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Faculty Publications for 2011


At the Greehey Children’s Cancer Research Institute, faculty members continue to achieve new advancements within their research. Below is a list of publications that have been published for this year.

 

Dr. Aune, Pediatrics

 

Policarpio-Nicolas ML, Valente PT, Aune GJ, Higgins RA. Isolated vaginal myeloid sarcoma in a 16-year-old girl. Ann Diagn Pathol. 2011 Jun 7. [Epub ahead of print] [PMID: 21658983].


Dr. Beuten, Pediatrics

 

Beuten J, Gelfond JAL, Piwkham D, Pollock BH, Winick NJ, Collier AB 3rd, Tomlinson GE.  Candidate gene association analysis of acute lymphoblastic leukemia identifies new susceptibility locus at 11p15 (LMO1). Carcinogenesis. 2011 Sep;32(9):1349-53. Epub 2011 May 21. [PMID: 21602560]

 

Beuten J, Halder I, Fowler SP, Goring HH, Duggirala R, Arya R, Thompson IM, Leach RJ, Lehman DM.  Wide disparity in genetic admixture among Mexican Americans from San Antonio, TX.  Ann Hum Genet. 2011 Jul;75(4):529-38. doi: 10.1111/j.1469-1809.2011.00655.x. Epub 2011 May 18 [PMID: 21592109]

 

Swinney RM, Beuten J, Collier AB 3rd, Chen T, Winick NJ, Pollock BH,  Tomlinson GE.  Polymorphisms in CYP1A1 and ethnic-specific susceptibility to acute lymphoblastic leukemia in children. Cancer Epidemiol Biomarkers Prev. 2011 Jul;20(7):1537-42. Epub 2011 May 17 [PMID: 21586621]

 

Mitra N, Banda K, Altheide TK, Schaffer L, Johnson-Pais TL, Beuten J, Leach RJ, Angata T, Varki N, Varki A.  SIGLEC12:  A human-specific segregationg (pseudo) gene encodes a signaling molecular expressed in prostate carcinomas. J Biol Chem 2011; Jul; 286 (26): 23003-11. Epub 2011 May 9 [PMID: 21555517]


Piwkham D, Gelfond JA, Rerkamnuaychoke B, Pakakasama S, Rebel VI, Pollock BH, Winick NJ, Collier AB 3rd, Tomlinson GE, Beuten J. Multilocus association of genetic variants in MLL, CREBBP, EP300 and TOP2A with childhood acute lymphoblastic leukemia in Hispanics from Texas.  Cancer Epidemiol Biomarkers Prev. 2011 Jun;20(6):1204-12. Epub 2011 Apr 14. [PMID: 21493871]

Dr. Bishop, Cellular & Structural Biology

Zimmer SN, Lemieux ME, Karia BP, Day C, Zhou T, Zhou Q, Kung AL, Suresh U, Chen Y, Kinney MC, Bishop AJ and Rebel VI. Mice heterozygous for CREB binding protein are hypersensitive to γ-radiation and invariably develop myelodysplastic/myeloproliferative disease. Exp Hematol. 2011 Dec 20. [Epub ahead of print] [PMID: 22198154]

 

Lin S, Yu L, Yang J, Liu Z, Karia B, Bishop AJ, Jackson J, Lozano G, Copland JA, Mu X, Sun B, Sun LZ. Mutant p53 disrupts the role of ShcA in balancing the Smad Protein-dependent and -independent signaling activity of transforming growth factor-beta (TGF-β). J Biol Chem. 2011 Dec 23;286(51):44023-34. Epub 2011 Oct 28. [PMID: 22039050]

 

Brown AD, Claybon AB, Bishop AJ.  A conditional mouse model for measuring the frequency of homologous recombination events in vivo in the absence of essential genes.  Mol Cell Biol. 2011 Sep; 31(17):3593-602. Epub 2011 Jun 27. [PMID: 21709021]

 

