Faculty

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Darryl Shibata, MD
Professor of Pathology
Pathology
NOR 2424 Health Sciences Campus Los Angeles
+1 323 865 3298

Overview

After attending UCLA for his undergraduate degree, Dr. Shibata obtained his medical degree from the Keck School of Medicine of USC. After completing his internship training in pediatrics from UC San Diego, Dr. Shibata returned to USC for his residency and fellowship at LAC+USC Medical Center. Currently, Dr. Shibata has clinical appointments at both LAC+USC Medical Center and USC/Norris Comprehensive Cancer Center. In addition to his wide array of responsibilities in the research, education and practitioner capacities, Dr. Shibata sits on the editorial board of the BMC Cancer Journal and the American Journal of Pathology.

Publications

Raub CB, Lee CC, Shibata D, Taylor C, Kartalov E. HistoMosaic Detecting KRAS G12V Mutation Across Colorectal Cancer Tissue Slices through in Situ PCR. Anal Chem. 2016 Mar 1; 88(5):2792-8. View in: PubMed

Siegmund K, Shibata D. At least two well-spaced samples are needed to genotype a solid tumor. BMC Cancer. 2016; 16(1):250. View in: PubMed

Kang H, Salomon MP, Sottoriva A, Zhao J, Toy M, Press MF, Curtis C, Marjoram P, Siegmund K, Shibata D. Many private mutations originate from the first few divisions of a human colorectal adenoma. J Pathol. 2015 Nov; 237(3):355-62. View in: PubMed

Walther V, Hiley CT, Shibata D, Swanton C, Turner PE, Maley CC. Can oncology recapitulate paleontology? Lessons from species extinctions. Nat Rev Clin Oncol. 2015 May; 12(5):273-85. View in: PubMed

Sottoriva A, Kang H, Ma Z, Graham TA, Salomon MP, Zhao J, Marjoram P, Siegmund K, Press MF, Shibata D, Curtis C. A Big Bang model of human colorectal tumor growth. Nat Genet. 2015 Mar; 47(3):209-16. View in: PubMed

Ramaswamy K, Yik WY, Wang XM, Oliphant EN, Lu W, Shibata D, Ryder OA, Hacia JG. Derivation of induced pluripotent stem cells from orangutan skin fibroblasts. BMC Res Notes. 2015; 8(1):577. View in: PubMed

Siddiqi IN, Shibata D. Diffuse Large B-cell Lymphoma of Germinal Center and Nongerminal Center Phenotypes Presenting Concurrently at the Same Anatomic Site: Intratumoral Heterogeneity or Composite Lymphoma? Appl Immunohistochem Mol Morphol. 2015 Jan; 23(1):78-80. View in: PubMed

Wang XM, Yik WY, Zhang P, Lu W, Huang N, Kim BR, Shibata D, Zitting M, Chow RH, Moser AB, Steinberg SJ, Hacia JG. Induced pluripotent stem cell models of Zellweger spectrum disorder show impaired peroxisome assembly and cell type-specific lipid abnormalities. Stem Cell Res Ther. 2015; 6(1):158. View in: PubMed

Zhao J, Siegmund KD, Shibata D, Marjoram P. Ancestral inference in tumors: How much can we know? J Theor Biol. 2014 Oct 21; 359:136-45. View in: PubMed

Siddiqi IN, Ailawadhi S, Huang Q, Shibata RK, Kang H, Shibata D. Deep sequencing reveals lack of a clonal relationship between a metachronous classical hodgkin and diffuse large B-cell lymphoma. Clin Lymphoma Myeloma Leuk. 2014 Jun; 14(3):e87-93. View in: PubMed

Fischer JM, Schepers AG, Clevers H, Shibata D, Liskay RM. Occult progression by Apc-deficient intestinal crypts as a target for chemoprevention. Carcinogenesis. 2014 Jan; 35(1):237-46. View in: PubMed

Kreso A, O'Brien CA, van Galen P, Gan OI, Notta F, Brown AM, Ng K, Ma J, Wienholds E, Dunant C, Pollett A, Gallinger S, McPherson J, Mullighan CG, Shibata D, Dick JE. Variable clonal repopulation dynamics influence chemotherapy response in colorectal cancer. Science. 2013 Feb 1; 339(6119):543-8. View in: PubMed

Kang H, Shibata D. Direct measurements of human colon crypt stem cell niche genetic fidelity: the role of chance in non-darwinian mutation selection. Front Oncol. 2013; 3:264. View in: PubMed

Sottoriva A, Spiteri I, Shibata D, Curtis C, Tavaré S. Single-molecule genomic data delineate patient-specific tumor profiles and cancer stem cell organization. Cancer Res. 2013 Jan 1; 73(1):41-9. View in: PubMed

