JQ6JohnQuackenbushJohn Quackenbush, Ph.D.42.33546850000000-71.1015102000000043077Quackenbush, JohnJohn Quackenbush is Professor of Computational Biology and Bioinformatics and Chair of the Department of Biostatistics at the Harvard T.H. Chan School of Public Health, Professor in the Channing Division of Network Medicine, and Professor at the Dana-Farber Cancer Institute. John's PhD was in Theoretical Physics, but in 1992 he received a fellowship to work on the Human Genome Project. This led him through the Salk Institute, Stanford, The Institute for Genomic Research (TIGR), and to Harvard in 2005. John uses massive data to probe how many small effects combine to influence human health and disease. He has more than 300 scientific papers and over 73,000 citations. Among his honors is recognition in 2013 as a White House Open Science Champion of Change.617/432-9028Henry Pickering Walcott Professor of Computational Biology and Bioinformaticscatalyst:eCommonsLogineCommons Loginprns:coAuthorOfcoauthor ofprns:endDateend dateFaculty Rankprns:fullNamefull nameprns:hasAuthorListauthor listprns:hasFacultyRankhas faculty rankprns:hasNetworkhas networkprns:hasPublicationVenuepublished inprns:informationResourceReferenceinformation resource referenceprns:isPrimaryPositionis primary positionprns:latitudelatitudeprns:longitudelongitudeprns:mainImagephotoprns:maxWeightmaximum weightprns:medlineTAjournal title abbreviationprns:meshDescriptorUIMeSH DescriptorUIprns:meshSemanticGroupNameMeSH semantic group nameprns:minWeightminimum weightprns:numberOfAuthorsnumber of authorsprns:numberOfConnectionsnumber of connectionsprns:numberOfPublicationsnumber of publicationsprns:personIdPerson IDprns:personInPrimaryPositionperson in primary positionprns:physicalNeighborOfphysical neighborprns:positionInDepartmentposition in departmentprns:positionInDivisionposition in divisionprns:predicateNodepredicate nodeprns:principalInvestigatorNameprincipal investigator nameprns:publicationDatepublication dateprns:similarTosimilar toprns:sortOrdersort orderprns:startDatestart dateprns:uniquenessWeightuniqueness weightprns:yearyearAcademic ArticleArticleDocumentbibo:pmidPubMed IdentifierAddressvivo:address1address line 1vivo:address2address line 2vivo:address3address line 3vivo:addressCitycityvivo:addressPostalCodepostal codevivo:addressStatestate or provincevivo:authorInAuthorshipselected publicationsvivo:authorRankauthor rank in publicationAuthorshipDepartmentDivisionGrantvivo:hasResearchArearesearch areasvivo:hasResearcherRoleresearch activitiesvivo:hrJobTitleHR job titleInformation Resourcevivo:linkAnchorTextlink anchor textvivo:linkedAuthorlinked authorvivo:linkedInformationResourcelinked information resourcevivo:mailingAddressmailing addressvivo:overviewoverviewvivo:personInPositionpositionsvivo:phoneNumberphonePositionvivo:positionInOrganizationposition in organizationvivo:preferredTitlepreferred titleResearcher Rolevivo:researcherRoleOfresearcher role ofvivo:roleContributesTocontributes tovivo:sponsorAwardIdsponsor award idURLLinkvivo:webpagewebpagerdf:predicatepredicaterdf:typetyperdfs:labellabelConceptAgentfoaf:firstNamefirst namefoaf:lastNamelast nameOrganizationPerson12819153Kasukawa T, Furuno M, Nikaido I, Bono H, Hume DA, Bult C, Hill DP, Baldarelli R, Gough J, Kanapin A, Matsuda H, Schriml LM, Hayashizaki Y, Okazaki Y, Quackenbush JGenome researchDevelopment and evaluation of an automated annotation pipeline and cDNA annotation system. Genome Res. 2003 Jun; 13(6B):1542-51.Genome Res2003-06-01T00:00:002003Development and evaluation of an automated annotation pipeline and cDNA annotation system.Authorship 10527331829511081Carette X, Platig J, Young DC, Helmel M, Young AT, Wang Z, Potluri LP, Moody CS, Zeng J, Prisic S, Paulson JN, Muntel J, Madduri AVR, Velarde J, Mayfield JA, Locher C, Wang T, Quackenbush J, Rhee KY, Moody DB, Steen H, Husson RNmBioMultisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface. mBio. 2018 03 06; 9(2).mBio2018-03-06T00:00:002018Multisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface.15528642Microbiology (Reading, England)An open letter on microarray data from the MGED Society. Microbiology (Reading). 2004 Nov; 150(Pt 11):3522-3524.Microbiology (Reading)2004-11-01T00:00:002004An open letter on microarray data from the MGED Society.Authorship 10539311729572535Domenyuk V, Gatalica Z, Santhanam R, Wei X, Stark A, Kennedy P, Toussaint B, Levenberg S, Wang J, Xiao N, Greil R, Rinnerthaler G, Gampenrieder SP, Heimberger AB, Berry DA, Barker A, Quackenbush J, Marshall JL, Poste G, Vacirca JL, Vidal GA, Schwartzberg LS, Halbert DD, Voss A, Magee D, Miglarese MR, Famulok M, Mayer G, Spetzler DNature communicationsPoly-ligand profiling differentiates trastuzumab-treated breast cancer patients according to their outcomes. Nat Commun. 2018 03 23; 9(1):1219.Nat Commun2018-03-23T00:00:002018Poly-ligand profiling differentiates trastuzumab-treated breast cancer patients according to their outcomes.29581134Parmar C, Barry JD, Hosny A, Quackenbush J, Aerts HJWLClinical cancer research : an official journal of the American Association for Cancer ResearchData Analysis Strategies in Medical Imaging. Clin Cancer Res. 2018 08 01; 24(15):3492-3499.Clin Cancer Res2018-03-26T00:00:002018Data Analysis Strategies in Medical Imaging.16141072Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schönbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki YScience (New York, N.Y.)The transcriptional landscape of the mammalian genome. Science. 2005 Sep 02; 309(5740):1559-63.Science2005-09-02T00:00:002005The transcriptional landscape of the mammalian genome.Authorship 1054584411244096Yuan Q, Quackenbush J, Sultana R, Pertea M, Salzberg SL, Buell CRPlant physiologyRice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species. Plant Physiol. 2001 Mar; 125(3):1166-74.Plant Physiol2001-03-01T00:00:002001Rice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species.11875039Lee Y, Sultana R, Pertea G, Cho J, Karamycheva S, Tsai J, Parvizi B, Cheung F, Antonescu V, White J, Holt I, Liang F, Quackenbush JGenome researchCross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA). Genome Res. 2002 Mar; 12(3):493-502.Genome Res2002-03-01T00:00:002002Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA).19808870Speers C, Tsimelzon A, Sexton K, Herrick AM, Gutierrez C, Culhane A, Quackenbush J, Hilsenbeck S, Chang J, Brown PClinical cancer research : an official journal of the American Association for Cancer ResearchIdentification of novel kinase targets for the treatment of estrogen receptor-negative breast cancer. Clin Cancer Res. 2009 Oct 15; 15(20):6327-40.Clin Cancer Res2009-10-06T00:00:002009Identification of novel kinase targets for the treatment of estrogen receptor-negative breast cancer.18688244Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann SNature biotechnologyPromoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol. 2008 Aug; 26(8):889-96.Nat Biotechnol2008-08-01T00:00:002008Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.19939294Quackenbush JGenome medicineData reporting standards: making the things we use better. Genome Med. 2009 Nov 25; 1(11):111.Genome Med2009-11-25T00:00:002009Data reporting standards: making the things we use better.19997620April C, Klotzle B, Royce T, Wickham-Garcia E, Boyaniwsky T, Izzo J, Cox D, Jones W, Rubio R, Holton K, Matulonis U, Quackenbush J, Fan JBPloS oneWhole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples. PLoS One. 2009 Dec 03; 4(12):e8162.PLoS One2009-12-03T00:00:002009Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples.21370078Chervitz SA, Deutsch EW, Field D, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Stoeckert CJ, Taylor CF, Taylor R, Ball CAMethods in molecular biology (Clifton, N.J.)Data standards for Omics data: the basis of data sharing and reuse. Methods Mol Biol. 2011; 719:31-69.Methods Mol Biol2011-01-01T00:00:002011Data standards for Omics data: the basis of data sharing and reuse.22110038Culhane AC, Schröder MS, Sultana R, Picard SC, Martinelli EN, Kelly C, Haibe-Kains B, Kapushesky M, St Pierre AA, Flahive W, Picard KC, Gusenleitner D, Papenhausen G, O'Connor N, Correll M, Quackenbush JNucleic acids researchGeneSigDB: a manually curated database and resource for analysis of gene expression signatures. Nucleic Acids Res. 2012 Jan; 40(Database issue):D1060-6.Nucleic Acids Res2011-11-21T00:00:002011GeneSigDB: a manually curated database and resource for analysis of gene expression signatures.Authorship 1062553229707235Padi M, Quackenbush JNPJ systems biology and applicationsDetecting phenotype-driven transitions in regulatory network structure. NPJ Syst Biol Appl. 2018; 4:16.NPJ Syst Biol Appl2018-04-19T00:00:002018Detecting phenotype-driven transitions in regulatory network structure.29777175Hosny A, Parmar C, Quackenbush J, Schwartz LH, Aerts HJWLNature reviews. CancerArtificial intelligence in radiology. Nat Rev Cancer. 2018 08; 18(8):500-510.Nat Rev Cancer2018-08-01T00:00:002018Artificial intelligence in radiology.17332024Song JS, Maghsoudi K, Li W, Fox E, Quackenbush J, Shirley Liu XBioinformatics (Oxford, England)Microarray blob-defect removal improves array analysis. Bioinformatics. 2007 Apr 15; 23(8):966-71.Bioinformatics2007-03-01T00:00:002007Microarray blob-defect removal improves array analysis.Authorship 10658913Authorship 1065043529765148Kuijjer ML, Paulson JN, Salzman P, Ding W, Quackenbush JBritish journal of cancerCancer subtype identification using somatic mutation data. Br J Cancer. 