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Endogenous Retroviruses and the Pregnancy Compensation Hypothesis: A Reply to David.

Natri H, Garcia AR, Buetow KH, Trumble BC, Wilson MA.

Trends Genet. 2019 Nov 18. pii: S0168-9525(19)30200-8. doi: 10.1016/j.tig.2019.10.006. [Epub ahead of print] No abstract available.


Novel mechanisms of cancer emerge when accounting for sex as a biological variable.

Wilson MA, Buetow KH.

Cancer Res. 2019 Nov 13. pii: canres.2634.2019. doi: 10.1158/0008-5472.CAN-19-2634. [Epub ahead of print]


Evolution of Immune Sexual Dimorphism in Response to Placental Invasiveness: A Reply to Greenbaum and Greenbaum.

Garcia AR, Natri H, Buetow KH, Trumble BC, Wilson MA.

Trends Genet. 2019 Nov 9. pii: S0168-9525(19)30201-X. doi: 10.1016/j.tig.2019.10.007. [Epub ahead of print] No abstract available.


Distinct molecular etiologies of male and female hepatocellular carcinoma.

Natri HM, Wilson MA, Buetow KH.

BMC Cancer. 2019 Oct 15;19(1):951. doi: 10.1186/s12885-019-6167-2.


High GILT Expression and an Active and Intact MHC Class II Antigen Presentation Pathway Are Associated with Improved Survival in Melanoma.

Buetow KH, Meador LR, Menon H, Lu YK, Brill J, Cui H, Roe DJ, DiCaudo DJ, Hastings KT.

J Immunol. 2019 Nov 15;203(10):2577-2587. doi: 10.4049/jimmunol.1900476. Epub 2019 Oct 7.


The Pregnancy Pickle: Evolved Immune Compensation Due to Pregnancy Underlies Sex Differences in Human Diseases.

Natri H, Garcia AR, Buetow KH, Trumble BC, Wilson MA.

Trends Genet. 2019 Jul;35(7):478-488. doi: 10.1016/j.tig.2019.04.008. Review.


Cell studio: A platform for interactive, 3D graphical simulation of immunological processes.

Liberman A, Kario D, Mussel M, Brill J, Buetow K, Efroni S, Nevo U.

APL Bioeng. 2018 Jun 4;2(2):026107. doi: 10.1063/1.5039473. eCollection 2018 Jun.


Tracking Cancer Genetic Evolution using OncoTrack.

Talukder AK, Agarwal M, Buetow KH, Denèfle PP.

Sci Rep. 2016 Jul 14;6:29647. doi: 10.1038/srep29647.


Quantification of read species behavior within whole genome sequencing of cancer genomes for the stratification and visualization of genomic variation.

Hibsh D, Buetow KH, Yaari G, Efroni S.

Nucleic Acids Res. 2016 May 19;44(9):e81. doi: 10.1093/nar/gkw031. Epub 2016 Jan 24.


Systematic genetic analysis identifies Cis-eQTL target genes associated with glioblastoma patient survival.

Chen QR, Hu Y, Yan C, Buetow K, Meerzaman D.

PLoS One. 2014 Aug 18;9(8):e105393. doi: 10.1371/journal.pone.0105393. eCollection 2014.


Addition of MR imaging features and genetic biomarkers strengthens glioblastoma survival prediction in TCGA patients.

Nicolasjilwan M, Hu Y, Yan C, Meerzaman D, Holder CA, Gutman D, Jain R, Colen R, Rubin DL, Zinn PO, Hwang SN, Raghavan P, Hammoud DA, Scarpace LM, Mikkelsen T, Chen J, Gevaert O, Buetow K, Freymann J, Kirby J, Flanders AE, Wintermark M; TCGA Glioma Phenotype Research Group.

J Neuroradiol. 2015 Jul;42(4):212-21. doi: 10.1016/j.neurad.2014.02.006. Epub 2014 Jul 2.


Systems analysis utilising pathway interactions identifies sonic hedgehog pathway as a primary biomarker and oncogenic target in hepatocellular carcinoma.

