Li Ding, Ph.D.,  The Genome Institute

Dr. Li Ding joined The Genome Institute at Washington University in 2002. Dr. Ding has extensive experience in cancer genetics/genomics. She successfully led and completed the integrated analysis of a multi-institute study on the genomics of lung adenocarcinomas and identified key genes and pathways leading to lung cancer. In addition, Dr. Ding worked with Drs. Ley, Wilson, and Mardis to analyze the tumor and skin genomes of a patient with acute myeloid leukemia (AML), the first cancer genome that has ever been fully sequenced and analyzed. Further, Dr. Ding led the analysis of several cancer metastasis/relapse studies including the genome remodeling of a basal-like breast cancer and the clonal evolution of relapsed AML. Dr. Ding’s research focuses on identifying and characterizing somatic/germline genetic changes relevant to cancer initiation and progression as well as drug response by integrating various data types including DNA, RNA, and proteomics data. Dr. Ding is also interested in developing algorithms to facilitate the translation of genomic findings to clinical practice.

Dr. Ding leads the Medical Genomics group, consisting of biologists, bioinformaticians, mathematicians, and statisticians. Dr. Ding’s team has developed a suite of variant detection and interpretation tools including VarScan, SomaticSniper, CMDS, BreakDancer, BreakFusion, PathScan, and MuSiC; many of them are widely used by the research community and have been applied in several large-scale projects such as The Cancer Genome Atlas (TCGA) project and the Pediatric Cancer Genome Project (PCGP).

Dr. Ding received a B.S. degree from Fudan University, a Ph.D. from the University of Utah under Dr. Stephen Prescott's guidance, and did her postdoctoral research in the Biochemistry Department at Stanford University. Prior to her move to St. Louis, Dr. Ding was at Incyte Genomics, where she used in silico approaches to discover novel drugable genes and identify gene expression changes during development and disease progression.

Selected Publications

Ding L, Wendl MC, McMichael JF, Raphael BJ. Expanding the computational toolbox for mining cancer genomes. Nat Rev Genet. 2014 July. PMID: 25001846.

Kanchi K, Johnson K, Lu C, McLellan MD, Leiserson MD, Wendl MC, Zhang Q6, Koboldt DC, Xie M, Kandoth C, McMichael JF, Wyczalkowski MA, Larson DE, Schmidt HK, Miller CA, Fulton RS, Spellman PT, Mardis ER, Druley TE, Graubert TA, Goodfellow PJ, Raphael BJ, Wilson RK, Ding L. Integrated analysis of germline and somatic variants in ovarian cancer. Nature Communications. 2014 Jan 22;5, Article number: 3156 doi:10.1038/ncomms4156 PMID: 24448499.

Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, Xie M, Zhang Q, McMichael JF, Wyczalkowski MA, Leiserson MD, Miller CA, Welch JS, Walter MJ, Wendl MC, Ley TJ, Wilson RK, Raphael BJ, Ding L. Mutational landscape and significance across 12 major cancer types. Nature. 2013 Oct 17;502(7471):333-9. doi: 10.1038/nature12634. PMID: 24132290.

Dees ND, Zhang Q, Kandoth C, Wendl MC, Schierding W, Koboldt DC, Mooney TB, Callaway MB, Dooling D, Mardis ER, Wilson RK, Ding L. MuSiC: Identifying mutational significance in cancer genomes. Genome Res. 2012 Aug;22(8):1589-98. PMID: 22759861.

Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012 Mar;22(3):568-76. PMID: 22300766.

Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DC, Welch JS, Ritchey JK, Young MA, Lamprecht T, McLellan MD, McMichael JF, Wallis JW, Lu C, Shen D, Harris CC, Dooling DJ, Fulton RS, Fulton LL, Chen K, Schmidt H, Kalicki-Veizer J, Magrini VJ, Cook L, McGrath SD, Vickery TL, Wendl MC, Heath S, Watson MA, Link DC, Tomasson MH, Shannon WD, Payton JE, Kulkarni S, Westervelt P, Walter MJ, Graubert TA, Mardis ER, Wilson RK, DiPersio JF. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature. 2012 Jan 11;481(7382):506-10. PMID: 22237025.