2018 05; 118(11):1492-1501.Br J Cancer2018-05-16T00:00:002018Cancer subtype identification using somatic mutation data.16902087Bruggmann R, Bharti AK, Gundlach H, Lai J, Young S, Pontaroli AC, Wei F, Haberer G, Fuks G, Du C, Raymond C, Estep MC, Liu R, Bennetzen JL, Chan AP, Rabinowicz PD, Quackenbush J, Barbazuk WB, Wing RA, Birren B, Nusbaum C, Rounsley S, Mayer KF, Messing JGenome researchUneven chromosome contraction and expansion in the maize genome. Genome Res. 2006 Oct; 16(10):1241-51.Genome Res2006-08-10T00:00:002006Uneven chromosome contraction and expansion in the maize genome.18697859Kitami T, Rubio R, O'Brien W, Quackenbush J, Nadeau JHPhysiological genomicsGene-environment interactions reveal a homeostatic role for cholesterol metabolism during dietary folate perturbation in mice. Physiol Genomics. 2008 Oct 08; 35(2):182-90.Physiol Genomics2008-08-12T00:00:002008Gene-environment interactions reveal a homeostatic role for cholesterol metabolism during dietary folate perturbation in mice.18846086Kahvejian A, Quackenbush J, Thompson JFNature biotechnologyWhat would you do if you could sequence everything? Nat Biotechnol. 2008 Oct; 26(10):1125-33.Nat Biotechnol2008-10-01T00:00:002008What would you do if you could sequence everything?19204204Parker JS, Mullins M, Cheang MC, Leung S, Voduc D, Vickery T, Davies S, Fauron C, He X, Hu Z, Quackenbush JF, Stijleman IJ, Palazzo J, Marron JS, Nobel AB, Mardis E, Nielsen TO, Ellis MJ, Perou CM, Bernard PSJournal of clinical oncology : official journal of the American Society of Clinical OncologySupervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol. 2009 Mar 10; 27(8):1160-7.J Clin Oncol2009-02-09T00:00:002009Supervised risk predictor of breast cancer based on intrinsic subtypes.12074166Andersson T, Unneberg P, Nilsson P, Odeberg J, Quackenbush J, Lundeberg JBioTechniquesMonitoring of representational difference analysis subtraction procedures by global microarrays. Biotechniques. 2002 Jun; 32(6):1348-50, 1352, 1354-6, 1358.Biotechniques2002-06-01T00:00:002002Monitoring of representational difference analysis subtraction procedures by global microarrays.12429061Yang IV, Chen E, Hasseman JP, Liang W, Frank BC, Wang S, Sharov V, Saeed AI, White J, Li J, Lee NH, Yeatman TJ, Quackenbush JGenome biologyWithin the fold: assessing differential expression measures and reproducibility in microarray assays. Genome Biol. 2002 Oct 24; 3(11):research0062.Genome Biol2002-10-24T00:00:002002Within the fold: assessing differential expression measures and reproducibility in microarray assays.14593198Brentani H, Caballero OL, Camargo AA, da Silva AM, da Silva WA, Dias Neto E, Grivet M, Gruber A, Guimaraes PE, Hide W, Iseli C, Jongeneel CV, Kelso J, Nagai MA, Ojopi EP, Osorio EC, Reis EM, Riggins GJ, Simpson AJ, de Souza S, Stevenson BJ, Strausberg RL, Tajara EH, Verjovski-Almeida S, Acencio ML, Bengtson MH, Bettoni F, Bodmer WF, Briones MR, Camargo LP, Cavenee W, Cerutti JM, Coelho Andrade LE, Costa dos Santos PC, Ramos Costa MC, da Silva IT, Estécio MR, Sa Ferreira K, Furnari FB, Faria M, Galante PA, Guimaraes GS, Holanda AJ, Kimura ET, Leerkes MR, Lu X, Maciel RM, Martins EA, Massirer KB, Melo AS, Mestriner CA, Miracca EC, Miranda LL, Nobrega FG, Oliveira PS, Paquola AC, Pandolfi JR, Campos Pardini MI, Passetti F, Quackenbush J, Schnabel B, Sogayar MC, Souza JE, Valentini SR, Zaiats AC, Amaral EJ, Arnaldi LA, de Araújo AG, de Bessa SA, Bicknell DC, Ribeiro de Camaro ME, Carraro DM, Carrer H, Carvalho AF, Colin C, Costa F, Curcio C, Guerreiro da Silva ID, Pereira da Silva N, Dellamano M, El-Dorry H, Espreafico EM, Scattone Ferreira AJ, Ayres Ferreira C, Fortes MA, Gama AH, Giannella-Neto D, Giannella ML, Giorgi RR, Goldman GH, Goldman MH, Hackel C, Ho PL, Kimura EM, Kowalski LP, Krieger JE, Leite LC, Lopes A, Luna AM, Mackay A, Mari SK, Marques AA, Martins WK, Montagnini A, Mourão Neto M, Nascimento AL, Neville AM, Nobrega MP, O'Hare MJ, Otsuka AY, Ruas de Melo AI, Paco-Larson ML, Guimarães Pereira G, Pereira da Silva N, Pesquero JB, Pessoa JG, Rahal P, Rainho CA, Rodrigues V, Rogatto SR, Romano CM, Romeiro JG, Rossi BM, Rusticci M, Guerra de Sá R, Sant' Anna SC, Sarmazo ML, Silva TC, Soares FA, Sonati Mde F, de Freitas Sousa J, Queiroz D, Valente V, Vettore AL, Villanova FE, Zago MA, Zalcberg HProceedings of the National Academy of Sciences of the United States of AmericaThe generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags. Proc Natl Acad Sci U S A. 2003 Nov 11; 100(23):13418-23.Proc Natl Acad Sci U S A2003-10-30T00:00:002003The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags.14744111Agrawal D, Chen T, Irby R, Quackenbush J, Chambers AF, Szabo M, Cantor A, Coppola D, Yeatman TJComptes rendus biologiesOsteopontin identified as colon cancer tumor progression marker. C R Biol. 2003 Oct-Nov; 326(10-11):1041-3.C R Biol2003-10-01T00:00:002003Osteopontin identified as colon cancer tumor progression marker.22253616Cannon EK, Birkett SM, Braun BL, Kodavali S, Jennewein DM, Yilmaz A, Antonescu V, Antonescu C, Harper LC, Gardiner JM, Schaeffer ML, Campbell DA, Andorf CM, Andorf D, Lisch D, Koch KE, McCarty DR, Quackenbush J, Grotewold E, Lushbough CM, Sen TZ, Lawrence CJInternational journal of plant genomicsPOPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data. Int J Plant Genomics. 2011; 2011:923035.Int J Plant Genomics2011-12-27T00:00:002011POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data.22789589Gusenleitner D, Howe EA, Bentink S, Quackenbush J, Culhane ACBioinformatics (Oxford, England)iBBiG: iterative binary bi-clustering of gene sets. Bioinformatics. 2012 Oct 01; 28(19):2484-92.Bioinformatics2012-07-12T00:00:002012iBBiG: iterative binary bi-clustering of gene sets.22823907Fountzilas E, Kelly AD, Perez-Atayde AR, Goldsmith J, Konstantinopoulos PA, Francoeur N, Correll M, Rubio R, Hu L, Gebhardt MC, Quackenbush J, Spentzos DBMC genomicsA microRNA activity map of human mesenchymal tumors: connections to oncogenic pathways; an integrative transcriptomic study. BMC Genomics. 2012 Jul 23; 13:332.BMC Genomics2012-07-23T00:00:002012A microRNA activity map of human mesenchymal tumors: connections to oncogenic pathways; an integrative transcriptomic study.15126644Larkin JE, Frank BC, Gaspard RM, Duka I, Gavras H, Quackenbush JPhysiological genomicsCardiac transcriptional response to acute and chronic angiotensin II treatments. Physiol Genomics. 2004 Jul 08; 18(2):152-66.Physiol Genomics2004-07-08T00:00:002004Cardiac transcriptional response to acute and chronic angiotensin II treatments.22912389Wang ZC, Birkbak NJ, Culhane AC, Drapkin R, Fatima A, Tian R, Schwede M, Alsop K, Daniels KE, Piao H, Liu J, Etemadmoghadam D, Miron A, Salvesen HB, Mitchell G, DeFazio A, Quackenbush J, Berkowitz RS, Iglehart JD, Bowtell DD, Matulonis UAClinical cancer research : an official journal of the American Association for Cancer ResearchProfiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome. Clin Cancer Res. 2012 Oct 15; 18(20):5806-15.Clin Cancer Res2012-08-21T00:00:002012Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome.15846360Larkin JE, Frank BC, Gavras H, Sultana R, Quackenbush JNature methodsIndependence and reproducibility across microarray platforms. Nat Methods. 2005 May; 2(5):337-44.Nat Methods2005-04-21T00:00:002005Independence and reproducibility across microarray platforms.16085323Cui L, Fan Q, Hu Y, Karamycheva SA, Quackenbush J, Khuntirat B, Sattabongkot J, Carlton JMMolecular and biochemical parasitologyGene discovery in Plasmodium vivax through sequencing of ESTs from mixed blood stages. Mol Biochem Parasitol. 2005 Nov; 144(1):1-9.Mol Biochem Parasitol2005-11-01T00:00:002005Gene discovery in Plasmodium vivax through sequencing of ESTs from mixed blood stages.16511469Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden NNatureTop-down standards will not serve systems biology. Nature. 2006 Mar 02; 440(7080):24.Nature2006-03-02T00:00:002006Top-down standards will not serve systems biology.16901212Brooksbank C, Quackenbush JOmics : a journal of integrative biologyData standards: a call to action. OMICS. 2006; 10(2):94-9.OMICS2006-01-01T00:00:002006Data standards: a call to action.17087822Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma ABMC bioinformaticsA simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics. 2006 Nov 06; 7:489.BMC Bioinformatics2006-11-06T00:00:002006A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.18413601Taoufik E, Petit E, Divoux D, Tseveleki V, Mengozzi M, Roberts ML, Valable S, Ghezzi P, Quackenbush J, Brines M, Cerami A, Probert LProceedings of the National Academy of Sciences of the United States of AmericaTNF receptor I sensitizes neurons to erythropoietin- and VEGF-mediated neuroprotection after ischemic and excitotoxic injury. Proc Natl Acad Sci U S A. 2008 Apr 22; 105(16):6185-90.Proc Natl Acad Sci U S A2008-04-14T00:00:002008TNF receptor I sensitizes neurons to erythropoietin- and VEGF-mediated neuroprotection after ischemic and excitotoxic injury.18642945Aryee MJ, Quackenbush JJournal of proteome researchAn optimized predictive strategy for interactome mapping. J Proteome Res. 2008 Sep; 7(9):4089-94.J Proteome Res2008-07-22T00:00:002008An optimized predictive strategy for interactome mapping.21543491Gewurz BE, Mar JC, Padi M, Zhao B, Shinners NP, Takasaki K, Bedoya E, Zou JY, Cahir-McFarland E, Quackenbush J, Kieff EJournal of virologyCanonical NF-kappaB activation is essential for Epstein-Barr virus latent membrane protein 1 TES2/CTAR2 gene regulation. J Virol. 2011 Jul; 85(13):6764-73.J Virol2011-05-04T00:00:002011Canonical NF-kappaB activation is essential for Epstein-Barr virus latent membrane protein 1 TES2/CTAR2 gene regulation.16626501Perreard L, Fan C, Quackenbush JF, Mullins M, Gauthier NP, Nelson E, Mone M, Hansen H, Buys SS, Rasmussen K, Orrico AR, Dreher D, Walters R, Parker J, Hu Z, He X, Palazzo JP, Olopade OI, Szabo A, Perou CM, Bernard PSBreast cancer research : BCRClassification and risk stratification of invasive breast carcinomas using a real-time quantitative RT-PCR assay. Breast Cancer Res. 2006; 8(2):R23.Breast Cancer Res2006-04-20T00:00:002006Classification and risk stratification of invasive breast carcinomas using a real-time quantitative RT-PCR assay.16939790Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, Li J, Thiagarajan M, White JA, Quackenbush JMethods in enzymologyTM4 microarray software suite. Methods Enzymol. 