Claybon AB and Bishop AJR. Dissection of the mouse eye for a whole mount of the retinal pigment epithelium. J Vis Exp. 2011 Feb 27;(48). pii: 2563. doi: 10.3791/2563. [PMID: 21403630]

 

Ravi D, Chen Y, Karia B, Brown A, Gu TT, Li J, Carey MS, Hennessy BT and Bishop AJR. 14-3-3 σ expression effects G2/M response to oxygen and correlates with ovarian cancer metastasis. PLoS One 2011 Jan 10;6(1):e15864. [PMID: 21249227]

Dr. Chen, DEB

 

Hsu FH, Serpedin E, Hsiao TZ, Bishop AJ, Dougherty ER, Chen Y. Identifying Genes Associated with Chemotherapy, Response in Ovarian Carcinomas Based on DNA Copy Number and Expression Profiles, IEEE Workshops on Genomic Signal Processing and Statistics 2011 (GENSIPS2011), Dec 4-6, 2011, San Antonio, TX. (Invited to Special Issue of BMC Genomics, 2011)

 

Zimmer SN, Lemieux ME, Karia BP, Day C, Zhou T, Zhou Q, Kung AL, Suresh U, Chen Y, Kinney MC, Bishop A, Rebel VI. Mice heterozygous for CREB binding protein are hypersensitive to γ-radiation and invariably develop myelodysplastic/myeloproliferative disease, accepted to Experimental Hematology, 2011

 

Killian JK, Walker RL, Bilke S, Chen Y, Davis S, Cornelison R, Smith WI, Meltzer PS. Genome-wide methylation profiling in archival formalin-fixed paraffin-embedded tissue samples, Methods Mol Biol. 2012; 823:107-18. [PMID: 22081342]
 
Roessler S, Long EL, Budhu A, Chen Y, Zhao X, Ji J, Walker R, Jia H-L, Ye Q-H, Qin L-X, Tang Z-Y, He P, Hunter KW, Thorgeirsson SS, Meltzer PS, Wang XW.  Integrative Genomic Identification of Genes on 8p Associated with Hepatocellular Carcinoma Progression and Patient Survival, accepted to Gastroenterology, Dec. 2011.

 

Chen HI, Hsiao TZ, Keller C, Chen Y. S-score: a Novel Scoring Method of Gene Signatures for Molecular Classification, IEEE Workshops on Genomic Signal Processing and Statistics 2011 (GENSIPS2011), Dec 4-6, 2011, San Antonio, TX.

 

Yue D, Chen Y, Huang Y. Computational Prediction of microRNA Regulatory Pathways, IEEE Workshops on Genomic Signal Processing and Statistics 2011 (GENSIPS2011), Dec 4-6, 2011, San Antonio, TX.

 

Doderer M, Anguiano Z, Suresh U, Dashnamoorthy R, Bishop AJ, Chen Y. Multisource Biological Pathway Consolidation. IEEE Workshops on Genomic Signal Processing and Statistics 2011 (GENSIPS2011), Dec 4-6, 2011, San Antonio, TX. (Invited to Special Issue of BMC Genomics, 2011)

 

Hsu FH, Serpedin E, Chen Y, Dougherty ER. Stochastic Modeling of Dynamic Effects of Copy Number Alterations upon Gene Expression Levels, IEEE Workshops on Genomic Signal Processing and Statistics 2011 (GENSIPS2011), Dec 4-6, 2011, San Antonio, TX. (Invited to Special Issue of BMC Genomics, 2011)

 

Xiao Y, Suresh U, Chen HH, Wu X, Wolf SE and Chen Y.  A Novel Significance Score for Gene Selection and Ranking, accepted to Bioinformatics, Nov. 2011.