Efroni S, Meerzaman D, Schaefer CF, Greenblum S, Soo-Lyu M, Hu Y, Cultraro C, Meshorer E, Buetow KH.

IET Syst Biol. 2013 Dec;7(6):243-51.


Genome-wide transcriptional sequencing identifies novel mutations in metabolic genes in human hepatocellular carcinoma.

Meerzaman DM, Yan C, Chen QR, Edmonson MN, Schaefer CF, Clifford RJ, Dunn BK, Dong L, Finney RP, Cultraro CM, Hu Y, Yang Z, Nguyen CV, Kelley JM, Cai S, Zhang H, Zhang J, Wilson R, Messmer L, Chung YH, Kim JA, Park NH, Lyu MS, Song IH, Komatsoulis G, Buetow KH.

Cancer Genomics Proteomics. 2014 Jan-Feb;11(1):1-12.


Turning the tide against cancer through sustained medical innovation: the pathway to progress.

Abernethy A, Abrahams E, Barker A, Buetow K, Burkholder R, Dalton WS, Foti M, Frueh F, Gaynor RB, Kean M, Khan Z, Lessor T, Lichtenfeld JL, Mendelsohn J, van't Veer L.

Clin Cancer Res. 2014 Mar 1;20(5):1081-6. doi: 10.1158/1078-0432.CCR-13-3430. Epub 2014 Feb 12. Review.


Multi-SNP analysis of GWAS data identifies pathways associated with nonalcoholic fatty liver disease.

Chen QR, Braun R, Hu Y, Yan C, Brunt EM, Meerzaman D, Sanyal AJ, Buetow K.

PLoS One. 2013 Jul 19;8(7):e65982. doi: 10.1371/journal.pone.0065982. Print 2013.


Discovery analysis of TCGA data reveals association between germline genotype and survival in ovarian cancer patients.

Braun R, Finney R, Yan C, Chen QR, Hu Y, Edmonson M, Meerzaman D, Buetow K.

PLoS One. 2013;8(3):e55037. doi: 10.1371/journal.pone.0055037. Epub 2013 Mar 21.


Tyrosine kinome sequencing of pediatric acute lymphoblastic leukemia: a report from the Children's Oncology Group TARGET Project.

Loh ML, Zhang J, Harvey RC, Roberts K, Payne-Turner D, Kang H, Wu G, Chen X, Becksfort J, Edmonson M, Buetow KH, Carroll WL, Chen IM, Wood B, Borowitz MJ, Devidas M, Gerhard DS, Bowman P, Larsen E, Winick N, Raetz E, Smith M, Downing JR, Willman CL, Mullighan CG, Hunger SP.

Blood. 2013 Jan 17;121(3):485-8. doi: 10.1182/blood-2012-04-422691. Epub 2012 Dec 4.


Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia.

Roberts KG, Morin RD, Zhang J, Hirst M, Zhao Y, Su X, Chen SC, Payne-Turner D, Churchman ML, Harvey RC, Chen X, Kasap C, Yan C, Becksfort J, Finney RP, Teachey DT, Maude SL, Tse K, Moore R, Jones S, Mungall K, Birol I, Edmonson MN, Hu Y, Buetow KE, Chen IM, Carroll WL, Wei L, Ma J, Kleppe M, Levine RL, Garcia-Manero G, Larsen E, Shah NP, Devidas M, Reaman G, Smith M, Paugh SW, Evans WE, Grupp SA, Jeha S, Pui CH, Gerhard DS, Downing JR, Willman CL, Loh M, Hunger SP, Marra MA, Mullighan CG.

Cancer Cell. 2012 Aug 14;22(2):153-66. doi: 10.1016/j.ccr.2012.06.005.


Life sciences domain analysis model.

Freimuth RR, Freund ET, Schick L, Sharma MK, Stafford GA, Suzek BE, Hernandez J, Hipp J, Kelley JM, Rokicki K, Pan S, Buckler A, Stokes TH, Fernandez A, Fore I, Buetow KH, Klemm JD.