2006; 411:134-93.Methods Enzymol2006-01-01T00:00:002006TM4 microarray software suite.Authorship 111012718287690Chan AP, Rabinowicz PD, Quackenbush J, Buell CR, Town CDMethods in molecular biology (Clifton, N.J.)Plant database resources at The Institute for Genomic Research. Methods Mol Biol. 2007; 406:113-36.Methods Mol Biol2007-01-01T00:00:002007Plant database resources at The Institute for Genomic Research.22194627Milbury CA, Correll M, Quackenbush J, Rubio R, Makrigiorgos GMClinical chemistryCOLD-PCR enrichment of rare cancer mutations prior to targeted amplicon resequencing. Clin Chem. 2012 Mar; 58(3):580-9.Clin Chem2011-12-21T00:00:002011COLD-PCR enrichment of rare cancer mutations prior to targeted amplicon resequencing.Authorship 114139219552933Hellner K, Mar J, Fang F, Quackenbush J, Münger KVirologyHPV16 E7 oncogene expression in normal human epithelial cells causes molecular changes indicative of an epithelial to mesenchymal transition. Virology. 2009 Aug 15; 391(1):57-63.Virology2009-06-23T00:00:002009HPV16 E7 oncogene expression in normal human epithelial cells causes molecular changes indicative of an epithelial to mesenchymal transition.19934259Culhane AC, Schwarzl T, Sultana R, Picard KC, Picard SC, Lu TH, Franklin KR, French SJ, Papenhausen G, Correll M, Quackenbush JNucleic acids researchGeneSigDB--a curated database of gene expression signatures. Nucleic Acids Res. 2010 Jan; 38(Database issue):D716-25.Nucleic Acids Res2009-11-24T00:00:002009GeneSigDB--a curated database of gene expression signatures.20041215Mar JC, Quackenbush JPLoS computational biologyDecomposition of gene expression state space trajectories. PLoS Comput Biol. 2009 Dec; 5(12):e1000626.PLoS Comput Biol2009-12-24T00:00:002009Decomposition of gene expression state space trajectories.22355044Skiadas CC, Duan S, Correll M, Rubio R, Karaca N, Ginsburg ES, Quackenbush J, Racowsky CMolecular human reproductionOvarian reserve status in young women is associated with altered gene expression in membrana granulosa cells. Mol Hum Reprod. 2012 Jul; 18(7):362-71.Mol Hum Reprod2012-02-20T00:00:002012Ovarian reserve status in young women is associated with altered gene expression in membrana granulosa cells.Authorship 119622118434084Chittenden TW, Howe EA, Culhane AC, Sultana R, Taylor JM, Holmes C, Quackenbush JGenomicsFunctional classification analysis of somatically mutated genes in human breast and colorectal cancers. Genomics. 2008 Jun; 91(6):508-11.Genomics2008-04-22T00:00:002008Functional classification analysis of somatically mutated genes in human breast and colorectal cancers.18958862Dutta B, Kanani H, Quackenbush J, Klapa MIBiotechnology and bioengineeringTime-series integrated "omic" analyses to elucidate short-term stress-induced responses in plant liquid cultures. Biotechnol Bioeng. 2009 Jan 01; 102(1):264-279.Biotechnol Bioeng2009-01-01T00:00:002009Time-series integrated "omic" analyses to elucidate short-term stress-induced responses in plant liquid cultures.30240647Barry JD, Fagny M, Paulson JN, Aerts HJWL, Platig J, Quackenbush JiScienceHistopathological Image QTL Discovery of Immune Infiltration Variants. iScience. 2018 Jul 27; 5:80-89.iScience2018-07-06T00:00:002018Histopathological Image QTL Discovery of Immune Infiltration Variants.Authorship 10943276CL325CamilaLopes-RamosCamila Miranda Lopes-Ramos, Ph.D.140526Lopes-Ramos, CamilaInstructor in MedicineAuthorship 1097140730275053Lopes-Ramos CM, Kuijjer ML, Ogino S, Fuchs CS, DeMeo DL, Glass K, Quackenbush JCancer researchGene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. Cancer Res. 2018 10 01; 78(19):5538-5547.Cancer Res2018-10-01T00:00:002018Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism.15917849Pinent M, Bladé MC, Salvadó MJ, Arola L, Hackl H, Quackenbush J, Trajanoski Z, Ardévol AInternational journal of obesity (2005)Grape-seed derived procyanidins interfere with adipogenesis of 3T3-L1 cells at the onset of differentiation. Int J Obes (Lond). 2005 Aug; 29(8):934-41.Int J Obes (Lond)2005-08-01T00:00:002005Grape-seed derived procyanidins interfere with adipogenesis of 3T3-L1 cells at the onset of differentiation.16381977Chan AP, Pertea G, Cheung F, Lee D, Zheng L, Whitelaw C, Pontaroli AC, SanMiguel P, Yuan Y, Bennetzen J, Barbazuk WB, Quackenbush J, Rabinowicz PDNucleic acids researchThe TIGR Maize Database. Nucleic Acids Res. 2006 Jan 01; 34(Database issue):D771-6.Nucleic Acids Res2006-01-01T00:00:002006The TIGR Maize Database.19202193Bateman A, Quackenbush JBioinformatics (Oxford, England)Bioinformatics for next generation sequencing. Bioinformatics. 2009 Feb 15; 25(4):429.Bioinformatics2009-02-08T00:00:002009Bioinformatics for next generation sequencing.19936203Santagata S, Maire CL, Idbaih A, Geffers L, Correll M, Holton K, Quackenbush J, Ligon KLPloS oneCRX is a diagnostic marker of retinal and pineal lineage tumors. PLoS One. 2009 Nov 20; 4(11):e7932.PLoS One2009-11-20T00:00:002009CRX is a diagnostic marker of retinal and pineal lineage tumors.Authorship 132895111691794Hegde P, Qi R, Gaspard R, Abernathy K, Dharap S, Earle-Hughes J, Gay C, Nwokekeh NU, Chen T, Saeed AI, Sharov V, Lee NH, Yeatman TJ, Quackenbush JCancer researchIdentification of tumor markers in models of human colorectal cancer using a 19,200-element complementary DNA microarray. 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Mamm Genome. 2002 Jul; 13(7):373-9.Mamm Genome2002-07-01T00:00:002002Analysis of bovine mammary gland EST and functional annotation of the Bos taurus gene index.16683036Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, Engström PG, Lenhard B, Aturaliya RN, Batalov S, Beisel KW, Bult CJ, Fletcher CF, Forrest AR, Furuno M, Hill D, Itoh M, Kanamori-Katayama M, Katayama S, Katoh M, Kawashima T, Quackenbush J, Ravasi T, Ring BZ, Shibata K, Sugiura K, Takenaka Y, Teasdale RD, Wells CA, Zhu Y, Kai C, Kawai J, Hume DA, Carninci P, Hayashizaki YPLoS geneticsTranscript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet. 2006 Apr; 2(4):e62.PLoS Genet2006-04-01T00:00:002006Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.16887002Quackenbush JAnimal geneticsFrom 'omes to biology. Anim Genet. 2006 Aug; 37 Suppl 1:48-56.Anim Genet2006-08-01T00:00:002006From 'omes to biology.17468134Raj JU, Aliferis C, Caprioli RM, Cowley AW, Davies PF, Duncan MW, Erle DJ, Erzurum SC, Finn PW, Ischiropoulos H, Kaminski N, Kleeberger SR, Leikauf GD, Loyd JE, Martin TR, Matalon S, Moore JH, Quackenbush J, Sabo-Attwood T, Shapiro SD, Schnitzer JE, Schwartz DA, Schwiebert LM, Sheppard D, Ware LB, Weiss ST, Whitsett JA, Wurfel MM, Matthay MAAmerican journal of physiology. Lung cellular and molecular physiologyGenomics and proteomics of lung disease: conference summary. Am J Physiol Lung Cell Mol Physiol. 2007 Jul; 293(1):L45-51.Am J Physiol Lung Cell Mol Physiol2007-04-27T00:00:002007Genomics and proteomics of lung disease: conference summary.18428690Lee Y, Quackenbush JCurrent protocols in bioinformaticsUsing the TIGR gene index databases for biological discovery. Curr Protoc Bioinformatics. 2003 Nov; Chapter 1:Unit 1.6.Curr Protoc Bioinformatics2003-11-01T00:00:002003Using the TIGR gene index databases for biological discovery.18601736Djebbari A, Quackenbush JBMC systems biologySeeded Bayesian Networks: constructing genetic networks from microarray data. BMC Syst Biol. 2008 Jul 04; 2:57.BMC Syst Biol2008-07-04T00:00:002008Seeded Bayesian Networks: constructing genetic networks from microarray data.19240299Fedorov VB, Goropashnaya AV, Tøien Ø, Stewart NC, Gracey AY, Chang C, Qin S, Pertea G, Quackenbush J, Showe LC, Showe MK, Boyer BB, Barnes BMPhysiological genomicsElevated expression of protein biosynthesis genes in liver and muscle of hibernating black bears (Ursus americanus). Physiol Genomics. 2009 04 10; 37(2):108-18.Physiol Genomics2009-02-24T00:00:002009Elevated expression of protein biosynthesis genes in liver and muscle of hibernating black bears (Ursus americanus).19723662Culhane AC, Quackenbush JCancer researchConfounding effects in "A six-gene signature predicting breast cancer lung metastasis". Cancer Res. 2009 Sep 15; 69(18):7480-5.Cancer Res2009-09-01T00:00:002009Confounding effects in "A six-gene signature predicting breast cancer lung metastasis".21037082Tanaka N, Huttenhower C, Nosho K, Baba Y, Shima K, Quackenbush J, Haigis KM, Giovannucci E, Fuchs CS, Ogino SThe American journal of pathologyNovel application of structural equation modeling to correlation structure analysis of CpG island methylation in colorectal cancer. Am J Pathol. 2010 Dec; 177(6):2731-40.Am J Pathol2010-10-29T00:00:002010Novel application of structural equation modeling to correlation structure analysis of CpG island methylation in colorectal cancer.21852951Mar JC, Matigian NA, Mackay-Sim A, Mellick GD, Sue CM, Silburn PA, McGrath JJ, Quackenbush J, Wells CAPLoS geneticsVariance of gene expression identifies altered network constraints in neurological disease. PLoS Genet. 2011 Aug; 7(8):e1002207.PLoS Genet2011-08-11T00:00:002011Variance of gene expression identifies altered network constraints in neurological disease.22247278Chittenden TW, Howe EA, Taylor JM, Mar JC, Aryee MJ, Gómez H, Sultana R, Braisted J, Nair SJ, Quackenbush J, Holmes CBioinformatics (Oxford, England)nEASE: a method for gene ontology subclassification of high-throughput gene expression data. Bioinformatics. 