2023
Proceedings of the Association for Pathology Informatics Bootcamp 2022
Obstfeld A, Brodsky V, Carter A, Gershkovich P, Haymond S, Levy B, Sinard J, Sellers D, Stoffel M, Jackups R. Proceedings of the Association for Pathology Informatics Bootcamp 2022. Journal Of Pathology Informatics 2023, 14: 100331. PMID: 37705688, PMCID: PMC10495674, DOI: 10.1016/j.jpi.2023.100331.Peer-Reviewed Original Research
2022
NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health
Lee P, Benz C, Blood P, Börner K, Campisi J, Chen F, Daldrup-Link H, De Jager P, Ding L, Duncan F, Eickelberg O, Fan R, Finkel T, Furman D, Garovic V, Gehlenborg N, Glass C, Heckenbach I, Joseph Z, Katiyar P, Kim S, Königshoff M, Kuchel G, Lee H, Lee J, Ma J, Ma Q, Melov S, Metis K, Mora A, Musi N, Neretti N, Passos J, Rahman I, Rivera-Mulia J, Robson P, Rojas M, Roy A, Scheibye-Knudsen M, Schilling B, Shi P, Silverstein J, Suryadevara V, Xie J, Wang J, Wong A, Niedernhofer L, Wang S, Anvari H, Balough J, Benz C, Bons J, Brenerman B, Evans W, Gerencser A, Gregory H, Hansen M, Justice J, Kapahi P, Murad N, O’Broin A, Pavone M, Powell M, Scott G, Shanes E, Shankaran M, Verdin E, Winer D, Wu F, Adams A, Blood P, Bueckle A, Cao-Berg I, Chen H, Davis M, Filus S, Hao Y, Hartman A, Hasanaj E, Helfer J, Herr B, Joseph Z, Molla G, Mou G, Puerto J, Quardokus E, Ropelewski A, Ruffalo M, Satija R, Schwenk M, Scibek R, Shirey W, Sibilla M, Welling J, Yuan Z, Bonneau R, Christiano A, Izar B, Menon V, Owens D, Phatnani H, Smith C, Suh Y, Teich A, Bekker V, Chan C, Coutavas E, Hartwig M, Ji Z, Nixon A, Dou Z, Rajagopal J, Slavov N, Holmes D, Jurk D, Kirkland J, Lagnado A, Tchkonia T, Abraham K, Dibattista A, Fridell Y, Howcroft T, Jhappan C, Montes V, Prabhudas M, Resat H, Taylor V, Kumar M, Suryadevara V, Cigarroa F, Cohn R, Cortes T, Courtois E, Chuang J, Davé M, Domanskyi S, Enninga E, Eryilmaz G, Espinoza S, Gelfond J, Kirkland J, Kuchel G, Kuo C, Lehman J, Aguayo-Mazzucato C, Meves A, Rani M, Sanders S, Thibodeau A, Tullius S, Ucar D, White B, Wu Q, Xu M, Yamaguchi S, Assarzadegan N, Cho C, Hwang I, Hwang Y, Xi J, Adeyi O, Aliferis C, Bartolomucci A, Dong X, DuFresne-To M, Ikramuddin S, Johnson S, Nelson A, Niedernhofer L, Revelo X, Trevilla-Garcia C, Sedivy J, Thompson E, Robbins P, Wang J, Aird K, Alder J, Beaulieu D, Bueno M, Calyeca J, Chamucero-Millaris J, Chan S, Chung D, Corbett A, Gorbunova V, Gowdy K, Gurkar A, Horowitz J, Hu Q, Kaur G, Khaliullin T, Lafyatis R, Lanna S, Li D, Ma A, Morris A, Muthumalage T, Peters V, Pryhuber G, Reader B, Rosas L, Sembrat J, Shaikh S, Shi H, Stacey S, Croix C, Wang C, Wang Q, Watts A, Gu L, Lin Y, Rabinovitch P, Sweetwyne M, Artyomov M, Ballentine S, Chheda M, Davies S, DiPersio J, Fields R, Fitzpatrick J, Fulton R, Imai S, Jain S, Ju T, Kushnir V, Link D, Ben Major M, Oh S, Rapp D, Rettig M, Stewart S, Veis D, Vij K, Wendl M, Wyczalkowski M, Craft J, Enninful A, Farzad N, Gershkovich P, Halene S, Kluger Y, VanOudenhove J, Xu M, Yang J, Yang M. NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health. Nature Aging 2022, 2: 1090-1100. PMID: 36936385, PMCID: PMC10019484, DOI: 10.1038/s43587-022-00326-5.Peer-Reviewed Original ResearchConceptsSenescence-associated secretory phenotypeSenescent cellsSecretory phenotypeMulti-omics datasetsStable growth arrestHuman lifespanDiverse rolesGrowth arrestProinflammatory senescence-associated secretory phenotypeHuman tissuesPhenotypeMetabolic changesCellsHuman healthLifespanPhysiological healthCommon Coordinate FrameworkSystems approach to enhance Lynch syndrome diagnosis through tumour testing