J Am Med Inform Assoc. 2012 Nov-Dec;19(6):1095-102. doi: 10.1136/amiajnl-2011-000763. Epub 2012 Jun 28.


The general transcription factor TAF7 is essential for embryonic development but not essential for the survival or differentiation of mature T cells.

Gegonne A, Tai X, Zhang J, Wu G, Zhu J, Yoshimoto A, Hanson J, Cultraro C, Chen QR, Guinter T, Yang Z, Hathcock K, Singer A, Rodriguez-Canales J, Tessarollo L, Mackem S, Meerzaman D, Buetow K, Singer DS.

Mol Cell Biol. 2012 May;32(10):1984-97. doi: 10.1128/MCB.06305-11. Epub 2012 Mar 12.


Integrated cross-species transcriptional network analysis of metastatic susceptibility.

Hu Y, Wu G, Rusch M, Lukes L, Buetow KH, Zhang J, Hunter KW.

Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):3184-9. doi: 10.1073/pnas.1117872109. Epub 2012 Jan 30.


Using patient-initiated study participation in the development of evidence for personalized cancer therapy.

Ambrose LF, Freedman J, Buetow K, Friend S, Schilsky RL.

Clin Cancer Res. 2011 Nov 1;17(21):6651-7. doi: 10.1158/1078-0432.CCR-11-1110.


Pathways of distinction analysis: a new technique for multi-SNP analysis of GWAS data.

Braun R, Buetow K.

PLoS Genet. 2011 Jun;7(6):e1002101. doi: 10.1371/journal.pgen.1002101. Epub 2011 Jun 9.


Key pathways are frequently mutated in high-risk childhood acute lymphoblastic leukemia: a report from the Children's Oncology Group.

Zhang J, Mullighan CG, Harvey RC, Wu G, Chen X, Edmonson M, Buetow KH, Carroll WL, Chen IM, Devidas M, Gerhard DS, Loh ML, Reaman GH, Relling MV, Camitta BM, Bowman WP, Smith MA, Willman CL, Downing JR, Hunger SP.

Blood. 2011 Sep 15;118(11):3080-7. doi: 10.1182/blood-2011-03-341412. Epub 2011 Jun 16.


The PathOlogist: an automated tool for pathway-centric analysis.

Greenblum SI, Efroni S, Schaefer CF, Buetow KH.

BMC Bioinformatics. 2011 May 4;12:133. doi: 10.1186/1471-2105-12-133.


Cyberinfrastructure and the biomedical sciences.

Hesse BW, Croyle RT, Buetow KH.

Am J Prev Med. 2011 May;40(5 Suppl 2):S97-102. doi: 10.1016/j.amepre.2011.01.006. No abstract available.


CREBBP mutations in relapsed acute lymphoblastic leukaemia.

Mullighan CG, Zhang J, Kasper LH, Lerach S, Payne-Turner D, Phillips LA, Heatley SL, Holmfeldt L, Collins-Underwood JR, Ma J, Buetow KH, Pui CH, Baker SD, Brindle PK, Downing JR.

Nature. 2011 Mar 10;471(7337):235-9. doi: 10.1038/nature09727.


Detecting cancer gene networks characterized by recurrent genomic alterations in a population.

Efroni S, Ben-Hamo R, Edmonson M, Greenblum S, Schaefer CF, Buetow KH.

PLoS One. 2011 Jan 4;6(1):e14437. doi: 10.1371/journal.pone.0014437.


Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format.

Edmonson MN, Zhang J, Yan C, Finney RP, Meerzaman DM, Buetow KH.

Bioinformatics. 2011 Mar 15;27(6):865-6. doi: 10.1093/bioinformatics/btr032. Epub 2011 Jan 28.


Novel pathway analysis of genomic polymorphism-cancer risk interaction in the Breast Cancer Prevention Trial.

Dunn BK, Greene MH, Kelley JM, Costantino JP, Clifford RJ, Hu Y, Tang G, Kazerouni N, Rosenberg PS, Meerzaman DM, Buetow KH.