 

Xiao Y, Suresh U, Chen HH, Wu X, Wolf SE and Chen Y. Gene Sets Enrichment Analysis of miRNA Expression Profile, BIBM 2011, Nov. 2011, Atlanta, GA

 

Meng J, Zhang JM, Chen Y, Huang Y. Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks, Proteome Sci. 2011 Oct 14;9 Suppl 1:S9, [PMID: 22166063]

 

Hsu FH, Serpedin E, Chen Y, Dougherty ER.  Stochastic Modeling of the Relationship between Copy Number and Gene Expression Based on Transcriptional Logic, IEEE Trans Biomed Eng. 2011 Oct 24, [PMID: 22042124]

 

Hsu FH, Chen HI, Tsai MH, Lai LC, Huang CC, Tu SH, Chuang EY, Chen Y.  A model-based circular binary segmentation algorithm for the analysis of array CGH data, BMC Res Notes. 2011 Oct 10; 4(1):394, [PMID: 21985277]

 

Nguyen N, Chiao YA, Huang Y, Gao SJ, Lindsey ML, Chen Y, Jin Y. Temporal Clustering of Gene Expression Patterns Using Short-Time Segments, accepted to International Journal of Functional Informatics and Personalized Medicine (IJFIPM), May 2011.

 

Valenzuela MS, Chen Y (co-first author), Davis S, Yang F, Walker RL, Bilke S, Lueders J, Martin MM, Aladjem MI, Massion PP, Meltzer PS. Preferential localization of human origins of DNA replication at the 5'-ends of expressed genes and at evolutionarily conserved DNA sequences. PLoS One. 2011; 6(5):e17308. Epub 2011 May 13. [PMID: 21602917]

 

Rubin BP, Nishijo K, Chen HI, Yi X, Schuetze DP, Pal R, Prajapati SI, Abraham J, Arenkiel BR, Chen QR, Davis S, McCleish AT, Capecchi MR, Michalek JE, Zarzabal LA, Khan J, Yu Z, Parham DM, Barr FG, Meltzer PS, Chen Y, Keller C. Evidence for an Unanticipated Relationship between Undifferentiated Pleomorphic Sarcoma and Embryonal Rhabdomyosarcoma, Cancer Cell. 2011 Feb 15; 19(2):177-91. [PMID: 21316601]

 

Dashnamoorthy R, Chen Y, Karia B, Brown A, Gu TT, Li J, Carey MS, Hennessy BT, Bishop AJ. 14-3-3 σ expression effects G2/M response to oxygen and correlates with ovarian cancer metastasis, PLoS One. 2011 Jan 10; 6(1):e15864. [PMID: 21249227]

 

Dr. Gao, Pediatrics

 

Zhang W, Greene W, Gao SJ. Microtubule- and dynein-dependent nuclear trafficking of rhesus rhadinovirus in rhesus fibroblasts. J Virol. 2011 Oct 26. [Epub ahead of print]

 

Ye F, Lei X, Gao SJ. Mechanisms of Kaposi's Sarcoma-Associated Herpesvirus Latency and Reactivation. Adv Virol. 2011; pii: 193860. [PMID: 21625290]

 

Ye F, Zhou F, Bedolla RG, Jones T, Lei X, Kang T, Guadalupe M, Gao SJ. Reactive oxygen species hydrogen peroxide mediates Kaposi's sarcoma-associated herpesvirus reactivation from latency. PLoS Pathog. 2011 May; 7(5):e1002054. Epub 2011 May 19. [PMID: 21625536]

 

Zhou F, Gao SJ. Recent advances in cloning herpesviral genomes as infectious bacterial artificial chromosomes. Cell Cycle. 2011 Feb 1; 10(3):434-40. Epub 2011 Feb 1. [PMID: 21245660]

 

Guadalupe M, Pollock BH, Westbrook S, Redding S, Bullock D, Anstead G, Agan BK, Marconi VC, Barbieri S, Sankar V, Rebeles J, Flahive Y, Schoolfield J, Wang L, Lei X, Dow D, Yeh CK, Dang H, Infante AJ, Gao SJ. Risk factors influencing antibody responses to Kaposi's sarcoma-associated herpesvirus latent and lytic antigens in patients under antiretroviral therapy. J Acquir Immune Defic Syndr. 2011 Jan; 56(1):83-90. [PMID: 21084997]

 

