| General Category |
Specific
Task |
Person |
Address |
|
|
|
|
| Preparations for genome sequencing |
20x incrossing of remanei PB4641 and brenneri PB2801 |
Scott E. Baird |
Department of Biological Sciences, Wright State
University, Dayton, Ohio, USA |
|
20x incrossing of japonica DF5081 |
Karin C. Kiontke |
Department of Biology, New York University, New York, NY
10003, USA |
|
Physical determination of genome sizes |
J. Spencer Johnston |
Texas A&M University, College Station, TX 77843, USA |
|
|
|
|
Genome sequencing at WashU
|
Genomic library analysis |
Makedonka Mitreva |
Genome Sequencing Center, Washington University School of
Medicine, St Louis, MO 63108, USA |
|
|
Sahar Abubucker |
|
|
|
Zhengyuan Wang |
|
|
Genomic library assembly and submission |
Patrick Minx |
Genome Sequencing Center, Washington University School of
Medicine, St Louis, MO 63108, USA |
|
|
Joanne O. Nelson |
|
|
|
Asif T. Chinwala |
|
|
|
Shunfang Hou |
|
|
Genomic library finishing |
Robert S. Fulton |
Genome Sequencing Center, Washington University School of
Medicine, St Louis, MO 63108, USA |
|
|
Tina A. Graves |
|
|
|
Aye Wollam |
|
|
|
Lee Trani |
|
|
|
Scott S. Kruchowski |
|
|
|
Chad Tomlinson |
|
|
|
Laura P. Courtney |
|
|
|
Neha Shah |
|
|
|
Rachel M. Abbott |
|
|
|
Amy D. Kozlowicz-Reily |
|
|
|
Cynthia Strong |
|
|
Genomic library production |
Lucinda L. Fulton |
Genome Sequencing Center, Washington University School of
Medicine, St Louis, MO 63108, USA |
|
|
Kimberley D. Delehaunty |
|
|
|
Michelle O'Laughlin |
|
|
|
Catrina C. Fronick |
|
|
|
Elizabeth L. Appelbaum |
|
|
Reliable formatting for NCBI submission |
Philip Ozersky |
Genome Sequencing Center, Washington University School of
Medicine, St Louis, MO 63108, USA |
|
|
|
|
Genome sequencing outside
WashU
|
Caenorhabditis sp. 5 JU800 sequencing and
assembly
|
Sujai Kumar |
Institute of Evolutionary
Biology, University of Edinburgh,
King's Buildings Campus, Edinburgh EH9 3JT, UK |
|
|
Mark Blaxter |
|
|
C. angaria, revised sequencing and
assembly
|
Erich M. Schwarz
|
Division of Biology, 156-29,
California Institute of Technology, Pasadena, CA 91125, USA
|
|
|
Igor Antoshechkin
|
|
|
khmer-filtering of cDNA for
RNA-scaffolding
|
C. Titus Brown
|
MSU, Microb. & Mol. Gen.