Int J Mol Epidemiol Genet. 2010;1(4):332-49. Epub 2010 Sep 5.


Genetic variations at loci involved in the immune response are risk factors for hepatocellular carcinoma.

Clifford RJ, Zhang J, Meerzaman DM, Lyu MS, Hu Y, Cultraro CM, Finney RP, Kelley JM, Efroni S, Greenblum SI, Nguyen CV, Rowe WL, Sharma S, Wu G, Yan C, Zhang H, Chung YH, Kim JA, Park NH, Song IH, Buetow KH.

Hepatology. 2010 Dec;52(6):2034-43. doi: 10.1002/hep.23943.


The BioPAX community standard for pathway data sharing.

Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD.

Nat Biotechnol. 2010 Sep;28(9):935-42. doi: 10.1038/nbt.1666. Epub 2010 Sep 9. Erratum in: Nat Biotechnol. 2010 Dec;28(12):1308. Nat Biotechnol. 2012 Apr;30(4):365. Reubenacker, Oliver [corrected to Ruebenacker, Oliver].


Needles in the haystack: identifying individuals present in pooled genomic data.

Braun R, Rowe W, Schaefer C, Zhang J, Buetow K.

PLoS Genet. 2009 Oct;5(10):e1000668. doi: 10.1371/journal.pgen.1000668. Epub 2009 Oct 2.


The completion of the Mammalian Gene Collection (MGC).

MGC Project Team, Temple G, Gerhard DS, Rasooly R, Feingold EA, Good PJ, Robinson C, Mandich A, Derge JG, Lewis J, Shoaf D, Collins FS, Jang W, Wagner L, Shenmen CM, Misquitta L, Schaefer CF, Buetow KH, Bonner TI, Yankie L, Ward M, Phan L, Astashyn A, Brown G, Farrell C, Hart J, Landrum M, Maidak BL, Murphy M, Murphy T, Rajput B, Riddick L, Webb D, Weber J, Wu W, Pruitt KD, Maglott D, Siepel A, Brejova B, Diekhans M, Harte R, Baertsch R, Kent J, Haussler D, Brent M, Langton L, Comstock CL, Stevens M, Wei C, van Baren MJ, Salehi-Ashtiani K, Murray RR, Ghamsari L, Mello E, Lin C, Pennacchio C, Schreiber K, Shapiro N, Marsh A, Pardes E, Moore T, Lebeau A, Muratet M, Simmons B, Kloske D, Sieja S, Hudson J, Sethupathy P, Brownstein M, Bhat N, Lazar J, Jacob H, Gruber CE, Smith MR, McPherson J, Garcia AM, Gunaratne PH, Wu J, Muzny D, Gibbs RA, Young AC, Bouffard GG, Blakesley RW, Mullikin J, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Hirst M, Zeng T, Tse K, Moksa M, Deng M, Ma K, Mah D, Pang J, Taylor G, Chuah E, Deng A, Fichter K, Go A, Lee S, Wang J, Griffith M, Morin R, Moore RA, Mayo M, Munro S, Wagner S, Jones SJ, Holt RA, Marra MA, Lu S, Yang S, Hartigan J, Graf M, Wagner R, Letovksy S, Pulido JC, Robison K, Esposito D, Hartley J, Wall VE, Hopkins RF, Ohara O, Wiemann S.

Genome Res. 2009 Dec;19(12):2324-33. doi: 10.1101/gr.095976.109. Epub 2009 Sep 18.


An infrastructure for interconnecting research institutions.

Buetow KH.

Drug Discov Today. 2009 Jun;14(11-12):605-10. doi: 10.1016/j.drudis.2009.03.011. Epub 2009 Apr 1. Review.


Infrastructure for a learning health care system: CaBIG.

Buetow KH, Niederhuber J.

Health Aff (Millwood). 2009 May-Jun;28(3):923-4; author reply 924-5. doi: 10.1377/hlthaff.28.3.923-a. No abstract available.