Zhang J, Ding L, Holmfeldt L, Wu G, Heatley SL, Payne-Turner D, Easton J, Chen X, Wang J, Rusch M, Lu C, Chen SC, Wei L, Collins-Underwood JR, Ma J, Roberts KG, Pounds SB, Ulyanov A, Becksfort J, Gupta P, Huether R, Kriwacki RW, Parker M, McGoldrick DJ, Zhao D, Alford D, Espy S, Bobba KC, Song G, Pei D, Cheng C, Roberts S, Barbato MI, Campana D, Coustan-Smith E, Shurtleff SA, Raimondi SC, Kleppe M, Cools J, Shimano KA, Hermiston ML, Doulatov S, Eppert K, Laurenti E, Notta F, Dick JE, Basso G, Hunger SP, Loh ML, Devidas M, Wood B, Winter S, Dunsmore KP, Fulton RS, Fulton LL, Hong X, Harris CC, Dooling DJ, Ochoa K, Johnson KJ, Obenauer JC, Evans WE, Pui CH, Naeve CW, Ley TJ, Mardis ER, Wilson RK, Downing JR, Mullighan CG. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature. 2012 Jan 11;481(7380):157-63. PMID: 22237106.

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. PMID: 21498403.

Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, Larson DE, Kandoth C, Payton JE, Baty J, Welch J, Harris CC, Lichti CF, Townsend RR, Fulton RS, Dooling DJ, Koboldt DC, Schmidt H, Zhang Q, Osborne JR, Lin L, O'Laughlin M, McMichael JF, Delehaunty KD, McGrath SD, Fulton LA, Magrini VJ, Vickery TL, Hundal J, Cook LL, Conyers JJ, Swift GW, Reed JP, Alldredge PA, Wylie T, Walker J, Kalicki J, Watson MA, Heath S, Shannon WD, Varghese N, Nagarajan R, Westervelt P, Tomasson MH, Link DC, Graubert TA, DiPersio JF, Mardis ER, Wilson RK. DNMT3A mutations in acute myeloid leukemia. N Engl J Med. 2010 Dec 16;363(25):2424-33. PMID: 21067377.

Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, Harris CC, McLellan MD, Fulton RS, Fulton LL, Abbott RM, Hoog J, Dooling DJ, Koboldt DC, Schmidt H, Kalicki J, Zhang Q, Chen L, Lin L, Wendl MC, McMichael JF, Magrini VJ, Cook L, McGrath SD, Vickery TL, Appelbaum E, Deschryver K, Davies S, Guintoli T, Lin L, Crowder R, Tao Y, Snider JE, Smith SM, Dukes AF, Sanderson GE, Pohl CS, Delehaunty KD, Fronick CC, Pape KA, Reed JS, Robinson JS, Hodges JS, Schierding W, Dees ND, Shen D, Locke DP, Wiechert ME, Eldred JM, Peck JB, Oberkfell BJ, Lolofie JT, Du F, Hawkins AE, O'Laughlin MD, Bernard KE, Cunningham M, Elliott G, Mason MD, Thompson DM Jr, Ivanovich JL, Goodfellow PJ, Perou CM, Weinstock GM, Aft R, Watson M, Ley TJ, Wilson RK, Mardis ER. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 2010 Apr 15:464(7291):999-1005. PMID: 20393555

Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, Koboldt DC, Fulton RS, Delehaunty KD, McGrath SD, Fulton LA, Locke DP, Magrini VJ, Abbott RM, Vickery TL, Reed JS, Robinson JS, Wylie T, Smith SM, Carmichael L, Eldred JM, Harris CC, Walker J, Peck JB, Du F, Dukes AF, Sanderson GE, Brummett AM, Clark E, McMichael JF, Meyer RJ, Schindler JK, Pohl CS, Wallis JW, Shi X, Lin L, Schmidt H, Tang Y, Haipek C, Wiechert ME, Ivy JV, Kalicki J, Elliott G, Ries RE, Payton JE, Westervelt P, Tomasson MH, Watson MA, Baty J, Heath S, Shannon WD, Nagarajan R, Link DC, Walter MJ, Graubert TA, DiPersio JF, Wilson RK, Ley TJ. Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med 2009 Sep 10:361(11):1058-66. PMID: 19657110.

Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X, Fulton RS, Ley TJ, Wilson RK, Ding L, Mardis ER. BreakDancer: An algorithm for high-resolution mapping of genomic structural variation. Nat Methods 2009 Sep:6(9):677-81. PMID: 19668202

Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L. VarScan: Variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 2009 Sep 1:25(17):2283-5. PMID: 19542151.

Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, Dooling D, Dunford-Shore BH, McGrath S, Hickenbotham M, Cook L, Abbott R, Larson DE, Koboldt DC, Pohl C, Smith S, Hawkins A, Abbott S, Locke D, Hillier LW, Miner T, Fulton L, Magrini V, Wylie T, Glasscock J, Conyers J, Sander N, Shi X, Osborne JR, Minx P, Gordon D, Chinwalla A, Zhao Y, Ries RE, Payton JE, Westervelt P, Tomasson MH, Watson M, Baty J, Ivanovich J, Heath S, Shannon WD, Nagarajan R, Walter MJ, Link DC, Graubert TA, DiPersio JF, Wilson RK. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 2008 Nov 6:456(7218):66-72. PMID: 18987736

Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008 Oct 23:455(7216):1061-8. PMID: 18772890.

Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, Fulton L, Fulton RS, Zhang Q, Wendl MC, Lawrence MS, Larson DE, Chen K, Dooling DJ, Sabo A, Hawes AC, Shen H, Jhangiani SN, Lewis LR, Hall O, Zhu Y, Mathew T, Ren Y, Yao J, Scherer SE, Clerc K, Metcalf GA, Ng B, Milosavljevic A, Gonzalez-Garay ML, Osborne JR, Meyer R, Shi X, Tang Y, Koboldt DC, Lin L, Abbott R, Miner TL, Pohl C, Fewell G, Haipek C, Schmidt H, Dunford-Shore BH, Kraja A, Crosby SD, Sawyer CS, Vickery T, Sander S, Robinson J, Winckler W, Baldwin J, Chirieac LR, Dutt A, Fennell T, Hanna M, Johnson BE, Onofrio RC, Thomas RK, Tonon G, Weir BA, Zhao X, Ziaugra L, Zody MC, Giordano T, Orringer MB, Roth JA, Spitz MR, Wistuba II, Ozenberger B, Good PJ, Chang AC, Beer DG, Watson MA, Ladanyi M, Broderick S, Yoshizawa A, Travis WD, Pao W, Province MA, Weinstock GM, Varmus HE, Gabriel SB, Lander ES, Gibbs RA, Meyerson M, Wilson RK. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 2008 Oct 23:455(7216):1069-75. PMID: 18948947

Ding L, Sabo A, Berkowicz N, Meyer RR, Shotland Y, Johnson MR, Pepin KH, Wilson RK, Spieth J. EAnnot: A genome annotation tool using experimental evidence. Genome Res 2004 Dec:14(12):2503-9. PMID: 15574829.