Tsai AG, Chen DM, Lin M, Hsieh JC, Okitsu CY, Taghva A, Shibata D, Hsieh CL. Heterogeneity and randomness of DNA methylation patterns in human embryonic stem cells. DNA Cell Biol. 2012 Jun; 31(6):893-907. View in: PubMed

Wolkenhauer O, Shibata D, Mesarovic MD. The role of theorem proving in systems biology. J Theor Biol. 2012 May 7; 300:57-61. View in: PubMed

Shibata D. Cancer. Heterogeneity and tumor history. Science. 2012 Apr 20; 336(6079):304-5. View in: PubMed

Wang XM, Yik WY, Zhang P, Lu W, Dranchak PK, Shibata D, Steinberg SJ, Hacia JG. The gene expression profiles of induced pluripotent stem cells from individuals with childhood cerebral adrenoleukodystrophy are consistent with proposed mechanisms of pathogenesis. Stem Cell Res Ther. 2012; 3(5):39. View in: PubMed

Shibata D. Molecular tumor clocks to study the evolution of drug resistance. Mol Pharm. 2011 Dec 5; 8(6):2050-4. View in: PubMed

Oghamian S, Sodir NM, Bashir MU, Shen H, Cullins AE, Carroll CA, Kundu P, Shibata D, Laird PW. Reduction of pancreatic acinar cell tumor multiplicity in Dnmt1 hypomorphic mice. Carcinogenesis. 2011 Jun; 32(6):829-35. View in: PubMed

Shibata D. Mutation and epigenetic molecular clocks in cancer. Carcinogenesis. 2011 Feb; 32(2):123-8. View in: PubMed

Siegmund KD, Marjoram P, Tavaré S, Shibata D. High DNA methylation pattern intratumoral diversity implies weak selection in many human colorectal cancers. PLoS One. 2011; 6(6):e21657. View in: PubMed

Wolkenhauer O, Shibata DK, Mesarovic MD. A stem cell niche dominance theorem. BMC Syst Biol. 2011; 5:4. View in: PubMed

Wang X, Kang GH, Campan M, Weisenberger DJ, Long TI, Cozen W, Bernstein L, Wu AH, Siegmund KD, Shibata D, Laird PW. Epigenetic subgroups of esophageal and gastric adenocarcinoma with differential GATA5 DNA methylation associated with clinical and lifestyle factors. PLoS One. 2011; 6(10):e25985. View in: PubMed

Shibata D, Lieber MR. Is there any genetic instability in human cancer? DNA Repair (Amst). 2010 Aug 5; 9(8):858; discussion 859-60. View in: PubMed

Wu AH, Siegmund KD, Long TI, Cozen W, Wan P, Tseng CC, Shibata D, Laird PW. Hormone therapy, DNA methylation and colon cancer. Carcinogenesis. 2010 Jun; 31(6):1060-7. View in: PubMed

Wang XM, Greiner TC, Bibikova M, Pike BL, Siegmund KD, Sinha UK, Müschen M, Jaeger EB, Weisenburger DD, Chan WC, Shibata D, Fan JB, Hacia JG. Identification and functional relevance of de novo DNA methylation in cancerous B-cell populations. J Cell Biochem. 2010 Mar 1; 109(4):818-27. View in: PubMed

Calabrese P, Shibata D. A simple algebraic cancer equation: calculating how cancers may arise with normal mutation rates. BMC Cancer. 2010; 10:3. View in: PubMed

Hong YJ, Marjoram P, Shibata D, Siegmund KD. Using DNA methylation patterns to infer tumor ancestry. PLoS One. 2010; 5(8):e12002. View in: PubMed

Wolkenhauer O, Auffray C, Baltrusch S, Blüthgen N, Byrne H, Cascante M, Ciliberto A, Dale T, Drasdo D, Fell D, Ferrell JE, Gallahan D, Gatenby R, Günther U, Harms BD, Herzel H, Junghanss C, Kunz M, van Leeuwen I, Lenormand P, Levi F, Linnebacher M, Lowengrub J, Maini PK, Malik A, Rateitschak K, Sansom O, Schäfer R, Schürrle K, Sers C, Schnell S, Shibata D, Tyson J, Vera J, White M, Zhivotovsky B, Jaster R. Systems biologists seek fuller integration of systems biology approaches in new cancer research programs. Cancer Res. 2010 Jan 1; 70(1):12-3. View in: PubMed

Siegmund KD, Marjoram P, Tavaré S, Shibata D. Many colorectal cancers are "flat" clonal expansions. Cell Cycle. 2009 Jul 15; 8(14):2187-93. View in: PubMed

Siegmund KD, Marjoram P, Woo YJ, Tavaré S, Shibata D. Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers. Proc Natl Acad Sci U S A. 2009 Mar 24; 106(12):4828-33. View in: PubMed