and Comp. Sci. & Engineering, E. Lansing, MI, 48824
|
|
C. sp. 9, resequencing and assembly
|
Barbara J. Meyer
|
HHMI, Department of Molecular and Cell Biology, University
of California, Berkeley, CA 94720-3204, USA |
|
|
[Meyer lab members]
|
|
|
|
Erich M. Schwarz
|
|
|
|
|
|
| Genome heterozygosity |
Scan for heterozygosity |
Shiaw-Pyng Yang |
Monsanto Company, Chesterfield Ridge Center, 16401
Swingley Ridge, 5th Floor, Suite 500, Chesterfield, MO 63017
USA |
|
Complete, but non-summarized, genomic regions of likely
heterozygosity |
Shiaw-Pyng Yang |
|
|
Summarizing the heterozygosity data |
Erich M. Schwarz |
Division of Biology, 156-29, California Institute of
Technology, Pasadena, CA 91125, USA |
|
|
|
|
| Genome repeats |
Repeat prediction with Repeatmodeler, i.e., RepeatScout
and RECON |
Erich M. Schwarz |
Division of Biology, 156-29, California Institute of
Technology, Pasadena, CA 91125, USA |
|
Analysis of genomic repeats |
Ismael A. Vergara |
Department of Molecular Biology and Biochemistry, Simon
Fraser University, Burnaby, BC, V5A 1S6, Canada |
|
|
Nansheng [Jack] Chen |
|
|
|
David Baillie |
|
|
Filtered genomic repeats, compared vs.Caeno. spp. and
Pristionchus |
Ismael A. Vergara |
|
|
|
Nansheng [Jack] Chen |
|
|
Filter against prot.-coding, ncRNA genes |
Nansheng [Jack] Chen |
Department of Molecular Biology and Biochemistry, Simon
Fraser University, Burnaby, BC, V5A 1S6, Canada |
|
Repeatmask genome against filtered, merged set |
Michael Paulini |
Sanger Institute, Wellcome Trust Genome Campus Hinxton,
Cambridgeshire CB10 1SA, UK |
|
Chromosome-specific short DNA repeats |
Marc D. Perry |
Ontario Institute for Cancer Research, 101 College Street,
Suite 800, Toronto, Ontario M5G 0A3, Canada |
|
|
|
|
| Protein-coding gene prediction |
Gene sets, pre-2011 |
Kymberlie H. Pepin |
Genome Sequencing Center, Washington University School of
Medicine, St Louis, MO 63108, USA |
|
|
Tamberlyn Bieri |
|
|
|
Philip Ozersky |
|
|
|
William E. Nash |
|
|
|
Min-Ho Lee |
University at Albany, SUNY, Department of Biology, Albany,
NY 12222, USA, mhlee@albany.edu |
|
|
Darin Blasiar |
Monsanto Company, 700 Chesterfield Pkwy W, CC3A,
Chesterfield, MO 63017, USA
|
|
RNA-seq-based and ab initio gene sets, 2011-2012 |
Erich M. Schwarz |
Division of Biology, 156-29, California Institute of
Technology, Pasadena, CA 91125, USA |
|
Predicting small ORFs reliably |
Kousuke Hanada |
Plant Science Center and Bioinformatics and Systems
Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama, Kanagawa 230-0045, Japan |
|
|
Shin-Han Shiu |
Department of Plant Biology, Michigan State University,
East Lansing, MI, 48824, USA |
|
|
|
|
| ncRNA gene prediction |
RFAM/INFERNAL |
Sam Griffiths-Jones |
Faculty of Life Sciences, The University of Manchester,
Manchester M13 9PL, UK |
|
|
Hubert Rogers |
Faculty of Life Sciences, Michael Smith Building,
University of Manchester, Oxford Road, Manchester, M13 9PT,
UK |
|
de novo ncRNA prediction with RNAz, along with other
prediction tools |
Frank Jühling |
Bioinformatics Group, Department of Computer Science, and
Interdisciplinary Center for Bioinformatics, University of
Leipzig, Härtelstraße 16-18, D-04107 Leipzig,
Germany |
|
|
Hakim Tafer |
Department of Theoretical Chemistry University of Vienna,
Währingerstraße 17, A-1090 Wien, Austria |
|
|
Dominic Rose |
|
|
|
Manja Marz |
Institut für Pharmazeutische Chemie, Bau C, Marbacher
Weg 6, D-35032 Marburg, Germany |
|
|
Jana Hertel |
|
|
|
Sebastian Bartschat |