Publications

title citation publication date
C11orf95-rela fusions drive oncogenic NF-kb signaling in ependymoma. Neuro Oncol. 2014 Jul;16 Suppl 3:iii16. doi: 10.1093/neuonc/nou206.57. 2014-07-01
Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin Cell. 2014 Aug 14;158(4):929-44. doi: 10.1016/j.cell.2014.06.049. Epub 2014 Aug 7. 2014-08-14
SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution. PLoS Comput Biol. 2014 Aug 7;10(8):e1003665. doi: 10.1371/journal.pcbi.1003665. eCollection 2014. 2014-08-07
Proteogenomic characterization of human colon and rectal cancer. Nature. 2014 Jul 20. doi: 10.1038/nature13438. [Epub ahead of print] 2014-07-20
Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014 Jul 23. doi: 10.1038/nature13480. [Epub ahead of print] 2014-07-23
Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014 Jul 31;511(7511):543-50. doi: 10.1038/nature13385. Epub 2014 Jul 9. 2014-07-09
Expanding the computational toolbox for mining cancer genomes. Nat Rev Genet. 2014 Aug;15(8):556-70. doi: 10.1038/nrg3767. Epub 2014 Jul 8. 2014-08-01
Clonal architecture of secondary acute myeloid leukemia defined by single-cell sequencing. PLoS Genet. 2014 Jul 10;10(7):e1004462. doi: 10.1371/journal.pgen.1004462. eCollection 2014. 2014-07-10
The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes. Nat Commun. 2014 Apr 8;5:3630. doi: 10.1038/ncomms4630. 2014-04-08
Recurrent somatic structural variations contribute to tumorigenesis in pediatric osteosarcoma. Cell Rep. 2014 Apr 10;7(1):104-12. doi: 10.1016/j.celrep.2014.03.003. Epub 2014 Apr 3. 2014-04-10
The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma. Nat Genet. 2014 May;46(5):444-50. doi: 10.1038/ng.2938. Epub 2014 Apr 6. 2014-05-01
C11orf95-RELA fusions drive oncogenic NF-kappaB signalling in ependymoma. Nature. 2014 Feb 27;506(7489):451-5. doi: 10.1038/nature13109. Epub 2014 Feb 19. 2014-02-27
Integrated analysis of germline and somatic variants in ovarian cancer. Nat Commun. 2014 Jan 22;5:3156. doi: 10.1038/ncomms4156. 2014-01-22
MSIsensor: microsatellite instability detection using paired tumor-normal sequence data. Bioinformatics. 2013 Dec 25. [Epub ahead of print] 2013-12-24
Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif. Nat Commun. 2013;4:2730. doi: 10.1038/ncomms3730. 2013-11-13
Targeting oxidative stress in embryonal rhabdomyosarcoma. Cancer Cell. 2013 Dec 9;24(6):710-24. doi: 10.1016/j.ccr.2013.11.002. 2013-12-09
Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci Rep. 2013 Oct 2;3:2650. doi: 10.1038/srep02650. 2013-10-03
TIGRA: A Targeted Iterative Graph Routing Assembler for breakpoint assembly. Genome Res. 2013 Dec 4. [Epub ahead of print] 2013-12-04
High Frequency Strand Slippage Mutations in CTCF in MSI-Positive Endometrial Cancers. Hum Mutat. 2013 Oct 15. doi: 10.1002/humu.22463. [Epub ahead of print] 2013-10-15
Mutational landscape and significance across 12 major cancer types. Nature. 2013 Oct 17;502(7471):333-9. doi: 10.1038/nature12634. 2013-10-17
The Somatic Genomic Landscape of Glioblastoma. Cell. 2013 Oct 10;155(2):462-477. doi: 10.1016/j.cell.2013.09.034. 2013-10-10
Differences that matter in cancer genomics. Nat Biotechnol. 2013 Oct 8;31(10):892-893. doi: 10.1038/nbt.2715. 2013-10-08
DGIdb: mining the druggable genome. Nat Methods. 2013 Oct 13. doi: 10.1038/nmeth.2689. [Epub ahead of print] 2013-10-13
The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Sep 26;45(10):1113-20. doi: 10.1038/ng.2764. 2013-09-26