2012 Mar 01; 28(5):726-8.Bioinformatics2012-01-13T00:00:002012nEASE: a method for gene ontology subclassification of high-throughput gene expression data.Authorship 11224381030592451Hersh CP, Adcock IM, Celedón JC, Cho MH, Christiani DC, Himes BE, Kaminski N, Mathias RA, Meyers DA, Quackenbush J, Redline S, Steiling KA, Tabor HK, Tobin MD, Wurfel MM, Yang IV, Koppelman GHAnnals of the American Thoracic SocietyHigh-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report. Ann Am Thorac Soc. 2019 01; 16(1):1-16.Ann Am Thorac Soc2019-01-01T00:00:002019High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report.Authorship 114685211493695Kappe SH, Gardner MJ, Brown SM, Ross J, Matuschewski K, Ribeiro JM, Adams JH, Quackenbush J, Cho J, Carucci DJ, Hoffman SL, Nussenzweig VProceedings of the National Academy of Sciences of the United States of AmericaExploring the transcriptome of the malaria sporozoite stage. Proc Natl Acad Sci U S A. 2001 Aug 14; 98(17):9895-900.Proc Natl Acad Sci U S A2001-08-07T00:00:002001Exploring the transcriptome of the malaria sporozoite stage.12664684Dudoit S, Gentleman RC, Quackenbush JBioTechniquesOpen source software for the analysis of microarray data. Biotechniques. 2003 Mar; Suppl:45-51.Biotechniques2003-03-01T00:00:002003Open source software for the analysis of microarray data.2025-08-31QUACKENBUSH, JOHN2018-09-01Unraveling the Complexities of Risk and Mechanism in CancerR35CA220523Principal Investigator15122299Quackenbush JNature biotechnologyData standards for 'omic' science. Nat Biotechnol. 2004 May; 22(5):613-4.Nat Biotechnol2004-05-01T00:00:002004Data standards for 'omic' science.16415889Malek RL, Wang HY, Kwitek AE, Greene AS, Bhagabati N, Borchardt G, Cahill L, Currier T, Frank B, Fu X, Hasinoff M, Howe E, Letwin N, Luu TV, Saeed A, Sajadi H, Salzberg SL, Sultana R, Thiagarajan M, Tsai J, Veratti K, White J, Quackenbush J, Jacob HJ, Lee NHNature geneticsPhysiogenomic resources for rat models of heart, lung and blood disorders. Nat Genet. 2006 Feb; 38(2):234-9.Nat Genet2006-01-15T00:00:002006Physiogenomic resources for rat models of heart, lung and blood disorders.16766564Quackenbush J, Salzberg SLBioinformatics (Oxford, England)It is time to end the patenting of software. Bioinformatics. 2006 Jun 15; 22(12):1416-7.Bioinformatics2006-06-15T00:00:002006It is time to end the patenting of software.17102808Quackenbush JMolecular systems biologyWeighing our measures of gene expression. Mol Syst Biol. 2006; 2:63.Mol Syst Biol2006-11-14T00:00:002006Weighing our measures of gene expression.17449816Quackenbush JThe Journal of experimental biologyExtracting biology from high-dimensional biological data. J Exp Biol. 2007 May; 210(Pt 9):1507-17.J Exp Biol2007-05-01T00:00:002007Extracting biology from high-dimensional biological data.20205187Antonescu C, Antonescu V, Sultana R, Quackenbush JCurrent protocols in bioinformaticsUsing the DFCI gene index databases for biological discovery. Curr Protoc Bioinformatics. 2010 Mar; Chapter 1:Unit1.6.1-36.Curr Protoc Bioinformatics2010-03-01T00:00:002010Using the DFCI gene index databases for biological discovery.20540791Colak D, Chishti MA, Al-Bakheet AB, Al-Qahtani A, Shoukri MM, Goyns MH, Ozand PT, Quackenbush J, Park BH, Kaya NMolecular cancerIntegrative and comparative genomics analysis of early hepatocellular carcinoma differentiated from liver regeneration in young and old. Mol Cancer. 2010 Jun 12; 9:146.Mol Cancer2010-06-12T00:00:002010Integrative and comparative genomics analysis of early hepatocellular carcinoma differentiated from liver regeneration in young and old.21828086Sathirapongsasuti JF, Lee H, Horst BA, Brunner G, Cochran AJ, Binder S, Quackenbush J, Nelson SFBioinformatics (Oxford, England)Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics. 2011 Oct 01; 27(19):2648-54.Bioinformatics2011-08-09T00:00:002011Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.Authorship 1114806Authorship 11700212Authorship 1138729530864334Garmire LX, Yuan GC, Fan R, Yeo GW, Quackenbush JPacific Symposium on Biocomputing. Pacific Symposium on BiocomputingSINGLE CELL ANALYSIS, WHAT IS IN THE FUTURE? Pac Symp Biocomput. 2019; 24:332-337.Pac Symp Biocomput2019-01-01T00:00:002019SINGLE CELL ANALYSIS, WHAT IS IN THE FUTURE?Authorship 1228957D053263Physiology88717060.51988Gene Regulatory NetworksD020411DevicesProcedures143939220.515471Oligonucleotide Array Sequence AnalysisD030541Concepts & Ideas79017770.578496Databases, GeneticD020869Concepts & IdeasGenes & Molecular SequencesProcedures290093870.309717Gene Expression ProfilingAuthorship 11456124Authorship 1144167730981959Kuijjer ML, Tung MG, Yuan G, Quackenbush J, Glass KiScienceEstimating Sample-Specific Regulatory Networks. iScience. 2019 Apr 26; 14:226-240.iScience2019-03-28T00:00:002019Estimating Sample-Specific Regulatory Networks.30987980Lopes-Ramos CM, Kuijjer ML, Ogino S, Fuchs CS, DeMeo DL, Glass K, Quackenbush JCancer researchCorrection: Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. Cancer Res. 2019 Apr 15; 79(8):2084.Cancer Res2019-04-15T00:00:002019Correction: Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism.D019295Occupations148035060.404415Computational BiologyAuthorship 11515774Authorship 11519901831069578Campbell PT, Ambrosone CB, Nishihara R, Aerts HJWL, Bondy M, Chatterjee N, Garcia-Closas M, Giannakis M, Golden JA, Heng YJ, Kip NS, Koshiol J, Liu XS, Lopes-Ramos CM, Mucci LA, Nowak JA, Phipps AI, Quackenbush J, Schoen RE, Sholl LM, Tamimi RM, Wang M, Weijenberg MP, Wu CJ, Wu K, Yao S, Yu KH, Zhang X, Rebbeck TR, Ogino SCancer causes & control : CCCProceedings of the fourth international molecular pathological epidemiology (MPE) meeting. Cancer Causes Control. 2019 Aug; 30(8):799-811.Cancer Causes Control2019-05-08T00:00:002019Proceedings of the fourth international molecular pathological epidemiology (MPE) meeting.31062858Gaynor SM, Sun R, Lin X, Quackenbush JBioinformatics (Oxford, England)Identification of differentially expressed gene sets using the Generalized Berk-Jones statistic. Bioinformatics. 2019 11 01; 35(22):4568-4576.Bioinformatics2019-11-01T00:00:002019Identification of differentially expressed gene sets using the Generalized Berk-Jones statistic.BiostatisticsGeneticsMedicineRadiation OncologyWyss InstituteChanning Division of Network MedicineBrigham and Women's HospitalDana-Farber Cancer InstituteHarvard Medical SchoolHarvard T.H. Chan School of Public HealthHarvard UniversityGMC2GeorgeChurchGeorge McDonald Church, Ph.D.42.33837200000000-71.1032690000000021797Church, GeorgeRobert Winthrop Professor of GeneticsISK1ZakKohaneZak Kohane, M.D.,Ph.D.42.33743600000000-71.1054470000000025477Kohane, ZakMarion V. Nelson Professor of Biomedical Informatics11323selected publications5.339670.00448809903research areas3.639380.00934439180coauthor of76.471324.905260similar toTM33ThomasMangioneThomas William Mangione, Ph.D.42.33546850000000-71.1015102000000064751Mangione, ThomasInstructorLMR9LouiseRyanLouise Marie Ryan, Ph.D.42.33546850000000-71.1015102000000077364Ryan, LouiseAdjunct Professor of BiostatisticsDLD1DawnDemeoDawn Lisa Demeo, M.D.42.33669100000000-71.1020890000000024539Demeo, DawnAssociate Professor of MedicineCH132CurtisHuttenhowerCurtis Huttenhower, Ph.D.42.33546850000000-71.1015102000000016016Huttenhower, CurtisProfessor of Computational Biology and BioinformaticsJJC4JamesCollinsJames J. Collins, Ph.D.42.33594500000000-71.1029580000000055767Collins, JamesVisiting Professor of Systems Biology in the Wyss InstituteFD27FrancescaDominiciFrancesca Dominici, Ph.D.42.33546850000000-71.1015102000000045147Dominici, FrancescaClarence James Gamble Professor of Biostatistics, Population, and Data ScienceAGR5AndreaRotnitzkyAndrea Gloria Rotnitzky, Ph.D.42.33546850000000-71.1015102000000042041Rotnitzky, AndreaAdjunct Professor of BiostatisticsPJP8PeterParkPeter Park, Ph.D.42.33837200000000-71.1032690000000062138Park, PeterProfessor of Biomedical InformaticsHA62HugoAertsHugo Aerts, Ph.D.100404Aerts, HugoAssociate Professor of Radiation OncologyAuthorship 1173711331285997Millington AL, Houskeeper JA, Quackenbush JF, Trauba JM, Wittwer CTBiomolecular detection and quantificationThe kinetic requirements of extreme qPCR. Biomol Detect Quantif. 2019 Mar; 17:100081.Biomol Detect Quantif2019-03-13T00:00:002019The kinetic requirements of extreme qPCR.Authorship 13215Authorship 14375728Authorship 11797101231389890Lozano Calderón SA, Garbutt C, Kim J, Lietz CE, Chen YL, Bernstein K, Chebib I, Nielsen GP, Deshpande V, Rubio R, Wang YE, Quackenbush J, Delaney T, Raskin K, Schwab J, Cote G, Spentzos DClinical orthopaedics and related researchClinical and Molecular Analysis of Pathologic Fracture-associated Osteosarcoma: MicroRNA profile Is Different and Correlates with Prognosis. Clin Orthop Relat Res. 2019 Sep; 477(9):2114-2126.Clin Orthop Relat Res2019-09-01T00:00:002019Clinical and Molecular Analysis of Pathologic Fracture-associated Osteosarcoma: MicroRNA profile Is Different and Correlates with Prognosis.Authorship 135622102024-08-31QUACKENBUSH, JOHN2019-09-01WebMeV: A Robust Platform for Intuitive Genomic Data AnalysisU24CA231846Principal InvestigatorAuthorship 11940715Authorship 1099248Authorship 11197817Authorship 11993123Authorship 1199491331639475Altenbuchinger M, Weihs A, Quackenbush J, Grabe HJ, Zacharias HUBiochimica et biophysica acta. Gene regulatory mechanismsGaussian and Mixed Graphical Models as (multi-)omics data analysis tools. Biochim Biophys Acta Gene Regul Mech. 2020 06; 1863(6):194418.Biochim Biophys Acta Gene Regul Mech2019-10-19T00:00:002019Gaussian and Mixed Graphical Models as (multi-)omics data analysis tools.31653243Kuijjer ML, Hsieh PH, Quackenbush J, Glass KBMC cancerlionessR: single sample network inference in R. BMC Cancer. 