|
|
|
Stephanie Kehr |
|
|
|
Wolfgang Otto |
|
|
|
Alexander Donath |
|
|
|
Andrea Tanzer |
Department of Theoretical Chemistry University of Vienna,
Währingerstraße 17, A-1090 Wien, Austria |
|
|
Clara Bermudez-Santana |
Department of Biology, Universidad Nacional de Colombia,
Carrera 45 No 26-85, Edificio Uriel Guitierrez,
Bogotá, DC. Colombia |
|
|
Andreas R. Gruber |
Department of Theoretical Chemistry University of Vienna,
Währingerstraße 17, A-1090 Wien, Austria |
|
|
Jan Engelhardt |
|
|
|
Anke Busch |
|
|
|
Michael Hiller |
Department of Developmental Biology, Stanford University,
Stanford, CA 94305, USA |
|
|
Peter F. Stadler |
Bioinformatics Group, Department of Computer Science, and
Interdisciplinary Center for Bioinformatics, University of
Leipzig, Härtelstraße 16-18, D-04107 Leipzig,
Germany |
|
|
|
Max Planck Institute for Mathematics in the Sciences,
Inselstraße 22, D-04103 Leipzig, Germany |
|
|
|
Fraunhofer Institut für Zelltherapie und Immunologie,
IZI, Perlickstraße 1, D-04103 Leipzig, Germany |
|
|
|
Department of Theoretical Chemistry University of Vienna,
Währingerstraße 17, A-1090 Wien, Austria |
|
|
|
Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM
87501, USA |
|
de novo discovery of snoRNAs |
Paul Po-Shen Wang |
Department of Ecology and Evolution and Institute for
Genomics and Systems Biology, University of Chicago,
Chicago, Illinois 60637, USA |
|
|
Ilya Ruvinsky |
|
|
|
|
|
| Multigenome alignment and conserved ncDNA |
FSA whole-genome alignment |
Robert K. Bradley |
Departments of Mathematics and of Molecular & Cellular
Biology, University of California Berkeley, Berkeley, CA
94720, USA |
|
|
Lior Pachter |
|
|
|
Colin N. Dewey |
Departments of Computer Sciences and of Biostatistics and
Medical Informatics, University of Wisconsin, Madison, WI
53706, USA
|
|
PECAN genomic alignments/synteny |
Michael Paulini |
Sanger Institute, Wellcome Trust Genome Campus Hinxton,
Cambridgeshire CB10 1SA, UK |
|
Multiz whole-genome alignment |
Hiram Clawson |
Center for Biomolecular Science and Engineering, School of
Engineering, University of California Santa Cruz (UCSC),
Santa Cruz, CA 95064, USA |
|
Conserved ncDNA blocks in the nematode phylum |
Sujai Kumar |
Institute of Evolutionary Biology, School of Biological
Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK |
|
|
Mark Blaxter |
|
|
Sanger PECAN/GERP whole-genome analysis |
Michael Paulini |
Sanger Institute, Wellcome Trust Genome Campus Hinxton,
Cambridgeshire CB10 1SA, UK |
|
|
|
|
| Transcriptomics |
RNAseq data and analyses for C. briggsae |
LaDeana W. Hillier |
Department of Genome Sciences, University of Washington,
1705 NE Pacific Street, Seattle, WA 98195, USA |
|
|
Robert H. Waterston |
Department of Genome Sciences, University of Washington,
Seattle, Washington, USA |
|
|
|
|
| Gene organization and synteny |
Operons and conserved gene ordering |
Wenfeng Qian |
|
|
|
Jianzhi Zhang |
Department of Ecology and Evolutionary Biology, University
of Michigan, Ann Arbor, Michigan 48109, USA |
|
OrthoCluster |
Nansheng [Jack] Chen |
|
|
CYNTENATOR |
Christoph Dieterich |
Max Delbrück Center for
Molecular Medicine, Berlin-Buch, Robert-Rössle-Str. 10,
Berlin 13092, Germany |
|
|
|
|
| Cis-regulatory motifs |
Core promoter motif predictions |
Uladzislau 'Vlad' Hryshkevich |
Department of Biology,
Technion–Israel Institute of Technology, Haifa 30900, Israel |
|
|
Itai Yanai |
|
|
Motif-aware FSA |
Rahul Satija |
Department of Statistics, University of Oxford, 1 South
