Senior statistical programmer in thea classreference external hrefhttp://www.well.ox.ac.uk/gil-mcvean>McVean Group/a> at thea classreference external hrefhttps://www.bdi.ox.ac.uk/>Big Data Institute/a> (and formerly at thea classreference external hrefhttp://www.well.ox.ac.uk/home>Wellcome Centre for Human Genetics/a>),University of Oxford./dd>dt>2008-2014/dt>dd>Postdoc, primarily at the a classreference external hrefhttp://www.ed.ac.uk/biology/evolutionary-biology>Institute of Evolutionary Biology/a>, Universityof Edinburgh and also at thea classreference external hrefhttps://www.stats.ox.ac.uk/>Department of Statistics/a>, Universityof Oxford./dd>dt>2005-2008/dt>dd>Seniour Software Architect, a classreference external hrefhttp://www.mpstor.com/>MPSTOR/a>./dd>dt>2002-2005/dt>dd>PhD Computer Science,a classreference external hrefhttp://www.ucc.ie/>University College Cork/a>(a classreference external hrefhttp://jeromekelleher.net/downloads/k06.pdf>thesis/a>)./dd>dt>1998-2002/dt>dd>BSc Computer Science,  a classreference external hrefhttp://www.ucc.ie/>University College Cork/a>./dd>/dl>/div>div classsection idbook-chapters>h2>Book Chapters/h2>p>strong>Jerome Kelleher and Konrad Lohse./strong>Coalescent simulation with msprime.Chapter 9 in em>Statistical Population Genomics/em>, 2020.a classreference external hrefhttps://doi.org/10.1007/978-1-0716-0199-0_9>link/a>/p>p>strong>Jerome Kelleher and Gil McVean./strong>Linkage Disequilibrium, Recombination and Haplotype Structure.Chapter 2 in em>Handbook of Statistical Genomics/em>, 2019.a classreference external hrefhttps://doi.org/10.1002/9781119487845.ch2>link/a>/p>/div>div classsection idpublications>h2>Publications/h2>p>strong>Dominic Nelson, Jerome Kelleher, Aaron P. Ragsdale, Claudia Moreau, Gil McVean and Simon Gravel./strong>Accounting for long-range correlations in genome-wide simulations of large cohorts.em>PLOS Genetics/em> 16(5): e1008619, 2020.a classreference external hrefhttps://doi.org/10.1371/journal.pgen.1008619>link/a>/p>p>strong>Peter Ralph, Kevin Thornton and Jerome Kelleher/strong>.Efficiently Summarizing Relationships in Large Samples: A General Duality BetweenStatistics of Genealogies and Genomes.em>Genetics/em>, 2020.a classreference external hrefhttps://doi.org/10.1534/genetics.120.303253>link/a>/p>p>strong>Jerome Kelleher, Yan Wong, Anthony W. Wohns, Chaimaa Fadil, Patrick K. Albers and Gil McVean./strong>Inferring whole-genome histories in large population datasets.em>Nature Genetics/em>, 51:1330–1338, 2019.a classreference external hrefhttps://doi.org/10.1038/s41588-019-0483-y>link/a>/p>p>strong>Benjamin C. Haller,  Jared Galloway, Jerome Kelleher,  Philipp W. Messer and Peter L. Ralph./strong>Tree‐sequence recording in SLiM opens new horizons for forward‐time simulation of whole genomes.em>Molecular Ecology Resources/em>, 19:552–566, 2019.a classreference external hrefhttps://doi.org/10.1111/1755-0998.12968>link/a>/p>p>strong>Jerome Kelleher, Kevin R. Thornton, Jaime Ashander and Peter L. Ralph./strong>Efficient pedigree recording for fast population genetics simulation.em>PLoS Computational Biology/em>, 14(11): e1006581, 2018.a classreference external hrefhttps://doi.org/10.1371/journal.pcbi.1006581>link/a>/p>p>strong>Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe,Christopher H. Tomkins-Tinch, Renan Valieris, Johannes Köster and Bioconda Team./strong>Bioconda: sustainable and comprehensive