2019 Oct 25; 19(1):1003.BMC Cancer2019-10-25T00:00:002019lionessR: single sample network inference in R.Authorship 1205834531723161St Hilaire MA, Kristal BS, Rahman SA, Sullivan JP, Quackenbush J, Duffy JF, Barger LK, Gooley JJ, Czeisler CA, Lockley SWScientific reportsUsing a Single Daytime Performance Test to Identify Most Individuals at High-Risk for Performance Impairment during Extended Wake. Sci Rep. 2019 11 13; 9(1):16681.Sci Rep2019-11-13T00:00:002019Using a Single Daytime Performance Test to Identify Most Individuals at High-Risk for Performance Impairment during Extended Wake.true1Associate Professor of Radiation OncologyAssociate Professor of Radiation Oncologytrue1Associate Professor of MedicineAssociate Professor of MedicineAuthorship 12880610Authorship 1206648531806877Fagny M, Platig J, Kuijjer ML, Lin X, Quackenbush JBritish journal of cancerNongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function. Br J Cancer. 2020 02; 122(4):569-577.Br J Cancer2019-12-06T00:00:002019Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function.RAI3Rafael A.IrizarryRafael A. Irizarry, Ph.D.117919Irizarry, Rafael A.Professor of BiostatisticsAuthorship 12132861031871106Schwede M, Waldron L, Mok SC, Wei W, Basunia A, Merritt MA, Mitsiades CS, Parmigiani G, Harrington DP, Quackenbush J, Birrer MJ, Culhane ACCancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive OncologyThe Impact of Stroma Admixture on Molecular Subtypes and Prognostic Gene Signatures in Serous Ovarian Cancer. Cancer Epidemiol Biomarkers Prev. 2020 02; 29(2):509-519.Cancer Epidemiol Biomarkers Prev2019-12-23T00:00:002019The Impact of Stroma Admixture on Molecular Subtypes and Prognostic Gene Signatures in Serous Ovarian Cancer.Authorship 11893423Authorship 1222092731995399Morrow JD, Make B, Regan E, Han M, Hersh CP, Tal-Singer R, Quackenbush J, Choi AMK, Silverman EK, DeMeo DLAmerican journal of respiratory and critical care medicineDNA Methylation Is Predictive of Mortality in Current and Former Smokers. Am J Respir Crit Care Med. 2020 05 01; 201(9):1099-1109.Am J Respir Crit Care Med2020-05-01T00:00:002020DNA Methylation Is Predictive of Mortality in Current and Former Smokers.Authorship 1628665Authorship 12320961632157112Lietz CE, Garbutt C, Barry WT, Deshpande V, Chen YL, Lozano-Calderon SA, Wang Y, Lawney B, Ebb D, Cote GM, Duan Z, Hornicek FJ, Choy E, Petur Nielsen G, Haibe-Kains B, Quackenbush J, Spentzos DScientific reportsMicroRNA-mRNA networks define translatable molecular outcome phenotypes in osteosarcoma. Sci Rep. 2020 03 10; 10(1):4409.Sci Rep2020-03-10T00:00:002020MicroRNA-mRNA networks define translatable molecular outcome phenotypes in osteosarcoma.32307915Silverman EK, Schmidt HHHW, Anastasiadou E, Altucci L, Angelini M, Badimon L, Balligand JL, Benincasa G, Capasso G, Conte F, Di Costanzo A, Farina L, Fiscon G, Gatto L, Gentili M, Loscalzo J, Marchese C, Napoli C, Paci P, Petti M, Quackenbush J, Tieri P, Viggiano D, Vilahur G, Glass K, Baumbach JWiley interdisciplinary reviews. Systems biology and medicineMolecular networks in Network Medicine: Development and applications. Wiley Interdiscip Rev Syst Biol Med. 2020 11; 12(6):e1489.Wiley Interdiscip Rev Syst Biol Med2020-04-19T00:00:002020Molecular networks in Network Medicine: Development and applications.Authorship 124119521Authorship 1259363932579922Lopes-Ramos CM, Chen CY, Kuijjer ML, Paulson JN, Sonawane AR, Fagny M, Platig J, Glass K, Quackenbush J, DeMeo DLCell reportsSex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues. Cell Rep. 2020 06 23; 31(12):107795.Cell Rep2020-06-23T00:00:002020Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues.Authorship 144509Authorship 1446364Authorship 14337415Authorship 13971221Authorship 1473510Authorship 1532914Authorship 1545613Authorship 1281024432860050Kuijjer ML, Fagny M, Marin A, Quackenbush J, Glass KBioinformatics (Oxford, England)PUMA: PANDA Using MicroRNA Associations. Bioinformatics. 2020 09 15; 36(18):4765-4773.Bioinformatics2020-09-15T00:00:002020PUMA: PANDA Using MicroRNA Associations.Authorship 12923334432998967Paulson JN, Williams BL, Hehnly C, Mishra N, Sinnar SA, Zhang L, Ssentongo P, Mbabazi-Kabachelor E, Wijetunge DSS, von Bredow B, Mulondo R, Kiwanuka J, Bajunirwe F, Bazira J, Bebell LM, Burgoine K, Couto-Rodriguez M, Ericson JE, Erickson T, Ferrari M, Gladstone M, Guo C, Haran M, Hornig M, Isaacs AM, Kaaya BN, Kangere SM, Kulkarni AV, Kumbakumba E, Li X, Limbrick DD, Magombe J, Morton SU, Mugamba J, Ng J, Olupot-Olupot P, Onen J, Peterson MR, Roy F, Sheldon K, Townsend R, Weeks AD, Whalen AJ, Quackenbush J, Ssenyonga P, Galperin MY, Almeida M, Atkins H, Warf BC, Lipkin WI, Broach JR, Schiff SJScience translational medicinePaenibacillus infection with frequent viral coinfection contributes to postinfectious hydrocephalus in Ugandan infants. Sci Transl Med. 2020 09 30; 12(563).Sci Transl Med2020-09-30T00:00:002020Paenibacillus infection with frequent viral coinfection contributes to postinfectious hydrocephalus in Ugandan infants.Authorship 12974902233057217Haibe-Kains B, Adam GA, Hosny A, Khodakarami F, Waldron L, Wang B, McIntosh C, Goldenberg A, Kundaje A, Greene CS, Broderick T, Hoffman MM, Leek JT, Korthauer K, Huber W, Brazma A, Pineau J, Tibshirani R, Hastie T, Ioannidis JPA, Quackenbush J, Aerts HJWLNatureTransparency and reproducibility in artificial intelligence. Nature. 2020 10; 586(7829):E14-E16.Nature2020-10-14T00:00:002020Transparency and reproducibility in artificial intelligence.Authorship 13038441833136096Lam HC, Cloonan SM, Bhashyam AR, Haspel JA, Singh A, Sathirapongsasuti JF, Cervo M, Yao H, Chung AL, Mizumura K, An CH, Shan B, Franks JM, Haley KJ, Owen CA, Tesfaigzi Y, Washko GR, Quackenbush J, Silverman EK, Rahman I, Kim HP, Mahmood A, Biswal SS, Ryter SW, Choi AMThe Journal of clinical investigationHistone deacetylase 6-mediated selective autophagy regulates COPD-associated cilia dysfunction. J Clin Invest. 2020 11 02; 130(11):6189.J Clin Invest2020-11-02T00:00:002020Histone deacetylase 6-mediated selective autophagy regulates COPD-associated cilia dysfunction.https://www.hsph.harvard.edu/john-quackenbush/Faculty Website33330090Lopes-Ramos CM, Quackenbush J, DeMeo DLFrontiers in oncologyGenome-Wide Sex and Gender Differences in Cancer. Front Oncol. 2020; 10:597788.Front Oncol2020-11-23T00:00:002020Genome-Wide Sex and Gender Differences in Cancer.Authorship 13104812Authorship 1548026https://www.hsph.harvard.edu/profile/john-quackenbush/Academic ProfileAuthorship 1323648633514755Young AT, Carette X, Helmel M, Steen H, Husson RN, Quackenbush J, Platig JNPJ systems biology and applicationsMulti-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis. NPJ Syst Biol Appl. 2021 01 29; 7(1):8.NPJ Syst Biol Appl2021-01-29T00:00:002021Multi-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis.Authorship 13259871033536619Hatchi E, Goehring L, Landini S, Skourti-Stathaki K, DeConti DK, Abderazzaq FO, Banerjee P, Demers TM, Wang YE, Quackenbush J, Livingston DMNatureBRCA1 and RNAi factors promote repair mediated by small RNAs and PALB2-RAD52. Nature. 2021 03; 591(7851):665-670.Nature2021-02-03T00:00:002021BRCA1 and RNAi factors promote repair mediated by small RNAs and PALB2-RAD52.Authorship 19523712Authorship 1597074Authorship 1867231true1Professor of Biomedical InformaticsProfessor of Biomedical Informaticstrue1Robert Winthrop Professor of GeneticsRobert Winthrop Professor of GeneticsAuthorship 24976720Authorship 1355567633968133Weighill D, Ben Guebila M, Glass K, Platig J, Yeh JJ, Quackenbush JFrontiers in geneticsGene Targeting in Disease Networks. Front Genet. 2021; 12:649942.Front Genet2021-04-23T00:00:002021Gene Targeting in Disease Networks.Authorship 1364079234133929Burkholz R, Quackenbush J, Bojar DCell reportsUsing graph convolutional neural networks to learn a representation for glycans. Cell Rep. 2021 06 15; 35(11):109251.Cell Rep2021-06-15T00:00:002021Using graph convolutional neural networks to learn a representation for glycans.ens519EnakshiSahaEnakshi Saha, Ph.D.199390Saha, EnakshiResearch AssociateAuthorship 17235641Co-Principal Investigator34409295Snyder JM, Huang RY, Bai H, Rao VR, Cornes S, Barnholtz-Sloan JS, Gutman D, Fasano R, Van Meir EG, Brat D, Eschbacher J, Quackenbush J, Wen PY, Lee JWNeuro-oncology advancesAnalysis of morphological characteristics of IDH-mutant/wildtype brain tumors using whole-lesion phenotype analysis. Neurooncol Adv. 2021 Jan-Dec; 3(1):vdab088.Neurooncol Adv2021-06-24T00:00:002021Analysis of morphological characteristics of IDH-mutant/wildtype brain tumors using whole-lesion phenotype analysis.Authorship 138707112Authorship 16560592025-06-30DEMEO, DAWN L ;QUACKENBUSH, JOHN2021-09-01Networks Tools to Understand Sex- and Gender-Specific Drivers of DiseaseR01HG011393Co-Principal InvestigatorAuthorship 139221610Authorship 1393372634493595Lopes-Ramos CM, Belova T, Brunner TH, Ben Guebila M, Osorio D, Quackenbush J, Kuijjer MLCancer researchRegulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme. Cancer Res. 2021 11 01; 81(21):5401-5412.Cancer Res2021-09-07T00:00:002021Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme.34508353Ben Guebila M, Lopes-Ramos CM, Weighill D, Sonawane AR, Burkholz R, Shamsaei B, Platig J, Glass K, Kuijjer ML, Quackenbush JNucleic acids researchGRAND: a database of gene regulatory network models across human conditions. Nucleic Acids Res. 2022 01 07; 50(D1):D610-D621.Nucleic Acids Res2022-01-07T00:00:002022GRAND: a database of gene regulatory network models across human conditions.Authorship 1804262Authorship 18256320Authorship 1406671534707916Weighill D, Guebila MB, Lopes-Ramos C, Glass K, Quackenbush J, Platig J, Burkholz RProceedings of the ... AAAI Conference on Artificial Intelligence. AAAI Conference on Artificial IntelligenceGene regulatory network inference as relaxed graph matching. Proc AAAI Conf Artif Intell. 