Endocrine-Therapy-Resistant ESR1 Variants Revealed by Genomic Characterization of Breast-Cancer-Derived Xenografts. Cell Rep. 2013 Sep 18. pii: S2211-1247(13)00463-4. doi: 10.1016/j.celrep.2013.08.022. [Epub ahead of print] 2013-09-18
BreakTrans: uncovering the genomic architecture of gene fusions. Genome Biol. 2013 Aug 23;14(8):R87. [Epub ahead of print] 2013-08-23
Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods. 2013 Jul 30;10(8):723-9. doi: 10.1038/nmeth.2562. 2013-07-30
Activation of NFAT signaling establishes a tumorigenic microenvironment through cell autonomous and non-cell autonomous mechanisms. Oncogene. 2013 Apr 29. doi: 10.1038/onc.2013.132. [Epub ahead of print] 2013-04-29
Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia. N Engl J Med. 2013 May 1. [Epub ahead of print] 2013-05-01
Integrated genomic characterization of endometrial carcinoma. Nature. 2013 May 2;497(7447):67-73. doi: 10.1038/nature12113. 2013-05-02
Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas. Nat Genet. 2013 Apr 14. doi: 10.1038/ng.2611. [Epub ahead of print] 2013-04-14
Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. Genome Biol. 2013 Mar 13;14(3):R22. [Epub ahead of print] 2013-03-13
Advances for studying clonal evolution in cancer. Cancer Lett. 2013 Jan 23. pii: S0304-3835(13)00034-7. doi: 10.1016/j.canlet.2012.12.028. [Epub ahead of print] 2013-01-23
Clonal diversity of recurrently mutated genes in myelodysplastic syndromes. Leukemia. 2013 Feb 27. doi: 10.1038/leu.2013.58. [Epub ahead of print] 2013-02-27
The genomic landscape of hypodiploid acute lymphoblastic leukemia. Nat Genet. 2013 Jan 20. doi: 10.1038/ng.2532. [Epub ahead of print] 2013-01-20
Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma. Genome Res. 2012 Dec 5. [Epub ahead of print] 2012-12-05
Activating HER2 Mutations in HER2 Gene Amplification Negative Breast Cancer. Cancer Discov. 2012 Dec 7. [Epub ahead of print] 2012-12-07
Somatic Mutations of PIK3R1 Promote Gliomagenesis PLoS One. 2012;7(11):e49466. doi: 10.1371/journal.pone.0049466. Epub 2012 Nov 14. 2012-11-14
An Inv(16)(p13.3q24.3)-Encoded CBFA2T3-GLIS2 Fusion Protein Defines an Aggressive Subtype of Pediatric Acute Megakaryoblastic Leukemia. Cancer Cell. 2012 Nov 13;22(5):683-97. doi: 10.1016/j.ccr.2012.10.007. 2012-11-13
An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov 1;491(7422):56-65. doi: 10.1038/nature11632. 2012-11-01
Comprehensive molecular portraits of human breast tumours. Nature. 2012 Sep 23. doi: 10.1038/nature11412. [Epub ahead of print] 2012-09-23
Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers Cell. 2012 Sep 14;150(6):1121-34. doi: 10.1016/j.cell.2012.08.024. 2012-09-14
Comprehensive genomic characterization of squamous cell lung cancers Nature. 2012 Sep 9. doi: 10.1038/nature11404. [Epub ahead of print] 2012-09-09
Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature. 2012 Jun 10;486(7403):353-60. doi: 10.1038/nature11143. 2012-06-10
The origin and evolution of mutations in acute myeloid leukemia. Cell. 2012 Jul 20;150(2):264-78. 2012-07-20
The 1000 Genomes Project: data management and community access. Nat Methods. 2012 Apr 27;9(5):459-62. doi: 10.1038/nmeth.1974. 2012-04-27
Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 Jul 18;487(7407):330-7. doi: 10.1038/nature11252. 2012-07-18