Rembrandt: helping personalized medicine become a reality through integrative translational research.

Madhavan S, Zenklusen JC, Kotliarov Y, Sahni H, Fine HA, Buetow K.

Mol Cancer Res. 2009 Feb;7(2):157-67. doi: 10.1158/1541-7786.MCR-08-0435. Epub 2009 Feb 10.


e-Science, caGrid, and Translational Biomedical Research.

Saltz J, Kurc T, Hastings S, Langella S, Oster S, Ervin D, Sharma A, Pan T, Gurcan M, Permar J, Ferreira R, Payne P, Catalyurek U, Caserta E, Leone G, Ostrowski MC, Madduri R, Foster I, Madhavan S, Buetow KH, Shanbhag K, Siegel E.

Computer (Long Beach Calif). 2008 Nov;41(11):58-66.


PID: the Pathway Interaction Database.

Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, Buetow KH.

Nucleic Acids Res. 2009 Jan;37(Database issue):D674-9. doi: 10.1093/nar/gkn653. Epub 2008 Oct 2.


Superposition of transcriptional behaviors determines gene state.

Efroni S, Carmel L, Schaefer CG, Buetow KH.

PLoS One. 2008 Aug 6;3(8):e2901. doi: 10.1371/journal.pone.0002901.


Global transcription in pluripotent embryonic stem cells.

Efroni S, Duttagupta R, Cheng J, Dehghani H, Hoeppner DJ, Dash C, Bazett-Jones DP, Le Grice S, McKay RD, Buetow KH, Gingeras TR, Misteli T, Meshorer E.

Cell Stem Cell. 2008 May 8;2(5):437-47. doi: 10.1016/j.stem.2008.03.021.


Construction of reference genetic maps.

Buetow KH.

Curr Protoc Hum Genet. 2001 May;Chapter 1:Unit 1.5. doi: 10.1002/0471142905.hg0105s01.


Systematic analysis of genetic alterations in tumors using Cancer Genome WorkBench (CGWB).

Zhang J, Finney RP, Rowe W, Edmonson M, Yang SH, Dracheva T, Jen J, Struewing JP, Buetow KH.

Genome Res. 2007 Jul;17(7):1111-7. Epub 2007 May 24.


Allele-specific chromatin immunoprecipitation studies show genetic influence on chromatin state in human genome.

Kadota M, Yang HH, Hu N, Wang C, Hu Y, Taylor PR, Buetow KH, Lee MP.

PLoS Genet. 2007 May 18;3(5):e81.


The XIST noncoding RNA functions independently of BRCA1 in X inactivation.

Xiao C, Sharp JA, Kawahara M, Davalos AR, Difilippantonio MJ, Hu Y, Li W, Cao L, Buetow K, Ried T, Chadwick BP, Deng CX, Panning B.

Cell. 2007 Mar 9;128(5):977-89.


Cancer informatics vision: caBIG.

von Eschenbach AC, Buetow K.

Cancer Inform. 2007 Feb 6;2:22-4. No abstract available.


Genome-wide loss of heterozygosity and copy number alteration in esophageal squamous cell carcinoma using the Affymetrix GeneChip Mapping 10 K array.

Hu N, Wang C, Hu Y, Yang HH, Kong LH, Lu N, Su H, Wang QH, Goldstein AM, Buetow KH, Emmert-Buck MR, Taylor PR, Lee MP.

BMC Genomics. 2006 Nov 29;7:299.


Cancers as wounds that do not heal: differences and similarities between renal regeneration/repair and renal cell carcinoma.

Riss J, Khanna C, Koo S, Chandramouli GV, Yang HH, Hu Y, Kleiner DE, Rosenwald A, Schaefer CF, Ben-Sasson SA, Yang L, Powell J, Kane DW, Star RA, Aprelikova O, Bauer K, Vasselli JR, Maranchie JK, Kohn KW, Buetow KH, Linehan WM, Weinstein JN, Lee MP, Klausner RD, Barrett JC.

Cancer Res. 2006 Jul 15;66(14):7216-24.

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