Dr. McEwen, Biochemistry

Zuniga JE, Ilangovan U, Mahlawat P, Hinck CS, Huang T, Groppe JC, McEwen DG, Hinck AP. The TβR-I Pre-Helix Extension Is Structurally Ordered in the Unbound Form and Its Flanking Prolines Are Essential for Binding. J Mol Biol. 2011 Sep 30; 412(4):601-18. Epub 2011 Jul 29. [PMID: 21821041]



Dr. Penalva, Cellular & Structural Biology

 

Dávalos A, Goedeke L, Smibert P, Ramírez CM, Warrier NP, Andreo U, Cirera-Salinas D, Rayner K, Suresh U, Pastor-Pareja JC, Esplugues E, Fisher EA, Penalva LO, Moore KJ, Suárez Y, Lai EC, Fernández-Hernando C. miR-33a/b contribute to the regulation of fatty acid metabolism and insulin signaling. Proc Natl Acad Sci U S A. 2011 May 31; 108(22):9232-7. Epub 2011 May 16. [PMID:21576456][PubMed - indexed for MEDLINE]

 

Uren PJ, Burns SC, Ruan J, Singh KK, Smith AD, Penalva LO. Genomic analyses of the RNA binding protein Hu Antigen R (HuR) identify a complex network of target genes and novel characteristics of its binding sites. J Biol Chem. 2011 Oct 28; 286(43):37063-6. Epub 2011 Sep 2. [PMID: 21890634]

 

Chamorro-Jorganes A, Araldi E, Penalva LO, Sandhu D, Fernández-Hernando C, Suárez Y.MicroRNA-16 and MicroRNA-424 Regulate Cell-Autonomous Angiogenic Functions in Endothelial Cells via Targeting Vascular Endothelial Growth Factor Receptor-2 and Fibroblast Growth Factor Receptor-1. Arterioscler Thromb Vasc Biol. 2011 Nov; 31(11):2595-606.  [PMID: 21885851]

 

Vo DT, Qiao M, Smith AD, Burns SC, Brenner AJ, Penalva LO. The oncogenic RNA-binding protein Musashi1 is regulated by tumor suppressor miRNAs.  RNA Biol. 2011 Sep 1; 8(5). [Epub ahead of print][PMID: 21881409]

 

Boutz DR, Collins P, Suresh U, Lu M, Ramirez CM, Fernandez-Hernando C, Huang Y, Abreu Rde S, Le SY, Shapiro BA, Liu AM, Luk JM, Aldred SF, Trinklein N, Marcotte EM, Penalva LO. Two-Tiered Approach Identifies a Network of Cancer and Liver Disease- Related Genes Regulated by miR-122. J Biol Chem. 2011 May 20; 286(20):18066-78. Epub 2011 Mar 14. [PMID: 21402708]

 

Jain R, Devine T, George AD, Chittur SV, Baroni TE, Penalva LO, Tenenbaum SA.  RIP-Chip analysis:  RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling.  Methods Mol Biol 2011; 703:247-63. [PMID: 21125495]

 

Gelfond JAL, Zarzabal LA, Burton T, Burns S, Sogayar M, Penalva LOF. Latent rank change detection for analysis of splice-junction microarrays with nonlinear effects. Ann. Appl. Stat. 2011 March; 5(1):364-380.

Davalos A, Smibert P, Goedeke L, Warrier NP, Andreo U, Rayner K, Suresh U, Pastor-Pareja JC, EA Fisher, Penalva LOF, Moore KJ, Suárez Y, Laib EC, Fernández-Hernando C. Feedback loops involving SREBPs and miR-33 regulate fatty acid oxidation and insulin signaling: implication in metabolic syndrome. Proc Natl Acad Sci USA 2011; 108(22): 9232-7.

 

ENCODE Project Consortium A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046. Epub 2011 Apr 19.


Vo DT, Gelfond J, Sandhu D, Penalva LOF. The RNA binding protein Musashi1, a critical regulator in glioblastomas and medulloblastoma. In Molecular Targets of CNS Tumors. InTech. Edited by: Miklos Garami. p. 549-564.