MuSiC: Identifying mutational significance in cancer genomes. Genome Res. 2012 Jul 3. [Epub ahead of print] 2012-07-03
Landscape of Somatic Retrotransposition in Human Cancers. Science. 2012 Jun 28. [Epub ahead of print] 2012-06-28
Novel mutations target distinct subgroups of medulloblastoma. Nature. 2012 Jun 20. doi: 10.1038/nature11213. [Epub ahead of print] 2012-06-20
The pediatric cancer genome project. Nat Genet. 2012 May 29;44(6):619-22. doi: 10.1038/ng.2287. 2012-05-29
BreakFusion: Targeted Assembly-based Identification of Gene Fusions in Whole Transcriptome Paired-end Sequencing Data. Bioinformatics. 2012 May 4. [Epub ahead of print] 2012-05-04
Background Mutations in Parental Cells Account for Most of the Genetic Heterogeneity of Induced Pluripotent Stem Cells. Cell Stem Cell. 2012 Apr 26. [Epub ahead of print] 2012-04-26
Clonal Architecture of Secondary Acute Myeloid Leukemia. N Engl J Med. 2012 Mar 22;366(12):1090-8. doi: 10.1056/NEJMoa1106968. Epub 2012 Mar 14. 2012-03-14
Association of age at diagnosis and genetic mutations in patients with neuroblastoma. JAMA. 2012 Mar 14;307(10):1062-71. 2012-03-14
Co-survival of the fittest few: mosaic amplification of receptor tyrosine kinases in glioblastoma. Genome Biol. 2012 Jan 30;13(1):141. [Epub ahead of print] 2012-01-30
VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012 Feb 2. [Epub ahead of print] 2012-02-12
Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas. Nat Genet. 2012 Jan 29 [Epub ahead of print] 2012-01-29
Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature. 2012 Jan 11. doi: 10.1038/nature10738. [Epub ahead of print] 2012-01-11
The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature. 2012 Jan 11;481(7380):157-63. doi: 10.1038/nature10725. 2012-01-11
A novel retinoblastoma therapy from genomic and epigenetic analyses. Nature. 2012 Jan 11. doi: 10.1038/nature10733. [Epub ahead of print] 2012-01-11
Massively parallel sequencing approaches for characterization of structural variation. Methods Mol Biol. 2012;838:369-84. 2012-01-06
SomaticSniper: Identification of Somatic Point Mutations in Whole Genome Sequencing Data. Bioinformatics. 2011 Dec 6. [Epub ahead of print] 2011-12-06
Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes. Nat Genet. 2011 Dec 11. doi: 10.1038/ng.1031. [Epub ahead of print] 2011-12-11
The variant call format and VCFtools. Bioinformatics. 2011 Aug 1;27(15):2156-8. Epub 2011 Jun 7. 2011-08-01
The functional spectrum of low-frequency coding variation. Genome Biol. 2011 Sep 14;12(9):R84. [Epub ahead of print] 2011-09-14
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. 2011-06-12
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. 2011-07-19
Integrated genomic analyses of ovarian carcinoma Nature. 2011 Jun 29;474(7353):609-15. doi: 10.1038/nature10166. 2011-06-29
CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat Methods. 2011 Jun 12. doi: 10.1038/nmeth.1628. [Epub ahead of print] 2011-06-12
A dominant mutation in RPE65 identified by whole-exome sequencing causes retinitis pigmentosa with choroidal involvement. Eur J Hum Genet. 2011 Jun 8. doi: 10.1038/ejhg.2011.86. [Epub ahead of print] 2011-06-08
Identification of a Novel TP53 Cancer Susceptibility Mutation Through Whole-Genome Sequencing of a Patient With Therapy-Related AML JAMA. 2011 Apr 20;305(15):1568-1576. 2011-04-20
Use of Whole-Genome Sequencing to Diagnose a Cryptic Fusion Oncogene JAMA. 2011 Apr 20;305(15):1577-84. 2011-04-20
