Sujai Kumar

sujai@ylog.org
twitter: @sujaik
github.com/sujaikumar
www.ylog.org/sujai-googlescholar
orcid.org/0000-0001-5902-6641
Pubmed: Sujai Kumar
www.TheWanderOfScience.com
goat.genomehubs.org
 

Experience

• 2020-current - Senior Bioinformatician at the Darwin Tree of Life, Wellcome Sanger Institute, Cambridge, UK
• 2017-2020 - Bioinformatician at the Buck Lab, University of Edinburgh, UK
• 2014-2017 - Bioinformatician, Lepidopteran Genomics at the Blaxter Lab, University of Edinburgh, UK
• 2013-2014 - Bioinformatics Research Fellow at the Aboobaker Lab, University of Oxford, UK
• 2009-2012 - Postgraduate research at the Blaxter Lab, University of Edinburgh, UK
• 2007-2008 - Bioinformatician at the GenePool Sequencing Centre, University of Edinburgh, UK
• 2004-2006 - Research associate at the Centre for Research on Cognitive Systems, New Delhi, India
• 2004-2005 - Senior researcher at NEEV (Network of Enterprising Educational Ventures, Delhi)
• 2000-2004 - Research assistant at the Cognitive Development Lab, University of Illinois, USA
• 1998-2000 - Freelance Mathematics Education Consultant
• 1996-1998 - Co-author and illustrator of Tata McGraw Hill's Mathematics for Middle School textbooks

Education

• 2013 - PhD in evolutionary genomics, Institute of Evolutionary Biology, University of Edinburgh, UK
• 2007 - MSc Informatics, University of Edinburgh, UK
• 2004 - MS Educational Psychology, University of Illinois at Urbana- Champaign, USA
• 1998 - MSc Tech Information Systems, Birla Institute of Technology and Science, Pilani, India

Honors and Awards

• 2014 - Paul Nurse Junior Research Fellowship, Linacre College, Oxford
• 2013 - Amazon AWS Research Grant
• 2012 - James Rennie Bequest Travel Grant
• 2012 - NEMASYM Travel Award for 3rd meeting at Cold Spring Harbor Labs
• 2011 - Amazon AWS Research Grant
• 2011 - NEMASYM Travel Award for 2nd meeting at Oregon State University
• 2009 - University of Edinburgh School of Biological Sciences PhD Studentship
• 2009 - University of Edinburgh Overseas Research Studentship
• 2007 - University of Edinburgh Prize for best MSc Informatics student
• 2006 - Scottish International Scholarship Programme
• 2003 - University of Illinois Masters Thesis Grant
• 2000 - University of Illinois Distinguished Fellowship
• 1997 - Hughes Software Systems Best Student Award, Birla Institute of Technology and Science, Pilani, India
• 1992 - National Talent Search Scholarship, National Council of Educational Research and Training, India