Dr. Rao, Cellular & Structural Biology

 

Chang YF, Lee-Chang JS, Harris KY, Sinha-Hikim AP, Rao MK. Role of β-Catenin in Post-Meiotic Male Germ Cell Differentiation. PLoS One. 2011; 6(11):e28039. Epub 2011 Nov 18. [PMID: 22125654]

 

Chang YF, Lee-Chang JS, Panneerdoss S, Maclean JA, Rao MK. Isolation of Sertoli, Leydig, and spermatogenic cells from the mouse testis. Biotechniques. 2011 Nov;51(5):314-4

 

Dr. Rebel, Cellular & Structural Biology

 

Zimmer SN, Lemieux ME, Karia BP, Day C, Zhou T, Zhou Q, Kung AL, Suresh U, Chen Y, Kinney MC, Bishop AJ, Rebel VI. Mice heterozygous for CREB binding protein are hypersensitive to g-radiation and invariably develop myelodysplastic/myeloproliferative neoplasm. Exp Hematol. 2011 Dec 20. [Epub ahead of print] [PMID: 22198154]


Shim JH, Greenblatt MB, Singh A, Brady N, Hu D, Drapp R, Ogawa W, Kasuga M, Noda T, Yang SH, Lee SK, Rebel VI, Glimcher LH. Administration of BMP2/7 in utero partially reverses Rubinstein-Taybi syndromelike skeletal defects induced by Pdk1 or Cbp mutations in mice. J Clin Invest. 2011 Dec 1. pii: 59466. doi: 10.1172/JCI59466. [Epub ahead of print]


Harris SE, Macdougall M, Horn D, Woodruff K, Zimmer SN, Rebel VI, Fajardo R, Feng JQ, Heinrich-Gluhak J, Harris MA, Abboud Werner S. Meox2Cre-mediated disruption of CSF-1 leads to osteopetrosis and osteocyte defects. Bone. 2011 Sep 20. [Epub ahead of print][PMID: 21958845]


Lemieux ME, Cheng Z, Zhou Q, White R, Cornell J, Kung AL, Rebel VI. Inactivation of a Single Copy of Crebbp Selectively Alters Pre-mRNA Processing in Mouse Hematopoietic Stem Cells. PLoS One. 2011;6(8):e24153. Epub 2011 Aug 25. [PMID: 21901164]

 

Zimmer SN, Zhou Q, Zhou T, Cheng Z, Abboud-Werner SL, Horn D, Lecocke M, White R, Krivtsov AV, Armstrong SA, Kung AL, Livingston DM, Rebel VI. Crebbp haploinsufficiency in mice alters the bone marrow microenvironment leading to loss of stem cells and excessive myelopoiesis. Blood. 2011 Jul 7; 118(1):69-79. Epub 2011 May 9 [PMID: 21555743]

 

Piwkham D, Gelfond JA, Rerkamnuaychoke B, Pakakasama S, Rebel VI, Pollock BH, Winick NJ, Collier AB 3rd, Tomlinson GE, Beuten J. Multilocus association of genetic variants in MLL, CREBBP, EP300, and TOP2A with childhood acute lymphoblastic leukemia in Hispanics from Texas. Cancer Epidemiol Biomarkers Prev. 2011 Jun; 20(6):1204-12. Epub 2011 Apr 14. [PMID: 21493871].



Dr. Scott, Medicine

 

Scott LM. The JAK2 exon 12 mutations: a comprehensive review. Am J Hematol. 2011 Aug; 86(8):668-76. doi: 10.1002/ajh.22063. Epub 2011 Jun 14. [PMID: 21674578]

 

Dr. Shiio, Biochemistry

Song M,Hakala KW, Weintraub ST, Shiio Y.* Quantitative proteomic identification of the BRCA1 ubiquitination substrates. J Proteome Res. 2011 Sep 27. [Epub ahead of print] [PMID: 21950761]*Corresponding author

 