Parks Road, OX1 3TG Oxford, UK |
|
|
Lior Pachter |
Departments of Mathematics and of Molecular & Cellular
Biology, University of California Berkeley, Berkeley, CA
94720, USA |
|
|
|
|
| Protein-coding gene evolution and orthology |
Evolution of introns, codon divergence, and codon bias |
Asher D. Cutter |
Department of Ecology and Evolutionary Biology and the
Centre for the Analysis of Genome Evolution and Function,
University of Toronto, Toronto, Ontario M5S 3B2, Canada |
|
Large-scale ortholog evolutionary trees |
Asher D. Cutter |
Department of Ecology and Evolutionary Biology and the
Centre for the Analysis of Genome Evolution and Function,
University of Toronto, Toronto, Ontario M5S 3B2, Canada |
|
|
David H.A. Fitch |
Department of Biology, New York University, New York, NY
10003, USA |
|
|
Karin C. Kiontke |
|
|
CD-HIT/OrthoMCL |
Erich M. Schwarz |
Division of Biology, 156-29, California Institute of
Technology, Pasadena, CA 91125, USA |
|
Modified OrthoMCL orthologies for protein-coding genes |
Ana P.C. Rodrigues |
|
|
|
Gerard Manning |
Razavi Newman Center for Bioinformatics, Salk Institute
for Biological Studies, 10010 North Torrey Pines Road, La
Jolla, CA 92037, USA |
|
Compara |
Michael Paulini |
Sanger Institute, Wellcome Trust Genome Campus Hinxton,
Cambridgeshire CB10 1SA, UK |
|
TreeFam orthologies, and vs. OrthoMCL orthologies |
Avril Coghlan |
|
|
Scans for accelerated evolution and expansions of protein
domains |
Alexander Kanapin |
Wellcome Trust Centre for Human
Genetics, University of Oxford, Roosevelt Drive, Oxford OX3
7BN, UK
|
|
|
Lincoln D. Stein |
Ontario Institute for Cancer Research, 101 College Street,
Suite 800, Toronto, Ontario M5G 0A3, Canada |
|
Lineage-specific domains and domain architectures |
James Wasmuth |
|
|
|
John Parkinson |
Program in Molecular Structure and Function, Hospital for
Sick Children, Toronto, Ontario M5G 2L3, Canada |
|
|
|
|
| Comparisons with parasitic nematodes |
Genomic comparisons with Trichinella |
Zhengyuan Wang |
Genome Sequencing Center, Department of Genetics,
Washington University School of Medicine, St. Louis, MO
63110, USA |
|
|
Sahar Abubucker |
|
|
|
Makedonka Mitreva |
|
|
Analysis of parasite-specific gene families via NEMBASE4 |
Mark Blaxter |
Institute of Evolutionary Biology, School of Biological
Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK |
|
Nematode-specific genes, parasitism-related genes,
pathogenicity islands, etc. |
Mark Blaxter |
Institute of Evolutionary Biology, School of Biological
Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK |
|
Orthology groups conserved in free-living nematodes but
lost in parasites |
Erich M. Schwarz |
Division of Biology, 156-29, California Institute of
Technology, Pasadena, CA 91125, USA |
|
|
|
|
| Sex-determination and hermaphroditism |
Genome size and hermaphrodite-specific gene losses |
Erich M. Schwarz |
Division of Biology, 156-29, California Institute of
Technology, Pasadena, CA 91125, USA |
|
Specific evolution of sex-determination genes |
Eric S. Haag |
Department of Biology, University of Maryland, College
Park, MD 20742, USA |
|
|
Ronald E. Ellis |
Department of Molecular Biology, School of Osteopathic
Medicine, University of Medicine and Dentistry of New
Jersey, Stratford, NJ 08084, USA |
|
|
|
|
| Other analyses |
Stress-induced duplex destabilization (SIDD) of genomic
DNA |
Ian Korf |
UC Davis Genome Center, University of California Davis,
Davis, CA, USA |
|
|
Craig J. Benham |
|