2021 Feb; 35(11):10263-10272.Proc AAAI Conf Artif Intell2021-05-18T00:00:002021Gene regulatory network inference as relaxed graph matching.Authorship 1452072Authorship 1471423Authorship 1417907334887443Sonawane AR, DeMeo DL, Quackenbush J, Glass KNPJ systems biology and applicationsConstructing gene regulatory networks using epigenetic data. NPJ Syst Biol Appl. 2021 12 09; 7(1):45.NPJ Syst Biol Appl2021-12-09T00:00:002021Constructing gene regulatory networks using epigenetic data.Authorship 1421789211747377Litwin CM, Quackenbush JMicrobial pathogenesisCharacterization of a Vibrio vulnificus LysR homologue, HupR, which regulates expression of the haem uptake outer membrane protein, HupA. Microb Pathog. 2001 Dec; 31(6):295-307.Microb Pathog2001-12-01T00:00:002001Characterization of a Vibrio vulnificus LysR homologue, HupR, which regulates expression of the haem uptake outer membrane protein, HupA.Authorship 143540814Authorship 14383894Authorship 1442650635193937Weighill D, Ben Guebila M, Glass K, Quackenbush J, Platig JGenome researchPredicting genotype-specific gene regulatory networks. Genome Res. 2022 03; 32(3):524-533.Genome Res2022-02-22T00:00:002022Predicting genotype-specific gene regulatory networks.35156023Guebila MB, Morgan DC, Glass K, Kuijjer ML, DeMeo DL, Quackenbush JNAR genomics and bioinformaticsgpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit. NAR Genom Bioinform. 2022 Mar; 4(1):lqac002.NAR Genom Bioinform2022-02-08T00:00:002022gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit.34573415Neri de Souza Reis V, Tahira AC, Daguano Gastaldi V, Mari P, Portolese J, Feio Dos Santos AC, Lisboa B, Mari J, Caetano SC, Brunoni D, Bordini D, Silvestre de Paula C, Vêncio RZN, Quackenbush J, Brentani HGenesEnvironmental Influences Measured by Epigenetic Clock and Vulnerability Components at Birth Impact Clinical ASD Heterogeneity. Genes (Basel). 2021 09 17; 12(9).Genes (Basel)2021-09-17T00:00:002021Environmental Influences Measured by Epigenetic Clock and Vulnerability Components at Birth Impact Clinical ASD Heterogeneity.Authorship 14444471435459940Ben Guebila M, Weighill D, Lopes-Ramos CM, Burkholz R, Pop RT, Palepu K, Shapoval M, Fagny M, Schlauch D, Glass K, Altenbuchinger M, Kuijjer ML, Platig J, Quackenbush JNature methodsAn online notebook resource for reproducible inference, analysis and publication of gene regulatory networks. Nat Methods. 2022 05; 19(5):511-513.Nat Methods2022-05-01T00:00:002022An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks.Authorship 348119135715807Moll M, Hobbs BD, Menon A, Ghosh AJ, Putman RK, Hino T, Hata A, Silverman EK, Quackenbush J, Castaldi PJ, Hersh CP, McGeachie MJ, Sin DD, Tal-Singer R, Nishino M, Hatabu H, Hunninghake GM, Cho MHRespiratory researchBlood gene expression risk profiles and interstitial lung abnormalities: COPDGene and ECLIPSE cohort studies. Respir Res. 2022 Jun 17; 23(1):157.Respir Res2022-06-17T00:00:002022Blood gene expression risk profiles and interstitial lung abnormalities: COPDGene and ECLIPSE cohort studies.Authorship 14654914Authorship 14650615Authorship 146358518Authorship 1459257935759080Yao S, Campbell PT, Ugai T, Gierach G, Abubakar M, Adalsteinsson V, Almeida J, Brennan P, Chanock S, Golub T, Hanash S, Harris C, Hathaway CA, Kelsey K, Landi MT, Mahmood F, Newton C, Quackenbush J, Rodig S, Schultz N, Tearney G, Tworoger SS, Wang M, Zhang X, Garcia-Closas M, Rebbeck TR, Ambrosone CB, Ogino SCancer causes & control : CCCProceedings of the fifth international Molecular Pathological Epidemiology (MPE) meeting. Cancer Causes Control. 2022 Aug; 33(8):1107-1120.Cancer Causes Control2022-06-27T00:00:002022Proceedings of the fifth international Molecular Pathological Epidemiology (MPE) meeting.9120024Inoue I, Nakajima T, Williams CS, Quackenbush J, Puryear R, Powers M, Cheng T, Ludwig EH, Sharma AM, Hata A, Jeunemaitre X, Lalouel JMThe Journal of clinical investigationA nucleotide substitution in the promoter of human angiotensinogen is associated with essential hypertension and affects basal transcription in vitro. J Clin Invest. 1997 Apr 01; 99(7):1786-97.J Clin Invest1997-04-01T00:00:001997A nucleotide substitution in the promoter of human angiotensinogen is associated with essential hypertension and affects basal transcription in vitro.35637906Gaynor SM, Fagny M, Lin X, Platig J, Quackenbush JCell reports methodsConnectivity in eQTL networks dictates reproducibility and genomic properties. Cell Rep Methods. 2022 05 23; 2(5):100218.Cell Rep Methods2022-05-23T00:00:002022Connectivity in eQTL networks dictates reproducibility and genomic properties.Authorship 15940112Authorship 43162113Authorship 1502914436329870Qiang J, Ding W, Kuijjer M, Quackenbush J, Chen PIEEE access : practical innovations, open solutionsClustering Sparse Data With Feature Correlation With Application to Discover Subtypes in Cancer. IEEE Access. 2020; 8:67775-67789.IEEE Access2020-03-26T00:00:002020Clustering Sparse Data With Feature Correlation With Application to Discover Subtypes in Cancer.Authorship 2055441Authorship 1513784736533448Shutta KH, Weighill D, Burkholz R, Guebila MB, DeMeo DL, Zacharias HU, Quackenbush J, Altenbuchinger MNucleic acids researchDRAGON: Determining Regulatory Associations using Graphical models on multi-Omic Networks. Nucleic Acids Res. 2023 02 22; 51(3):e15.Nucleic Acids Res2023-02-22T00:00:002023DRAGON: Determining Regulatory Associations using Graphical models on multi-Omic Networks.Authorship 15325914Authorship 15321892536894939Ben Guebila M, Wang T, Lopes-Ramos CM, Fanfani V, Weighill D, Burkholz R, Schlauch D, Paulson JN, Altenbuchinger M, Shutta KH, Sonawane AR, Lim J, Calderer G, van IJzendoorn DGP, Morgan D, Marin A, Chen CY, Song Q, Saha E, DeMeo DL, Padi M, Platig J, Kuijjer ML, Glass K, Quackenbush JGenome biologyThe Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks. Genome Biol. 2023 03 09; 24(1):45.Genome Biol2023-03-09T00:00:002023The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks.36909563Hossain I, Fanfani V, Fischer J, Quackenbush J, Burkholz RbioRxiv : the preprint server for biologyBiologically informed NeuralODEs for genome-wide regulatory dynamics. bioRxiv. 2024 Jan 03.bioRxiv2024-01-03T00:00:002024Biologically informed NeuralODEs for genome-wide regulatory dynamics.Authorship 20899423Authorship 47214025Authorship 1553136336993392Hossain I, Fanfani V, Quackenbush J, Burkholz RResearch squareBiologically informed NeuralODEs for genome-wide regulatory dynamics. Res Sq. 2023 Mar 14.Res Sq2023-03-14T00:00:002023Biologically informed NeuralODEs for genome-wide regulatory dynamics.Authorship 15917851137672882Parker JS, Mullins M, Cheang MCU, Leung S, Voduc D, Vickery T, Davies S, Fauron C, He X, Hu Z, Quackenbush JF, Stijleman IJ, Palazzo J, Marron JS, Nobel AB, Mardis E, Nielsen TO, Ellis MJ, Perou CM, Bernard PSJournal of clinical oncology : official journal of the American Society of Clinical OncologySupervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes. J Clin Oncol. 2023 Sep 10; 41(26):4192-4199.J Clin Oncol2023-09-10T00:00:002023Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes.Authorship 1595144837790409Saha E, Guebila MB, Fanfani V, Fischer J, Shutta KH, Mandros P, DeMeo DL, Quackenbush J, Lopes-Ramos CMbioRxiv : the preprint server for biologyGene regulatory Networks Reveal Sex Difference in Lung Adenocarcinoma. bioRxiv. 2023 Sep 24.bioRxiv2023-09-24T00:00:002023Gene regulatory Networks Reveal Sex Difference in Lung Adenocarcinoma.Authorship 16113381038014256Saha E, Fanfani V, Mandros P, Ben-Guebila M, Fischer J, Hoff-Shutta K, Glass K, DeMeo DL, Lopes-Ramos C, Quackenbush JbioRxiv : the preprint server for biologyBayesian Optimized sample-specific Networks Obtained By Omics data (BONOBO). bioRxiv. 2023 Nov 17.bioRxiv2023-11-17T00:00:002023Bayesian Optimized sample-specific Networks Obtained By Omics data (BONOBO).Authorship 51668114Authorship 5224545Authorship 560786true1Instructor in MedicineInstructor in Medicinetrue1Professor of BiostatisticsProfessor of Biostatisticstrue1Visiting Professor of Systems Biology in the Wyss InstituteVisiting Professor of Systems Biology in the Wyss Institutetrue1Clarence James Gamble Professor of Biostatistics, Population, and Data ScienceClarence James Gamble Professor of Biostatistics, Population, and Data Sciencetrue1Marion V. Nelson Professor of Biomedical InformaticsMarion V. Nelson Professor of Biomedical Informaticstrue1Adjunct Professor of BiostatisticsAdjunct Professor of Biostatistics2Chair, Department of BiostatisticsChair, Department of Biostatisticstrue1Henry Pickering Walcott Professor of Computational Biology and BioinformaticsHenry Pickering Walcott Professor of Computational Biology and Bioinformaticstrue1InstructorInstructortrue1Assistant Professor of MedicineAssistant Professor of Medicinetrue1Research AssociateResearch Associatetrue1Professor of Computational Biology and BioinformaticsProfessor of Computational Biology and Bioinformaticstrue1Adjunct Professor of BiostatisticsAdjunct Professor of BiostatisticsAuthorship 16739715Authorship 2389036Authorship 3463348Authorship 3759262Authorship 24021311Authorship 2521833Authorship 2551776Authorship 49512221Authorship 6577927Authorship 65093820Authorship 6648153Authorship 6519678Authorship 6465946Authorship 6608538Authorship 667496323562991Kelly AD, Hill KE, Correll M, Hu L, Wang YE, Rubio R, Duan S, Quackenbush J, Spentzos DGenomicsNext-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: preliminary assessment of cross-platform concordance. Genomics. 