Lai Y, Song M, Hakala KW, Weintraub ST, Shiio Y. Proteomic dissection of the VHL interactome. J Proteome Res. 2011 Sep 26. [Epub ahead of print] [PMID: 21942715]

 

Lai Y, Qiao M, Song M, Weintraub ST, Shiio YQuantitative proteomics identifies the Myb-binding protein p160 as a novel target of the von Hippel-Lindau tumor suppressor.  PLoS One 2011 Feb 28:6(2):e16975. [PMID: 21386990]



Dr. Tomlinson, Pediatrics

Neklason DW, Done MW, Sargent NR, Schwartz AG, Anton-Culver H, Griffin, CA,  Ahnen D, Schildkraut JM, Tomlinson GE, Strong LC, Miller AR, Stopfer JE, Burt RW. Activating mutation in MET oncogene is inherited in familiar colorectal cancer.  BMC Cancer. 2011 Oct 4; 11(1):424. [Epub ahead of print] [PMID: 21970370]

 

Ding YC, John EM, Steele L, Kelley, Chu LH, Davis H, Tomlinson GE, Neuhausen SL, Germline mutations in PALB2 in African-American breast cancer cases. Breast Cancer Res Treat. 2011 Feb;126(1):227-30. Epub 2010 Nov 27. [PMID: 21113654]

 

Minnix JA, Robinson JD, Lam CY, Carter BL, Foreman JE, Vandenbergh DJ, Tomlinson GE, Wetter DW, Cinciripini PM. The serotonin transporter gene and startle response during nicotine deprivation. Biol Psychol. 2011 Jan;86(1):1-8. Epub 2010 Oct 1. [PMID: 20888887]

 

Plon SE, Wheeler D, Strong L, Tomlinson GE, Pirics M, Meng Q, Cheung H, Begin P, Biegel J, Muzny D, Lewis L, Gibbs R. Identification of genetic susceptibility to childhood cancer through analysis of genes in parallel. Cancer Genet. 2011 Jan; 204(1):19-25 [PMID: 21356188]

 

Spurdle AB, Marquart L, McGuffog L, Healey S, Sinilnikova O, Wan F, Chen X, Beesley J, Singer CF, Dressler AC, Gschwantler-Kaulich D, Blum JL, Tung N, Weitzel J, Lynch H, Garber J, Easton DF, Peock S, Cook M, Oliver CT, Frost D, Conroy D, Evans DG, Lalloo F, Eeles R, Izatt L, Davidson R, Chu C, Eccles D, Selkirk CG, Daly M, Isaacs C, Stoppa-Lyonnet D, Sinilnikova OM, Buecher B, Belotti M, Mazoyer S, Barjhoux L, Verny-Pierre C, Lasset C, Dreyfus H, Pujol P, Collonge-Rame MA; GEMO Study Collaborators, Rookus MA, Verhoef S, Kriege M, Hoogerbrugge N, Ausems MG, van Os TA, Wijnen J, Devilee P, Meijers-Heijboer HE, Blok MJ, Heikkinen T, Nevanlinna H, Jakubowska A, Lubinski J, Huzarski T, Byrski T, Durocher F, Couch FJ, Lindor NM, Wang X, Thomassen M, Domchek S, Nathanson K, Caligo M, Jernström H, Liljegren A, Ehrencrona H, Karlsson P; SWE-BRCA, Ganz PA, Olopade OI, Tomlinson G, Neuhausen S, Antoniou AC, Chenevix-Trench G, Rebbeck TR.  Common genetic variation at BARD1 is not associated with breast cancer risk in BRCA1 or BRCA2 mutation carriers. Cancer Epidemiol Biomarkers Prev. 2011 May;20(5):1032-8. Epub 2011 Mar 10. [PMID: 21393566]

 