Woo YJ, Siegmund KD, Tavaré S, Shibata D. Older individuals appear to acquire mitotically older colorectal cancers. J Pathol. 2009 Mar; 217(4):483-8. View in: PubMed

Jiang X, Castelao JE, Groshen S, Cortessis VK, Shibata DK, Conti DV, Gago-Dominguez M. Water intake and bladder cancer risk in Los Angeles County. Int J Cancer. 2008 Oct 1; 123(7):1649-56. View in: PubMed

Chu M, Siegmund KD, Hao QL, Crooks GM, Tavaré S, Shibata D. Inferring relative numbers of human leucocyte genome replications. Br J Haematol. 2008 Jun; 141(6):862-71. View in: PubMed

Alhopuro P, Phichith D, Tuupanen S, Sammalkorpi H, Nybondas M, Saharinen J, Robinson JP, Yang Z, Chen LQ, Orntoft T, Mecklin JP, Järvinen H, Eng C, Moeslein G, Shibata D, Houlston RS, Lucassen A, Tomlinson IP, Launonen V, Ristimäki A, Arango D, Karhu A, Sweeney HL, Aaltonen LA. Unregulated smooth-muscle myosin in human intestinal neoplasia. Proc Natl Acad Sci U S A. 2008 Apr 8; 105(14):5513-8. View in: PubMed

Miller AJ, Dudley SD, Tsao JL, Shibata D, Liskay RM. Tractable Cre-lox system for stochastic alteration of genes in mice. Nat Methods. 2008 Mar; 5(3):227-9. View in: PubMed

Shibata D. Mistakes make history: visualizing intestinal tectonics. Gastroenterology. 2008 Feb; 134(2):628-31. View in: PubMed

Basile LA, Gallaher TK, Shibata D, Miller JD, Douer D. Multilineage hematopoietic recovery with concomitant antitumor effects using low dose Interleukin-12 in myelosuppressed tumor-bearing mice. J Transl Med. 2008; 6:26. View in: PubMed

Siegmund KD, Marjoram P, Shibata D. Modeling DNA methylation in a population of cancer cells. Stat Appl Genet Mol Biol. 2008; 7(1):Article 18. View in: PubMed

Shibata DK, Kern SE. Ancestral trees for modeling stem cell lineages genetically rather than functionally: understanding mutation accumulation and distinguishing the restrictive cancer stem cell propagation theory and the unrestricted cell propagation theory of human tumorigenesis. Breast Dis. 2008; 29:15-25. View in: PubMed

Shibata D. Stem cells as common ancestors in a colorectal cancer ancestral tree. Curr Opin Gastroenterol. 2008 Jan; 24(1):59-63. View in: PubMed

Kern SE, Shibata D. The fuzzy math of solid tumor stem cells: a perspective. Cancer Res. 2007 Oct 1; 67(19):8985-8. View in: PubMed

Nicolas P, Kim KM, Shibata D, Tavaré S. The stem cell population of the human colon crypt: analysis via methylation patterns. PLoS Comput Biol. 2007 Mar 2; 3(3):e28. View in: PubMed

Chen T, Burke KA, Zhan Y, Wang X, Shibata D, Zhao Y. IL-12 facilitates both the recovery of endogenous hematopoiesis and the engraftment of stem cells after ionizing radiation. Exp Hematol. 2007 Feb; 35(2):203-13. View in: PubMed

Shibata D, Tavaré S. Stem cell chronicles: autobiographies within genomes. Stem Cell Rev. 2007 Jan; 3(1):94-103. View in: PubMed

Chu MW, Siegmund KD, Eckstam CL, Kim JY, Yang AS, Kanel GC, Tavaré S, Shibata D. Lack of increases in methylation at three CpG-rich genomic loci in non-mitotic adult tissues during aging. BMC Med Genet. 2007; 8:50. View in: PubMed

Sodir NM, Chen X, Park R, Nickel AE, Conti PS, Moats R, Bading JR, Shibata D, Laird PW. Smad3 deficiency promotes tumorigenesis in the distal colon of ApcMin/+ mice. Cancer Res. 2006 Sep 1; 66(17):8430-8. View in: PubMed

Shibata D. Clonal diversity in tumor progression. Nat Genet. 2006 Apr; 38(4):402-3. View in: PubMed

Shibata D, Tavaré S. Counting divisions in a human somatic cell tree: how, what and why? Cell Cycle. 2006 Mar; 5(6):610-4. View in: PubMed

Shibata D. When does MMR loss occur during HNPCC progression? Cancer Biomark. 2006; 2(1-2):29-35. View in: PubMed

Kim JY, Tavaré S, Shibata D. Human hair genealogies and stem cell latency. BMC Biol. 2006; 4:2. View in: PubMed