Publications

• Chow FW, Koutsovoulos G, Ovando-Vázquez C, Neophytou K, Bermúdez-Barrientos JR, Laetsch DR, Robertson E, Kumar S, Claycomb JM, Blaxter M, Abreu-Goodger C, Buck AH. (2019) Secretion of an Argonaute protein by a parasitic nematode and the evolution of its siRNA guides. Nucleic Acids Research, doi.org/10.1093/nar/gkz142
• Pinharanda A, Rousselle M, Martin SH, Hanly JJ, Davey JW, Kumar S, Galtier N, Jiggins CD (2018). Sexually dimorphic gene expression and transcriptome evolution provide mixed evidence for a fast-Z effect in Heliconius. J Evol Biol. https://doi.org/10.1111/jeb.13410
• Yoshida Y, Koutsovoulos G, Laetsch DR, Stevens L, Kumar S, Horikawa DD, Ishino K, Komine S, Kunieda T, Tomita M, Blaxter M, Arakawa K. (2017). Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus. PLOS Biology, doi.org/10.1371/journal.pbio.2002266
• Challis R, Kumar S, Stevens L, Blaxter M. (2017). GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species. Database, doi.org/10.1093/database/bax039
• Challis RJ, Kumar S, Dasmahapatra K, Jiggins CD, Blaxter M (2016) Lepbase: the Lepidopteran genome database. BioRxiv. dx.doi.org/10.1101/056994
• Koutsovoulos G, Kumar S, Laetsch DR, Stevens L, Daub J, Conlon C, Maroon H, Thomas F, Aboobaker AA, Blaxter M (2016) No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini. PNAS 113: 5053–5058. doi.org/10.1073/pnas.1600338113
• Buck AH, Coakley G, Simbari F, McSorley HJ, Quintana JF, Le Bihan T, Kumar S, Abreu-Goodger C, Lear M, Harcus Y, et al. (2014) Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity. Nature Communications 5: 5488. doi.org/10.1038/ncomms6488
• Armstrong SD, Babayan SA, Lhermitte-Vallarino N, Gray N, Xia D, Martin C, Kumar S. Taylor DW, Blaxter ML, Wastling JM  Makepeace BL. 2014 Comparative analysis of the secretome from a model filarial nematode (Litomosoides sigmodontis) reveals maximal diversity in gravid female parasites. Molecular and Cellular Proteomics 13(10):2527-2544 http://dx.doi.org/10.1074/mcp.M114.038539
• Lunt DH, Kumar S, Koutsovoulos G, Blaxter ML. (2014) The complex hybrid origins of the root knot nematodes revealed through comparative genomics. PeerJ 2:e356 https://doi.org/10.7717/peerj.356
• Kumar S, Jones M, Koutsovoulos G, Clarke M, Blaxter M, 2013. Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots. Frontiers in Genetics http://dx.doi.org/10.3389/fgene.2013.00237
• chiffer PH, Kroiher M, Kraus C, Koutsovoulos GD, Kumar S, Camps JI, Nsah NA, Stappert D, Morris K, Heger P, Altmueller J, Frommolt P, Nuernberg P, Thomas WK, Blaxter ML, Schierenberg E, 2013. The genome of Romanomermis culicivorax: revealing fundamental changes in the core developmental genetic toolkit in Nematoda. BMC Genomics http://dx.doi.org/10.1186/1471-2164-14-923
• Comandatore F, Sassera D, Montagna M, Kumar S, Koutsovoulos G, Thomas G, Repton C, Babayan SA, Gray N, Cordaux R, Darby A, Makepeace B, Blaxter M, 2013. Phylogenomics and analysis of shared genes suggest a single transition to mutualism in Wolbachia of nematodes. Genome Biology and Evolution http://dx.doi.org/10.1093/gbe/evt125
• Laxman S, Sutter BM, Wu X, Kumar S, Guo X, Trudgian DC, Mirzaei H, Tu BP, 2013. Sulfur amino acids regulate translational capacity and metabolic homeostasis through modulation of tRNA thiolation. Cell http://dx.doi.org/10.1016/j.cell.2013.06.043
• Wang J, Mitreva M, Berriman M, Thorne A, Magrini V, Koutsovoulos G, Kumar S, Blaxter ML, Davis RE, 2012. Silencing of Germline-Expressed Genes by DNA Elimination in Somatic Cells. Developmental Cell. http://dx.doi.org/10.1016/j.devcel.2012.09.020
• Godel C, Kumar S, Koutsovoulos G, Ludin P, Nilsson D, Comandatore F, Wrobel N, Thompson M, Schmid CD, Goto S, Bringaud F, Wolstenholme A, Bandi C, Epe C, Kaminsk R, Blaxter M, Maser P, 2012. The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets. FASEBJ. http://dx.doi.org/10.1096/fj.12-205096
• Kumar S, Blaxter M, 2012. Simultaneous genome sequencing of symbionts and their hosts. Symbiosis, 55 (3), 119-126. http://dx.doi.org/10.1007/s13199-012-0154-6
• Kumar S, Schiffer PH, Blaxter M, 2012. 959 nematode genomes: a semantic wiki for coordinating sequencing projects. Nucleic Acids Research 40 (D1), D1295-D1300. http://dx.doi.org/10.1093/nar/gkr826
• Kumar S, Koutsovoulos GD, Kaur G, Blaxter ML, 2012. Toward 959 nematode genomes. Worm 1 (1). http://dx.doi.org/10.4161/worm.19046
• Blaxter M, Kumar S, Kaur G, Koutsouvoulos G, Elsworth B, 2011. Genomics and transcriptomics across the diversity of the nematoda. Parasite Immunology 34 (2-3), 108-120. http://dx.doi.org/10.1111/j.1365-3024.2011.01342.x
• Kumar S, Blaxter M, 2010. Comparing de novo assemblers for 454 transcriptome data. BMC Genomics 11 (1), 571+. http://dx.doi.org/10.1186/1471-2164-11-571
• Hunt P, Martinelli A, Modrzynska K, Borges S, Creasey A, Rodrigues L, Beraldi D, Loewe L, Fawcett R, Kumar S, Thomson M, Trivedi U, Otto T, Pain A, Blaxter M, Cravo P, 2010. Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites. BMC Genomics 11 (1), 499+. http://dx.doi.org/10.1186/1471-2164-11-499
• Ferguson L, Lee SF, Chamberlain N, Nadeau N, Joron M, Baxter S, Wilkinson P, Papanicolaou A, Kumar S, Kee J, Clark R, Davidson C, Glithero R, Beasley H, Vogel H, Ffrench-Constant R, Jiggins C, 2010. Characterization of a hotspot for mimicry: assembly of a butterfly wing transcriptome to genomic sequence at the HmYb/sb locus. Molecular Ecology 19 (s1), 240-254. http://dx.doi.org/10.1111/j.1365-294X.2009.04475.x
• Keightley PD, Trivedi U, Thomson M, Oliver F, Kumar S, Blaxter ML, 2009. Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines. Genome Research 19 (7), 1195-1201. http://dx.doi.org/10.1101/gr.091231.109
• Kumar S, 2007. Evolutionary dynamics of conserved non-coding DNA elements: Big bang or gradual accretion? Thesis submitted for the MSc Informatics degree at the University of Edinburgh. http://www.inf.ed.ac.uk/publications/thesis/online/IM070463.pdf
• Kumar S, Mitra S, 2006. Self-Organizing traffic at a malfunctioning intersection. Journal of Artificial Societies and Social Simulation 9 (4). http://jasss.soc.surrey.ac.uk/9/4/3.html
• Mitra S, Kumar S, 2006. Fractal replication in time-manipulated one-dimensional cellular automata. Complex Systems 16 (3), 191-207. http://www.complex-systems.com/abstracts/v16_i03_a01.html
• Kumar S, Miller KF, 2005. Let SMIL be your umbrella: software tools for transcribing, coding, and presenting digital video in behavioral research. Behavior Research Methods 37 (2), 359-367. http://www.ncbi.nlm.nih.gov/pubmed/16171208
• Narasimhan J, Kumar S, 1998. Mathematics for Middle School - Volumes I, II, and III. Tata McGraw Hill: New Delhi