Piwkham D, Gelfond JA, Rerkamnuaychoke B, Pakakasama S, Rebel VI, Pollock BH, Winick NJ, Collier AB 3rd, Tomlinson GE, Beuten J. Multi-locus association of genetic variants in MLL, CREBBP, EP300 and TOP2A with childhood acute lymphoblastic leukemia in Hispanics from Texas. Cancer Epidemiol Biomarkers Prev. 2011 Jun;20(6):1204-12. Epub 2011 Apr 14. [PMID: 21493871]

 

Swinney RM, Beuten J, Collier AB 3rd, Chen TT, Winick NJ, Pollock BH, Tomlinson GE. Polymorphisms in CYP1A1 and ethnic-specific susceptibility to acute lymphoblastic leukemia in children. Cancer Epidemiol Biomarkers Prev. 2011 Jul; 20(7):1537-42. Epub 2011 May 17. [PMID: 21586621]

 

Litten JB, Chen TT, Schultz R, Herman K, Comstock J, Schiffman J, Tomlinson GE, Rakheja D. Activated NOTCH2 Is Overexpressed in Hepatoblastomas: An Immunohistochemical Study. Pediatr Dev Pathol. 2011 Sep-Oct; 14(5):378-83. Epub 2011 Jun 3 [PMID: 21639801].

 

Neuhausen SL, Brummel S, Ding YC, Steele L, Nathanson KL, Domchek S, Rebbeck TR, Singer CF, Pfeiler G, Lynch HT, Garber JE, Couch F, Weitzel JN, Godwin A, Narod SA, Ganz PA, Daly MB, Isaacs C, Olopade OI, Tomlinson GE, Rubinstein WS, Tung N, Blum JL, Gillen DL.  Genetic variation in IGF2 and HTRA1 and breast cancer risk among BRCA1 and BRCA2 carriers.  Cancer Epidemiol Biomarkers Prev. 2011 Aug;20(8):1690-702. Epub 2011 Jun 27 [PMID: 21708937]

 

Ziogas A, Horick N, Kinney A, Lowery J, Isaacs C, Griffin C, Moorman P, Edwards K, Hill D, Berg J, Tomlinson G, Anton-Culver H, Strong L, Dianne Finkelstein D, Plon S.  Clinically relevant changes in family history of cancer over time.  JAMA 2011 July 306(2): 172-8. [PMID: 21750294]

 

Beuten J, Gelfond JAL, Piwkham D, Pollock BH, Winick NJ, Collier A, Tomlinson GECandidate gene association analysis of acute lymphoblastic leukemia identifies new susceptibility locus at 11p15 (LMO1), Carcinogenesis, Carcinogenesis. 2011 Sep;32(9):1349-53. Epub 2011 May 21. [PMID: 21602560]

 

Rebbeck TR, Mitra N, Domchek SM, Wan F, Friebel TM, Tran TV, Singer CF, Tea MK, Blum JL, Tung N, Olopade OI, Weitzel JN, Lynch HT, Snyder CL, Garber JE, Antoniou AC, Peock S, Evans DG, Paterson J, Kennedy MJ, Donaldson A, Dorkins H, Easton DF; Epidemiological Study of BRCA1 and BRCA2 Mutation Carriers (EMBRACE), Rubinstein WS, Daly MB, Isaacs C, Nevanlinna H, Couch FJ, Andrulis IL, Freidman E, Laitman Y, Ganz PA, Tomlinson GE, Neuhausen SL, Narod SA, Phelan CM, Greenberg R, Nathanson KL .Modification of BRCA1-Associated Breast and Ovarian Cancer Risk by BRCA1 Interacting Genes.  Cancer Res. 2011 Sep 1;71(17):5792-805. Epub 2011 Jul 28 [PMID: 21799032]



Small Animal Imaging


Ohshima-Hosoyama S, Davare MA, Prajapati SI, Abraham J, Lal S, Nelon LD, Kilcoyne A, Giles FJ, Hanes MA, Rubin BP, Keller C. Preclinical Testing of Tandutinib in a Transgenic Medulloblastoma Mouse Model. J Pediatr Hematol Oncol. 2011 Dec 3. [Epub ahead of print] [PMID: 22146535]

 