Kim JY, Tavaré S, Shibata D. Counting human somatic cell replications: methylation mirrors endometrial stem cell divisions. Proc Natl Acad Sci U S A. 2005 Dec 6; 102(49):17739-44. View in: PubMed

Kabbarah O, Sotelo AK, Mallon MA, Winkeler EL, Fan MY, Pfeifer JD, Shibata D, Gutmann DH, Goodfellow PJ. Diethylstilbestrol effects and lymphomagenesis in Mlh1-deficient mice. Int J Cancer. 2005 Jul 1; 115(4):666-9. View in: PubMed

Irvine RA, Adachi N, Shibata DK, Cassell GD, Yu K, Karanjawala ZE, Hsieh CL, Lieber MR. Generation and characterization of endonuclease G null mice. Mol Cell Biol. 2005 Jan; 25(1):294-302. View in: PubMed

Kim JY, Beart RW, Shibata D. Stability of colon stem cell methylation after neo-adjuvant therapy in a patient with attenuated familial adenomatous polyposis. BMC Gastroenterol. 2005; 5:19. View in: PubMed

Calabrese P, Mecklin JP, Järvinen HJ, Aaltonen LA, Tavaré S, Shibata D. Numbers of mutations to different types of colorectal cancer. BMC Cancer. 2005; 5:126. View in: PubMed

Kim JY, Siegmund KD, Tavaré S, Shibata D. Age-related human small intestine methylation: evidence for stem cell niches. BMC Med. 2005; 3:10. View in: PubMed

Xie Y, Yang H, Cunanan C, Okamoto K, Shibata D, Pan J, Barnes DE, Lindahl T, McIlhatton M, Fishel R, Miller JH. Deficiencies in mouse Myh and Ogg1 result in tumor predisposition and G to T mutations in codon 12 of the K-ras oncogene in lung tumors. Cancer Res. 2004 May 1; 64(9):3096-102. View in: PubMed

Calabrese P, Tsao JL, Yatabe Y, Salovaara R, Mecklin JP, Järvinen HJ, Aaltonen LA, Tavaré S, Shibata D. Colorectal pretumor progression before and after loss of DNA mismatch repair. Am J Pathol. 2004 Apr; 164(4):1447-53. View in: PubMed

Kim KM, Calabrese P, Tavaré S, Shibata D. Enhanced stem cell survival in familial adenomatous polyposis. Am J Pathol. 2004 Apr; 164(4):1369-77. View in: PubMed

Calabrese P, Tavaré S, Shibata D. Pretumor progression: clonal evolution of human stem cell populations. Am J Pathol. 2004 Apr; 164(4):1337-46. View in: PubMed

Kim KM, Shibata D. Tracing ancestry with methylation patterns: most crypts appear distantly related in normal adult human colon. BMC Gastroenterol. 2004 Apr 1; 4:8. View in: PubMed

Karanjawala ZE, Adachi N, Irvine RA, Oh EK, Shibata D, Schwarz K, Hsieh CL, Lieber MR. The embryonic lethality in DNA ligase IV-deficient mice is rescued by deletion of Ku: implications for unifying the heterogeneous phenotypes of NHEJ mutants. DNA Repair (Amst). 2002 Dec 5; 1(12):1017-26. View in: PubMed

Shibata D. Molecular tumour clocks and colorectal cancer: seeing the unseen. Pathology. 2002 Dec; 34(6):534-40. View in: PubMed

Tsao JL, Dudley S, Kwok B, Nickel AE, Laird PW, Siegmund KD, Liskay RM, Shibata D. Diet, cancer and aging in DNA mismatch repair deficient mice. Carcinogenesis. 2002 Nov; 23(11):1807-10. View in: PubMed

Kim KM, Shibata D. Methylation reveals a niche: stem cell succession in human colon crypts. Oncogene. 2002 Aug 12; 21(35):5441-9. View in: PubMed

Trinh BN, Long TI, Nickel AE, Shibata D, Laird PW. DNA methyltransferase deficiency modifies cancer susceptibility in mice lacking DNA mismatch repair. Mol Cell Biol. 2002 May; 22(9):2906-17. View in: PubMed

Kim KM, Salovaara R, Mecklin JP, Järvinen HJ, Aaltonen LA, Shibata D. PolyA deletions in hereditary nonpolyposis colorectal cancer: mutations before a gatekeeper. Am J Pathol. 2002 Apr; 160(4):1503-6. View in: PubMed

Laiho P, Launonen V, Lahermo P, Esteller M, Guo M, Herman JG, Mecklin JP, Järvinen H, Sistonen P, Kim KM, Shibata D, Houlston RS, Aaltonen LA. Low-level microsatellite instability in most colorectal carcinomas. Cancer Res. 2002 Feb 15; 62(4):1166-70. View in: PubMed

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