Presentations

• Kumar S, September 2015. LepBase - lessons learnt from setting up a genome infrastructure for dozens of butterfly and moth species Talk presented at the 9th Edinburgh Bioinformatics Meeting, University of Edinburgh, UK
• Kumar S, August 2015. Lepbase – an Ensembl (and more) for the Lepidoptera Talk presented at the NextGen Bioinformatics User Group, University of Dundee, UK
• Kumar S, November 2013. Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots Invited talk presented at the Beatles and Bioinformatics meeting, University of Liverpool, UK
• Kumar S, Blaxter M, April 2012. Mammals and Fish share Genome Resident Elements. Do Nematodes? Poster presented at the Evolutionary Biology of Caenorhabditis and Other Nematodes Meeting, Cold Spring Harbor Laboratory, USA
• Kumar S, Koutsovoulos G, Blaxter M, July 2011. Assembling and annotating half a dozen draft nematode genomes using inexpensive Illumina sequencing. Paper presented at the annual meeting of the Sociey of Nematologists, Corvallis, OR, USA
• Kumar S, Blaxter M, July 2011. Novel ways of extracting complete Wolbachia genomes from 2nd gen nematode sequencing projects. Paper presented at the 3rd NemaSym RCN Meeting, Corvallis, OR, USA
• Kumar S, Thomas GT, Blaxter ML, June 2010. Preliminary genome assembly of the filarial nematode Litomosoides sigmodontis. Poster presented at the Evolutionary Biology of Caenorhabditis and Other Nematodes Meeting, Hinxton, UK
• Kumar S, June 2011. Evolution of cis-regulatory sequences. Paper presented at the Workshop on Evolution and Genomics, 17th International C elegans meeting, Los Angeles, USA
• Kumar S, April 2005. The Game of Life: An introduction to Cellular Automata. Invited talk presented to students of the Department of Physics at the Birla Institute of Technology and Science, Pilani, India
• Kumar S, Correa C, April 2004. Out of order: Extracting patterns from sequences of lesson codes. In KF Miller (Chair), Making Lesson Structure Visible: Alternative Analysis Techniques Applied to a Large International Mathematics Data Set. Paper presented at the annual meeting of American Educational Research Association, San Diego, CA, USA
• Correa C, Kumar S, April 2004. Charting the course: Navigating lesson data through visual representations. In KF Miller (Chair), Making Lesson Structure Visible: Alternative Analysis Techniques Applied to a Large International Mathematics Data Set. Paper presented at the annual meeting of the American Educational Research Association, San Diego, CA, USA
• Kumar S, Correa C, April 2004. Lightweight tools for working with digital video: Using SMIL to automate research tasks. Roundtable discussion at the annual meeting of the American Educational Research Association, San Diego, CA, USA
• Kumar S, Correa C, Sims LM, April 2003. First and Foremost: Examining lesson introductions by Chinese and American elementary school mathematics teachers. In KF Miller (Chair), Making Teaching Public: Studying Teacher Thinking Using Video Techniques. Paper presented at the annual meeting of the American Educational Research Association, Chicago, USA
• Sims LM, Kumar S, April 2002. Working with digital video: A guide for the perplexed. In KF Miller (Chair), Digital video records of classroom mathematics: How to make them and what we can learn from them. Paper presented at the annual meeting of the American Educational Research Association, New Orleans, LA, USA.