Moore CM, Dick EJ Jr, Hubbard GB, Gardner SM, Dunn BG, Brothman AR, Williams V, Prajapati SI, Keller C, Davis MD. Craniorachischisis and omphalocele in a stillborn cynomolgus monkey (Macaca fascicularis). Am J Med Genet A. 2011 Jun; 155A (6):1367-73. doi: 0.1002/ajmg.a.33627. Epub 2011 May 12. [PMID: 21567905]

 

Prajapati SI, Kilcoyne A, Samano AK, Green DP, McCarthy SD, Blackman BA, Brady MM, Zarzabal LA, Tatiparthy AK, Sledz TJ, Duong T, Ohshima-Hosoyama S, Giles FJ, Michalek JE, Rubin BP, Keller C. Micro-CT Based Virtual Histology Evaluation of Preclinical Medulloblastoma. Mol Imaging Biol. 2011 Jun; 13(3):493-9 [PMID: 20617390]

 

Hosoyama T, Aslam MI, Abraham J, Prajapati SI, Nishijo K, Michalek JE, Zarzabal LA, Nelon LD, Guttridge DC, Rubin BP, Keller C.  IL-4R drives dedifferentiation, mitogenesis, and metastasis in rhabdomyosarcoma. Clin Cancer Res. 2011 May 1; 17(9):2757-66. [PMID: 21536546]

 

Abraham J, Prajapati SI, Nishijo K, Schaffer BS, Taniguchi E, Kilcoyne A, McCleish AT, Nelon LD, Giles FG, Efstratiadis A, LeGallo RD, Nowak BM, Rubin BP, Malempati S, Keller C. Evasion mechanisms to Igf1r inhibition in rhabdomyosarcoma. Mol Cancer Ther. 2011 Apr; 10(4):697-707. Epub 2011 Mar 29. [PMID: 21447712]

 

Hosoyama T, Nishijo K, Prajapati SI, Li G, Keller C.  Rb1 gene inactivation expands satellite cell and postnatal myoblast pools. J Biol Chem. 2011 Jun 3; 286(22):19556-64. Epub 2011 Apr 8. [PMID: 21478154]

 

Rubin BP, Nishijo K, Chen HI, Yi X, Schuetze DP, Pal R, Prajapati SI, Abraham J, Arenkiel BR, Chen QR, Davis S, McCleish AT, Capecchi MR, Michalek JE, Zarzabal LA, Khan J, Yu Z, Parham DM, Barr FG, Meltzer PS, Chen Y, Keller C. Evidence for an unanticipated relationship between undifferentiated pleomorphic sarcoma and embryonal rhabdomyosarcoma. Cancer Cell. 2011 Feb 15; 19(2):177-91. [PMID: 21316601]

 

Prajapati SI, Keller C. Contrast enhanced vessel imaging using microCT.  J Vis Exp. 2011 Jan 27;(47). pii: 2377. doi: 10.3791/2377. [PMID: 21307830]

 

Computational Biology & Bioinformatics Initiative (CBBI)

Journal Publications submitted or accepted (CBBI members are in bold: Chen HI, Doderer M, Hsiao TH, Huang Y, Mohammad TA, Suresh U)

Mohammad TA, Nagarajaram HA, A hierarchical approach to protein fold prediction, J Integr Bioinform. 2011 Oct 19;8(1):185. doi: 10.2390/biecoll-ib-2011-185,  PMID: 22008449


Bashyam MD, Purushotham G, Chaudhary AK, Rao KM, Acharya V, Mohammad TA, Nagarajaram HA, Hariram V, Narasimhan C, A low prevalence of MYH7/MYBPC3 mutations among Familial Hypertrophic Cardiomyopathy patients in India, Mol Cell Biochem. 2012 Jan;360(1-2):373-82. Epub 2011 Sep 29, PMID: 21959974


Mohammad TA, Nagarajaram HA, SVM-based method for protein structural class prediction using secondary structural content and structural information of amino acids, J Bioinform Comput Biol. 2011 Aug;9(4):489-502, PMID: 21776605