2013 Jul; 102(1):8-14.Genomics2013-04-03T00:00:002013Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: preliminary assessment of cross-platform concordance.23741402Glass K, Huttenhower C, Quackenbush J, Yuan GCPloS onePassing messages between biological networks to refine predicted interactions. PLoS One. 2013; 8(5):e64832.PLoS One2013-05-31T00:00:002013Passing messages between biological networks to refine predicted interactions.23570996Larson JL, Huttenhower C, Quackenbush J, Yuan GCGenomicsA tiered hidden Markov model characterizes multi-scale chromatin states. Genomics. 2013 Jul; 102(1):1-7.Genomics2013-04-06T00:00:002013A tiered hidden Markov model characterizes multi-scale chromatin states.23493352De Rienzo A, Richards WG, Yeap BY, Coleman MH, Sugarbaker PE, Chirieac LR, Wang YE, Quackenbush J, Jensen RV, Bueno RClinical cancer research : an official journal of the American Association for Cancer ResearchSequential binary gene ratio tests define a novel molecular diagnostic strategy for malignant pleural mesothelioma. Clin Cancer Res. 2013 May 01; 19(9):2493-502.Clin Cancer Res2013-03-14T00:00:002013Sequential binary gene ratio tests define a novel molecular diagnostic strategy for malignant pleural mesothelioma.23462555Correll M, Johnson CK, Ferrari G, Brizzio M, Mak AW, Quackenbush J, Shaw RE, Zapolanski A, Grau JBGenomicsMutational analysis clopidogrel resistance and platelet function in patients scheduled for coronary artery bypass grafting. Genomics. 2013 Jun; 101(6):313-7.Genomics2013-02-24T00:00:002013Mutational analysis clopidogrel resistance and platelet function in patients scheduled for coronary artery bypass grafting.23355484Papillon-Cavanagh S, De Jay N, Hachem N, Olsen C, Bontempi G, Aerts HJ, Quackenbush J, Haibe-Kains BJournal of the American Medical Informatics Association : JAMIAComparison and validation of genomic predictors for anticancer drug sensitivity. J Am Med Inform Assoc. 2013 Jul-Aug; 20(4):597-602.J Am Med Inform Assoc2013-01-26T00:00:002013Comparison and validation of genomic predictors for anticancer drug sensitivity.Authorship 834917Authorship 1897991Authorship 5239916Authorship 2504213Authorship 2855547Authorship 6824636Authorship 684826712628980Cook DN, Wang S, Howles GP, Speer M, Churchhill G, Quackenbush J, Schwartz DAChestThe genetics of innate immunity in the lung. Chest. 2003 Mar; 123(3 Suppl):369S.Chest2003-03-01T00:00:002003The genetics of innate immunity in the lung.17701033Hollingsworth JW, Whitehead G, Berman KG, Tekippe EM, Gilmour MI, Larkin JE, Quackenbush J, Schwartz DAImmunogeneticsGenetic basis of murine antibacterial defense to streptococcal lung infection. Immunogenetics. 2007 Sep; 59(9):713-24.Immunogenetics2007-08-14T00:00:002007Genetic basis of murine antibacterial defense to streptococcal lung infection.24158781Li WQ, Han J, Widlund HR, Correll M, Wang YE, Quackenbush J, Mihm MC, Canales AL, Wu S, Golub T, Hoshida Y, Hunter DJ, Murphy G, Kupper TS, Qureshi AACancer causes & control : CCCCXCR4 pathway associated with family history of melanoma. Cancer Causes Control. 2014 Jan; 25(1):125-32.Cancer Causes Control2013-10-25T00:00:002013CXCR4 pathway associated with family history of melanoma.Authorship 691704724167291Portal D, Zhou H, Zhao B, Kharchenko PV, Lowry E, Wong L, Quackenbush J, Holloway D, Jiang S, Lu Y, Kieff EProceedings of the National Academy of Sciences of the United States of AmericaEpstein-Barr virus nuclear antigen leader protein localizes to promoters and enhancers with cell transcription factors and EBNA2. Proc Natl Acad Sci U S A. 2013 Nov 12; 110(46):18537-42.Proc Natl Acad Sci U S A2013-10-28T00:00:002013Epstein-Barr virus nuclear antigen leader protein localizes to promoters and enhancers with cell transcription factors and EBNA2.Authorship 693521124259003Quackenbush JF, Cassidy PB, Pfeffer LM, Boucher KM, Hawkes JE, Pfeffer SR, Kopelovich L, Leachman SAMethods in molecular biology (Clifton, N.J.)Isolation of circulating microRNAs from microvesicles found in human plasma. 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PLoS One. 2013; 8(11):e80314.PLoS One2013-11-26T00:00:002013Gene expression signature of normal cell-of-origin predicts ovarian tumor outcomes.24200693Lam HC, Cloonan SM, Bhashyam AR, Haspel JA, Singh A, Sathirapongsasuti JF, Cervo M, Yao H, Chung AL, Mizumura K, An CH, Shan B, Franks JM, Haley KJ, Owen CA, Tesfaigzi Y, Washko GR, Quackenbush J, Silverman EK, Rahman I, Kim HP, Mahmood A, Biswal SS, Ryter SW, Choi AMThe Journal of clinical investigationHistone deacetylase 6-mediated selective autophagy regulates COPD-associated cilia dysfunction. J Clin Invest. 2013 Dec; 123(12):5212-30.J Clin Invest2013-11-08T00:00:002013Histone deacetylase 6-mediated selective autophagy regulates COPD-associated cilia dysfunction.Authorship 6991077Authorship 20981111Authorship 2204526Authorship 7031336Authorship 2699641Authorship 257381424574459Adamia S, Bar-Natan M, Haibe-Kains B, Pilarski PM, Bach C, Pevzner S, Calimeri T, Avet-Loiseau H, Lode L, Verselis S, Fox EA, Galinsky I, Mathews S, Dagogo-Jack I, Wadleigh M, Steensma DP, Motyckova G, Deangelo DJ, Quackenbush J, Tenen DG, Stone RM, Griffin JDBloodNOTCH2 and FLT3 gene mis-splicings are common events in patients with acute myeloid leukemia (AML): new potential targets in AML. Blood. 2014 May 01; 123(18):2816-25.Blood2014-02-26T00:00:002014NOTCH2 and FLT3 gene mis-splicings are common events in patients with acute myeloid leukemia (AML): new potential targets in AML.Authorship 294538Authorship 2884958Authorship 4743401Authorship 7147245Authorship 72104917Authorship 3367068Authorship 725517915475305Nene V, Lee D, Kang'a S, Skilton R, Shah T, de Villiers E, Mwaura S, Taylor D, Quackenbush J, Bishop RInsect biochemistry and molecular biologyGenes transcribed in the salivary glands of female Rhipicephalus appendiculatus ticks infected with Theileria parva. Insect Biochem Mol Biol. 2004 Oct; 34(10):1117-28.Insect Biochem Mol Biol2004-10-01T00:00:002004Genes transcribed in the salivary glands of female Rhipicephalus appendiculatus ticks infected with Theileria parva.24284058Adamia S, Haibe-Kains B, Pilarski PM, Bar-Natan M, Pevzner S, Avet-Loiseau H, Lode L, Verselis S, Fox EA, Burke J, Galinsky I, Dagogo-Jack I, Wadleigh M, Steensma DP, Motyckova G, Deangelo DJ, Quackenbush J, Stone R, Griffin JDClinical cancer research : an official journal of the American Association for Cancer ResearchA genome-wide aberrant RNA splicing in patients with acute myeloid leukemia identifies novel potential disease markers and therapeutic targets. Clin Cancer Res. 2014 Mar 01; 20(5):1135-45.Clin Cancer Res2013-11-27T00:00:002013A genome-wide aberrant RNA splicing in patients with acute myeloid leukemia identifies novel potential disease markers and therapeutic targets.24055427Sharron Lin X, Hu L, Sandy K, Correll M, Quackenbush J, Wu CL, Scott McDougal WUrologic oncologyDifferentiating progressive from nonprogressive T1 bladder cancer by gene expression profiling: applying RNA-sequencing analysis on archived specimens. Urol Oncol. 2014 Apr; 32(3):327-36.Urol Oncol2013-09-18T00:00:002013Differentiating progressive from nonprogressive T1 bladder cancer by gene expression profiling: applying RNA-sequencing analysis on archived specimens.Authorship 2488712Authorship 25800510Authorship 72685919Authorship 73005115Authorship 730255623339462Kelly AD, Haibe-Kains B, Janeway KA, Hill KE, Howe E, Goldsmith J, Kurek K, Perez-Atayde AR, Francoeur N, Fan JB, April C, Schneider H, Gebhardt MC, Culhane A, Quackenbush J, Spentzos DGenome medicineMicroRNA paraffin-based studies in osteosarcoma reveal reproducible independent prognostic profiles at 14q32. Genome Med. 2013; 5(1):2.Genome Med2013-01-22T00:00:002013MicroRNA paraffin-based studies in osteosarcoma reveal reproducible independent prognostic profiles at 14q32.24690158Lee JW, Norden AD, Ligon KL, Golby AJ, Beroukhim R, Quackenbush J, Wells W, Oelschlager K, Maetzold D, Wen PYEpilepsy researchTumor associated seizures in glioblastomas are influenced by survival gene expression in a region-specific manner: a gene expression imaging study. Epilepsy Res. 2014 Jul; 108(5):843-52.Epilepsy Res2014-03-12T00:00:002014Tumor associated seizures in glioblastomas are influenced by survival gene expression in a region-specific manner: a gene expression imaging study.Authorship 35654912Authorship 3678473Authorship 7321151Authorship 7332951624870827Quackenbush JNaturePerspective: Learning to share. Nature. 2014 May 29; 509(7502):S68.Nature2014-05-29T00:00:002014Perspective: Learning to share.24892406Aerts HJ, Velazquez ER, Leijenaar RT, Parmar C, Grossmann P, Carvalho S, Cavalho S, Bussink J, Monshouwer R, Haibe-Kains B, Rietveld D, Hoebers F, Rietbergen MM, Leemans CR, Dekker A, Quackenbush J, Gillies RJ, Lambin PNature communicationsDecoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach. Nat Commun. 2014 Jun 03; 5:4006.Nat Commun2014-06-03T00:00:002014Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach.Authorship 737017824691108Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, Bontempi G, Haibe-Kains B, Quackenbush JGenomicsInference and validation of predictive gene networks from biomedical literature and gene expression data. Genomics. 2014 May-Jun; 103(5-6):329-36.Genomics2014-03-29T00:00:002014Inference and validation of predictive gene networks from biomedical literature and gene expression data.Authorship 1703982524964944Chu JH, Hersh CP, Castaldi PJ, Cho MH, Raby BA, Laird N, Bowler R, Rennard S, Loscalzo J, Quackenbush J, Silverman EKBMC systems biologyAnalyzing networks of phenotypes in complex diseases: methodology and applications in COPD. BMC Syst Biol. 2014 Jun 25; 8:78.BMC Syst Biol2014-06-25T00:00:002014Analyzing networks of phenotypes in complex diseases: methodology and applications in COPD.25015668Hatzis C, Bedard PL, Birkbak NJ, Beck AH, Aerts HJ, Stem DF, Stern DF, Shi L, Clarke R, Quackenbush J, Haibe-Kains BCancer researchEnhancing reproducibility in cancer drug screening: how do we move forward? Cancer Res. 2014 Aug 01; 74(15):4016-23.Cancer Res2014-07-11T00:00:002014Enhancing reproducibility in cancer drug screening: how do we move forward?Authorship 3330957Authorship 742272425009552Olsen C, Bontempi G, Emmert-Streib F, Quackenbush J, Haibe-Kains BFrontiers in geneticsRelevance of different prior knowledge sources for inferring gene interaction networks. Front Genet. 