John Wallis, Ph.D.
Research Accomplishments & Interests
John W. Wallis, Ph.D. joined The Genome Institute in 1999 as a member of the mapping group, where his responsibilities included the development of bioinformatic tools to aid in the construction of whole-genome fingerprint maps. He also developed software to integrate data from fingerprint, genetic, and physical maps to improve the sequence assemblies of human, mouse, rat, chicken, chimpanzee, platypus and macaque. Dr. Wallis recently joined the Medical Genomics group where he has written applications for genome annotation and the analysis of structural variation. He looks forward to combining his interests in computer science and molecular biology in future work for the 1000 Genomes Project, the Tumor Sequencing Project, The Cancer Genome Atlas, and other medical sequencing projects.
Other Biographical Information
Dr. Wallis received a B.A. degree from the University of California, Berkeley (1975, Biochemistry and Botany) and a Ph.D. degree from the University of California, Los Angeles (1983, Molecular Biology). He did postdoctoral research in the Department of Human Genetics, Columbia University College of Physicians and Surgeons (1984-1987). Dr. Wallis was a faculty member in the Department of Biochemisty at St. Louis University Medical School (1987-1996) where his lab focused on the genetic control of recombination in yeast. Dr. Wallis received a M.S. degree in Computer Science from Washington University in 1998.
Selected Publications
Chen K, Wallis JW, Kandoth C, Kalicki-Veizer JM, Mungall KL, Mungall AJ, Jones SJ, Marra…
BreakFusion: Targeted Assembly-based Identification of Gene Fusions in Whole Transcriptome Paired-end Sequencing Data.
Bioinformatics. 2012 May 4. [Epub ahead of print] PubMed | View Abstract
Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DC, Welch JS, Ritchey JK, Young…
Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing.
Nature. 2012 Jan 11. doi: 10.1038/nature10738. [Epub ahead of print] PubMed | View Abstract
Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge…
The functional spectrum of low-frequency coding variation.
Genome Biol. 2011 Sep 14;12(9):R84. [Epub ahead of print] PubMed | View Abstract
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter…
The variant call format and VCFtools.
Bioinformatics. 2011 Aug 1;27(15):2156-8. Epub 2011 Jun 7. PubMed | View Abstract
Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs…
Demographic history and rare allele sharing among human populations.
Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):11983-11988. Epub 2011 Jul 5. PubMed | View Abstract
The Cancer Genome Atlas Research Network
Integrated genomic analyses of ovarian carcinoma
Nature. 2011 Jun 29;474(7353):609-15. doi: 10.1038/nature10166. PubMed | View Abstract
The 1000 Genomes Project, Conrad DF, Keebler JE, Depristo MA, Lindsay SJ, Zhang Y, Casals…
Variation in genome-wide mutation rates within and between human families.
Nat Genet. 2011 Jun 12;43(7):712-714. doi: 10.1038/ng.862. PubMed | View Abstract
Welch JS, Westervelt P, Ding L, Larson DE, Klco JM, Kulkarni S, Wallis J, Chen…
Use of Whole-Genome Sequencing to Diagnose a Cryptic Fusion Oncogene
JAMA. 2011 Apr 20;305(15):1577-84. PubMed | View Abstract
Wendl MC, Wallis JW, Lin L, Kandoth C, Mardis ER, Wilson RK, Ding L.
PathScan: A Tool for Discerning Mutational Significance in Groups of Putative Cancer Genes.
Bioinformatics. 2011 Jun 15;27(12):1595-602. Epub 2011 Apr 14. PubMed | View Abstract
The 1000 Genomes Project Consortium
A map of human genome variation from population-scale sequencing
Nature. 2010 Oct 28;467(7319):1050-1. PubMed | View Abstract
Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, Harris CC, McLellan…
Genome remodelling in a basal-like breast cancer metastasis and xenograft.
Nature. 2010 Apr 15;464(7291):989-90. PubMed | View Abstract
Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, Koboldt DC, Fulton…
Recurring mutations found by sequencing an acute myeloid leukemia genome.
N Engl J Med. 2009 Sep 10;361(11):1058-66. Epub 2009 Aug 5. PubMed | View Abstract
Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl…
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.
Nat Methods. 2009 Sep;6(9):677-81. Epub 2009 Aug 9. PubMed | View Abstract
Cancer Genome Atlas Research Network.
Comprehensive genomic characterization defines human glioblastoma genes and core pathways.
Nature. 2008 Oct 23;455(7216):1061-8. Epub 2008 Sep 4. PubMed | View Abstract
Zody MC, Jiang Z, Fung HC, Antonacci F, Hillier LW, Cardone MF, Graves TA, Kidd…
Evolutionary toggling of the MAPT 17q21.31 inversion region.
Nat Genet. 2008 Aug 10. [Epub ahead of print] PubMed | View Abstract