software distribution for the life sciences.em>Nature Methods/em>, 15(7):475-476, 2018.a classreference external hrefhttps://doi.org/10.1038/s41592-018-0046-7>link/a>/p>p>strong>Jerome Kelleher, Mike Lin,  CH Albach,  Ewan Birney,  Robert Davies,Marina Gourtovaia, David Glazer,  Cristina Y Gonzalez,  David K Jackson,Aaron Kemp, John Marshall, Andrew Nowak, Alexander Senf,  Jaime M Tovar-Corona,Alexander Vikhorev, Thomas M Keane, and  GA4GH Streaming Task Team./strong>htsget: a protocol for securely streaming genomic data, em>Bioinformatics/em> 2018.a classreference external hrefhttps://doi.org/10.1093/bioinformatics/bty492>link/a>/p>p>strong>Jerome Kelleher, Alison M. Etheridge and Gilean McVean./strong>Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes.em>PLoS Computational Biology/em>, Volume 12, May 2016, e1004842.a classreference external hrefhttp://dx.doi.org/10.1371/journal.pcbi.1004842>link/a>/p>p>strong>Jerome Kelleher, Alison M. Etheridge, Amandine Véber and Nicholas H. Barton./strong>Spread of pedigree versus genetic ancestry in spatially distributed populations.em>Theoretical Population Biology/em>, Volume 108, April 2016, Pages 1–12.a classreference external hrefhttp://dx.doi.org/10.1016/j.tpb.2015.10.008>link/a>/p>p>strong>Jerome Kelleher, Alison M. Etheridge and Nicholas H. Barton./strong>Coalescent simulation in continuous space: Algorithms for large neighbourhood size.em>Theoretical Population Biology/em>, Volume 95, August 2014, Pages 13–23.a classreference external hrefhttp://www.sciencedirect.com/science/article/pii/S0040580914000355#>link/a>/p>p>strong>Jerome Kelleher, Rob W. Ness and Daniel L. Halligan./strong>Processing genome scale tabular data with wormtable.em>BMC Bioinformatics/em>, 14:356, 2013.a classreference external hrefhttp://www.biomedcentral.com/1471-2105/14/356>link/a>/p>p>strong>Jerome Kelleher, Nicholas H. Barton and Alison M. Etheridge./strong>Coalescent simulation in continuous space.em>Bioinformatics/em>, Volume 29, Issue 7, pp. 955-956, 2013.a classreference external hrefhttp://bioinformatics.oxfordjournals.org/content/29/7/955.abstract>link/a>/p>p>strong>Nicholas H. Barton, Alison M. Etheridge, Jerome Kelleher and Amandine Véber./strong>Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks.em>Theoretical Population Biology/em>, Volume 87, August 2013, Pages 105–119.a classreference external hrefhttp://www.sciencedirect.com/science/article/pii/S0040580913000233#>link/a>/p>p>strong>Nicholas H. Barton, Alison M. Etheridge, Jerome Kelleher and Amandine Véber./strong>Genetic hitchhiking in spatially extended populations.em>Theoretical Population Biology,/em> Volume 87, August 2013, Pages 75–89.a classreference external hrefhttp://www.sciencedirect.com/science/article/pii/S0040580912001359>link/a>/p>p>strong>Nicholas H. Barton, Jerome Kelleher and Alison M. Etheridge./strong>A new model for extinction and recolonisation in two dimensions: quantifying phylogeography.em>Evolution/em>, Volume 64, Issue 9, pp 2701-2715, 2010.a classreference external hrefhttp://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2010.01019.x/full>link/a>/p>p>strong>Konrad Lohse and Jerome Kelleher/strong>.Measuring the degree of starshape in genealogies --- summary statistics and demographic inference.em>Genetics Research/em>, Volume 91, Issue 04, pp 281-292, 2009.a classreference external hrefhttp://dx.doi.org/10.1017/S0016672309990139>link/a>/p>p>strong>William