2014; 5:177.Front Genet2014-06-24T00:00:002014Relevance of different prior knowledge sources for inferring gene interaction networks.Authorship 3680485Authorship 408864Authorship 4174513Authorship 31627112Authorship 3366415Authorship 35181211Authorship 4653302Authorship 39268120Authorship 4075443Authorship 4734201Authorship 4915746Authorship 7459732Authorship 75334910Authorship 7473711524858532Ferrari G, Quackenbush J, Strobeck J, Hu L, Johnson CK, Mak A, Shaw RE, Sayles K, Brizzio ME, Zapolanski A, Grau JBGenomicsComparative genome-wide transcriptional analysis of human left and right internal mammary arteries. Genomics. 2014 Jul; 104(1):36-44.Genomics2014-05-20T00:00:002014Comparative genome-wide transcriptional analysis of human left and right internal mammary arteries.25100327Aerts HJ, Velazquez ER, Leijenaar RT, Parmar C, Grossmann P, Carvalho S, Bussink J, Monshouwer R, Haibe-Kains B, Rietveld D, Hoebers F, Rietbergen MM, Leemans CR, Dekker A, Quackenbush J, Gillies RJ, Lambin PNature communicationsCorrigendum: Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach. Nat Commun. 2014; 5:4644.Nat Commun2014-08-07T00:00:002014Corrigendum: Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach.Authorship 3564462KRG4KimberlyGlassKimberly R. Glass, Ph.D.88900Glass, KimberlyAssistant Professor of MedicineAuthorship 55639827Authorship 75801110Authorship 2134264Authorship 3537109Authorship 36481310Authorship 759824525254348Mason EA, Mar JC, Laslett AL, Pera MF, Quackenbush J, Wolvetang E, Wells CAStem cell reportsGene expression variability as a unifying element of the pluripotency network. Stem Cell Reports. 2014 Aug 12; 3(2):365-77.Stem Cell Reports2014-07-25T00:00:002014Gene expression variability as a unifying element of the pluripotency network.Authorship 77217515Authorship 773132625486477Jirawatnotai S, Sharma S, Michowski W, Suktitipat B, Geng Y, Quackenbush J, Elias JE, Gygi SP, Wang YE, Sicinski PCell cycle (Georgetown, Tex.)The cyclin D1-CDK4 oncogenic interactome enables identification of potential novel oncogenes and clinical prognosis. Cell Cycle. 2014; 13(18):2889-900.Cell Cycle2014-01-01T00:00:002014The cyclin D1-CDK4 oncogenic interactome enables identification of potential novel oncogenes and clinical prognosis.25333685Yang IV, Pedersen BS, Rabinovich E, Hennessy CE, Davidson EJ, Murphy E, Guardela BJ, Tedrow JR, Zhang Y, Singh MK, Correll M, Schwarz MI, Geraci M, Sciurba FC, Quackenbush J, Spira A, Kaminski N, Schwartz DAAmerican journal of respiratory and critical care medicineRelationship of DNA methylation and gene expression in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med. 2014 Dec 01; 190(11):1263-72.Am J Respir Crit Care Med2014-12-01T00:00:002014Relationship of DNA methylation and gene expression in idiopathic pulmonary fibrosis.Authorship 46123255Authorship 4812873Authorship 50470011Authorship 5073567Authorship 51933560Authorship 5735296Authorship 261887158Authorship 2803545Authorship 312118Authorship 874378Authorship 668091Authorship 7953Authorship 4235041Authorship 3527137Authorship 4977396Authorship 501357103Authorship 4705503Authorship 3905939Authorship 2375485Authorship 3184416Authorship 50859811Authorship 5103123Authorship 517015Authorship 23648710Authorship 2338261Authorship 3207664Authorship 2150834Authorship 817951Authorship 913361Authorship 2359255Authorship 2681771Authorship 4218049Authorship 425991138Authorship 1187743Authorship 3012906Authorship 3096776Authorship 331077425763110Lao T, Glass K, Qiu W, Polverino F, Gupta K, Morrow J, Mancini JD, Vuong L, Perrella MA, Hersh CP, Owen CA, Quackenbush J, Yuan GC, Silverman EK, Zhou XGenome medicineHaploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring. Genome Med. 2015; 7(1):12.Genome Med2015-02-14T00:00:002015Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring.Authorship 4387715Authorship 4469643Authorship 25352449Authorship 3739835Authorship 37416810Authorship 4379897Authorship 4716093Authorship 479733825315895Castaldi PJ, Cho MH, Zhou X, Qiu W, Mcgeachie M, Celli B, Bakke P, Gulsvik A, Lomas DA, Crapo JD, Beaty TH, Rennard S, Harshfield B, Lange C, Singh D, Tal-Singer R, Riley JH, Quackenbush J, Raby BA, Carey VJ, Silverman EK, Hersh CPHuman molecular geneticsGenetic control of gene expression at novel and established chronic obstructive pulmonary disease loci. Hum Mol Genet. 2015 Feb 15; 24(4):1200-10.Hum Mol Genet2014-10-14T00:00:002014Genetic control of gene expression at novel and established chronic obstructive pulmonary disease loci.Authorship 34746311Authorship 507897Authorship 5325821Authorship 80463512Authorship 79605218Authorship 78957312Authorship 8071142Authorship 801435225888305Glass K, Quackenbush J, Spentzos D, Haibe-Kains B, Yuan GCBMC bioinformaticsA network model for angiogenesis in ovarian cancer. BMC Bioinformatics. 2015 Apr 11; 16:115.BMC Bioinformatics2015-04-11T00:00:002015A network model for angiogenesis in ovarian cancer.25431000Glass K, Quackenbush J, Silverman EK, Celli B, Rennard SI, Yuan GC, DeMeo DLBMC systems biologySexually-dimorphic targeting of functionally-related genes in COPD. 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Genom Data. 2013 Dec; 1:1.Genom Data2013-05-28T00:00:002013Accelerating genomic data publishing and sharing.Authorship 44859122Authorship 848274226576632Padi M, Quackenbush JBMC systems biologyIntegrating transcriptional and protein interaction networks to prioritize condition-specific master regulators. BMC Syst Biol. 2015 Nov 14; 9:80.BMC Syst Biol2015-11-14T00:00:002015Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators.26752519Cloonan SM, Glass K, Laucho-Contreras ME, Bhashyam AR, Cervo M, Pabón MA, Konrad C, Polverino F, Siempos II, Perez E, Mizumura K, Ghosh MC, Parameswaran H, Williams NC, Rooney KT, Chen ZH, Goldklang MP, Yuan GC, Moore SC, Demeo DL, Rouault TA, D'Armiento JM, Schon EA, Manfredi G, Quackenbush J, Mahmood A, Silverman EK, Owen CA, Choi AMNature medicineMitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice. Nat Med. 2016 Feb; 22(2):163-74.Nat Med2016-01-11T00:00:002016Mitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice.Authorship 8608231426554828De Rienzo A, Archer MA, Yeap BY, Dao N, Sciaranghella D, Sideris AC, Zheng Y, Holman AG, Wang YE, Dal Cin PS, Fletcher JA, Rubio R, Croft L, Quackenbush J, Sugarbaker PE, Munir KJ, Battilana JR, Gustafson CE, Chirieac LR, Ching SM, Wong J, Tay LC, Rudd S, Hercus R, Sugarbaker DJ, Richards WG, Bueno RCancer researchGender-Specific Molecular and Clinical Features Underlie Malignant Pleural Mesothelioma. 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Nature. 2016 11 30; 540(7631):E6-E8.Nature2016-11-30T00:00:002016Safikhani et al. reply.Authorship 937720927880818Berrios C, Padi M, Keibler MA, Park DE, Molla V, Cheng J, Lee SM, Stephanopoulos G, Quackenbush J, DeCaprio JAPLoS pathogensMerkel Cell Polyomavirus Small T Antigen Promotes Pro-Glycolytic Metabolic Perturbations Required for Transformation. PLoS Pathog. 2016 Nov; 12(11):e1006020.PLoS Pathog2016-11-23T00:00:002016Merkel Cell Polyomavirus Small T Antigen Promotes Pro-Glycolytic Metabolic Perturbations Required for Transformation.Authorship 2368126Authorship 2493425Authorship 35075714Authorship 9431996Authorship 9427503927540268Manimaran S, Selby HM, Okrah K, Ruberman C, Leek JT, Quackenbush J, Haibe-Kains B, Bravo HC, Johnson WEBioinformatics (Oxford, England)BatchQC: interactive software for evaluating sample and batch effects in genomic data. 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PLoS One. 2017; 12(2):e0170181.PLoS One2017-02-02T00:00:002017Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue.Authorship 832982655 Huntington AveHarvard School of Public HealthBiostatistics, Bldg 2-421655 Huntington AveBoston02115MAAuthorship 9581181227617304Elias KM, Emori MM, Westerling T, Long H, Budina-Kolomets A, Li F, MacDuffie E, Davis MR, Holman A, Lawney B, Freedman ML, Quackenbush J, Brown M, Drapkin RJCI insightEpigenetic remodeling regulates transcriptional changes between ovarian cancer and benign precursors. JCI Insight. 2016 Aug 18; 1(13).JCI Insight2016-08-18T00:00:002016Epigenetic remodeling regulates transcriptional changes between ovarian cancer and benign precursors.8849440Schuler GD, Boguski MS, Stewart EA, Stein LD, Gyapay G, Rice K, White RE, Rodriguez-Tomé P, Aggarwal A, Bajorek E, Bentolila S, Birren BB, Butler A, Castle AB, Chiannilkulchai N, Chu A, Clee C, Cowles S, Day PJ, Dibling T, Drouot N, Dunham I, Duprat S, East C, Edwards C, Fan JB, Fang N, Fizames C, Garrett C, Green L, Hadley D, Harris M, Harrison P, Brady S, Hicks A, Holloway E, Hui L, Hussain S, Louis-Dit-Sully C, Ma J, MacGilvery A, Mader C, Maratukulam A, Matise TC, McKusick KB, Morissette J, Mungall A, Muselet D, Nusbaum HC, Page DC, Peck A, Perkins S, Piercy M, Qin F, Quackenbush J, Ranby S, Reif T, Rozen S, Sanders C, She X, Silva J, Slonim DK, Soderlund C, Sun WL, Tabar P, Thangarajah T, Vega-Czarny N, Vollrath D, Voyticky S, Wilmer T, Wu X, Adams MD, Auffray C, Walter NA, Brandon R, Dehejia A, Goodfellow PN, Houlgatte R, Hudson JR, Ide SE, Iorio KR, Lee WY, Seki N, Nagase T, Ishikawa K, Nomura N, Phillips C, Polymeropoulos MH, Sandusky M, Schmitt K, Berry R, Swanson K, Torres R, Venter JC, Sikela JM, Beckmann JS, Weissenbach J, Myers RM, Cox DR, James MR, Bentley D, Deloukas P, Lander ES, Hudson TJScience (New York, N.Y.)A gene map of the human genome. 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