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. 2011-04-14
Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression. J Clin Invest. 2011 Mar 23. pii: 45284. doi: 10.1172/JCI45284. [Epub ahead of print] 2011-03-23
Recurrent DNMT3A mutations in patients with myelodysplastic syndromes. Leukemia. 2011 Jul;25(7):1153-8. doi: 10.1038/leu.2011.44. Epub 2011 Mar 18. 2011-03-18
Mapping copy number variation by population-scale genome sequencing. Nature. 2011 Feb 3;470(7332):59-65. 2011-02-03
Identification of Disease-Causing Mutations in Autosomal Dominant Retinitis Pigmentosa (adRP) Using Next-Generation DNA Sequencing. Invest Ophthalmol Vis Sci. 2010 Sep 22. [Epub ahead of print] 2010-09-22
Complete characterization of the microRNAome in a patient with acute myeloid leukemia. Blood. 2010 Dec 9;116(24):5316-26. Epub 2010 Sep 28. 2010-12-09
Diversity of human copy number variation and multicopy genes. Science. 2010 Oct 29;330(6004):641-6. 2010-10-29
Analysis of next-generation genomic data in cancer: accomplishments and challenges. Hum Mol Genet. 2010 Oct 15;19(R2):R188-96. Epub 2010 Sep 15. 2010-10-15
Challenges of sequencing human genomes. Brief Bioinform. 2010 Sep;11(5):484-98. Epub 2010 Jun 2. 2010-09-11
DNMT3A Mutations in Acute Myeloid Leukemia N Engl J Med. 2010 Nov 10. 2010-11-10
A map of human genome variation from population-scale sequencing Nature. 2010 Oct 28;467(7319):1050-1. 2010-10-28
Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell. 2010 May 18;17(5):510-22. Epub 2010 Apr 15. 2010-05-18
Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature. 2010 Apr 15;464(7291):989-90. 2010-04-15
Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell, Volume 17, Issue 1, 98-110, 19 January 2010. 2010-01-19
CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data. Bioinformatics. 2009 Dec 23. [Epub ahead of print] 2009-12-23
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 2009 Sep;6(9):677-81. Epub 2009 Aug 9. 2009-09-06
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. 2009-09-10
VarScan: Variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. 2009 Sep 1;25(17):2283-5. Epub 2009 Jun 19. 2009-06-19
The chromosome 3p21.3-encoded gene, LIMD1, is a critical tumor suppressor involved in human lung cancer development. Proc Natl Acad Sci U S A. 2008 Dec 16;105(50):19932-7. Epub 2008 Dec 5. 2008-12-16
DNA sequencing of a cytogenetically normal acute myeloid leukaemia (AML) genome. Nature. 2008 Nov 6;456(7218):66-72. 2008-11-06
Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 2008 Oct 23;455(7216):1069-75. 2008-10-23
Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008 Oct 23;455(7216):1061-8. Epub 2008 Sep 4. 2008-10-23
Novel MEK1 mutation identified by mutational analysis of epidermal growth factor receptor signaling pathway genes in lung adenocarcinoma. Cancer Res. 2008 Jul 15;68(14):5524-8. 2008-07-14
Characterizing the cancer genome in lung adenocarcinoma. Nature. 2007 Nov 4; [Epub ahead of print] 2007-11-04
PolyScan: An automatic indel and SNP detection approach to the analysis of human resequencing data. Genome Res. 2007 Apr 6; 2007-04-06
Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature. 2005 Apr 7;434(7034):724-31. 2005-04-07
EAnnot: a genome annotation tool using experimental evidence. Genome Res. 2004 Dec;14(12):2503-9. 2004-12-14
Finishing the euchromatic sequence of the human genome Nature. 2004 Oct 21;431(7011):931-45. 2004-10-21