Opperman and Jerome Kelleher/strong>.A Data Storage System, International Patent WO/2008/007348, 2008.a classreference external hrefhttp://www.wipo.int/pctdb/en/wo.jsp?wo2008007348>link/a>/p>p>strong>Jerome Kelleher./strong>Encoding Partitions as Ascending Compositions. PhD thesis, University College Cork, 2006.a classreference external hrefhttp://jeromekelleher.net/downloads/k06.pdf>pdf/a>/p>p>strong>Jerome Kelleher and Derek Bridge./strong>An Accurate and Scalable Collaborative Recommender.em>Artificial Intelligence Review/em>, Volume 21, Issue 3-4, pp.193-213, 2004.a classreference external hrefhttp://www.springerlink.com/content/v7458560x0733q58/>link/a>/p>p>strong>Stefano Bistarelli, Jerome Kelleher and Barry OSullivan/strong>.Tradeoff Generation using Soft Constraints,em>Recent Advances in Constraints/em>, Springer, LNAI 3010 2004.a classreference external hrefhttp://www.springerlink.com/content/8t9whlq4ll27hulf/>link/a>/p>p>strong>Jerome Kelleher and Barry OSullivan/strong>.Evaluation-Based Semiring Meta-Constraints.em>Proceedings of MICAI/em>, Springer, LNCS 2972 Mexico, 2004.a classreference external hrefhttp://jeromekelleher.net/downloads/ko04.pdf>pdf/a>/p>p>strong>Jerome Kelleher and Derek Bridge/strong>.RecTree Centroid: An Accurate, Scalable Collaborative Recommender.em>Proceedings of AICS/em>, Trinity College, Dublin, pp.89-94, 2003.a classreference external hrefhttp://jeromekelleher.net/downloads/kb03.pdf>pdf/a>/p>p>strong>Stefano Bistarelli, Jerome Kelleher and Barry OSullivan./strong>Symmetry Breaking in Soft CSPs.em>Proceedings of AI-2003/em>, Springer, Cambridge, UK, 2003.a classreference external hrefhttp://jeromekelleher.net/downloads/bko03.pdf>pdf/a>/p>p>strong>Jerome Kelleher and Barry OSullivan./strong>Evaluation-Based Semiring Meta-Constraints.em>Proceedings of AICS-2003/em>, Poster Paper, Dublin, Ireland, 2003./p>p>strong>Jerome Kelleher and Barry OSullivan/strong>.Optimising the Representation and Evaluation of Semiring Combination Constraints.Principles and Practice of Constraint Programming - CP2003, LNCS, 2003./p>p>strong>Derek Bridge and Jerome Kelleher/strong>.Experiments in Sparsity reduction: Using Clustering in Collaborative Recommenders.em>Proceedings of AICS-2002/em>, LNAI 2464, Springer, pp.144-149, 2002.a classreference external hrefhttp://jeromekelleher.net/downloads/bk02.pdf>pdf/a>/p>div classsection idpreprints>h3>Preprints/h3>p>strong>Jerome Kelleher/strong>.The large-parts formula for p(n).em>arXiv/em>, 1002.1458, 2010a classreference external hrefhttp://arxiv.org/abs/1002.1458>link/a>/p>p>strong>Jerome Kelleher and Barry OSullivan/strong>.Generating All Partitions: A Comparison Of Two Encodings.em>arXiv/em>, 0909.2331, 2009a classreference external hrefhttp://arxiv.org/abs/0909.2331>link/a>/p>/div>/div>/section>        section idextras classbody>        /section>!-- /#extras -->        footer idcontentinfo classbody>                address idabout classvcard body>                Proudly powered by a hrefhttps://getpelican.com/>Pelican/a>, which takes great advantage of a hrefhttps://www.python.org/>Python/a>.                /address>!-- /#about -->                p>The theme is by a hrefhttps://www.smashingmagazine.com/2009/08/designing-a-html-5-layout-from-scratch/>Smashing Magazine/a>, thanks!/p>        /footer>!-- /#contentinfo -->/body>/html>

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