Singh V, Mezzacappa C, Gershkovich P, Di Giovanna J, Ganzak A, Gibson J, Sinard J, Xicola RM, Llor X. Systems approach to enhance Lynch syndrome diagnosis through tumour testing. Journal Of Medical Genetics 2022, 60: 533-539. PMID: 36115663, PMCID: PMC10020126, DOI: 10.1136/jmg-2022-108770.Peer-Reviewed Original ResearchConceptsOriginal cohortColorectal adenocarcinomaLynch syndromeTumor testingGenetic testingPercentage of patientsProportion of patientsLynch syndrome diagnosisCG evaluationCancer genetic testingRace/ethnicityCRC testingCohort studyMMR immunohistochemistryLS diagnosisNew diagnosisMMR lossAcademic centersPatientsSyndrome diagnosisCohortCase identificationMethylation testingReferral differencesReferral mechanismsQIM22-192: Mismatch Repair Protein Immunohistochemistry: Quality of Mismatch Repair Deficiency Detection
Matsumoto N, Barbieri A, Gershkovich P, Cecchini M, Gibson J. QIM22-192: Mismatch Repair Protein Immunohistochemistry: Quality of Mismatch Repair Deficiency Detection. Journal Of The National Comprehensive Cancer Network 2022, 20: qim22-192. DOI: 10.6004/jnccn.2021.7192.Peer-Reviewed Original Research
2021
An independent assessment of an artificial intelligence system for prostate cancer detection shows strong diagnostic accuracy
Perincheri S, Levi AW, Celli R, Gershkovich P, Rimm D, Morrow JS, Rothrock B, Raciti P, Klimstra D, Sinard J. An independent assessment of an artificial intelligence system for prostate cancer detection shows strong diagnostic accuracy. Modern Pathology 2021, 34: 1588-1595. PMID: 33782551, PMCID: PMC8295034, DOI: 10.1038/s41379-021-00794-x.Peer-Reviewed Original ResearchConceptsMemorial Sloan-Kettering Cancer CenterCore biopsyPredictive valueDiagnostic accuracyProstate core needle biopsiesCore needle biopsySurgical pathology practiceNegative predictive valueProstate core biopsiesPositive predictive valueProstate cancer detectionStrong diagnostic accuracyPoor quality scansCancer detectionCancer CenterProstate biopsyLeading causeNeedle biopsyTransrectal approachProstate cancerProstatic adenocarcinomaProstate carcinomaBiopsyPathology practiceProstateMeasuring Faculty Effort: A Quantitative Approach That Aligns Personal and Institutional Goals in Pathology at Yale
Morrow JS, Gershkovich P, Gibson J, Gilshannon M, Kowalski D, Levi AW, Nguyen DX, Rimm DL, Xu ML, Sinard J. Measuring Faculty Effort: A Quantitative Approach That Aligns Personal and Institutional Goals in Pathology at Yale. Academic Pathology 2021, 8: 23742895211047985. PMID: 34646939, PMCID: PMC8504692, DOI: 10.1177/23742895211047985.Peer-Reviewed Original Research
2020
1 IMPROVING LYNCH SYNDROME IDENTIFICATION THROUGH THE IMPLEMENTATION OF ENHANCED TUMOR TESTING AND A COMPREHENSIVE SYSTEMS APPROACH
Singh V, Ganzak A, Gershkovich P, Gibson J, Llor X. 1 IMPROVING LYNCH SYNDROME IDENTIFICATION THROUGH THE IMPLEMENTATION OF ENHANCED TUMOR TESTING AND A COMPREHENSIVE SYSTEMS APPROACH. Gastroenterology 2020, 158: s-1. DOI: 10.1016/s0016-5085(20)30682-x.Peer-Reviewed Original Research
2018
TQuest, A Web-Based Platform to Enable Precision Medicine by Linking a Tumor’s Genetic Defects to Therapeutic Options
Gershkovich P, Platt J, Knopf J, Tasoulis MK, Shi W, Pusztai L, Hatzis C. TQuest, A Web-Based Platform to Enable Precision Medicine by Linking a Tumor’s Genetic Defects to Therapeutic Options. JCO Clinical Cancer Informatics 2018, 2: 1-13. PMID: 30652574, DOI: 10.1200/cci.17.00120.Peer-Reviewed Original ResearchConceptsData acquisition layerFull-text indexAcquisition layerUser interfaceData layersPrototype web applicationWeb-based platformWeb applicationRelevance scoresSearch enginesSource codeSoftware toolsSearch resultsInterventional clinical trialsLabel dataClinical trialsTherapeutic optionsPlatformUS FoodMolecular abnormalitiesMetastatic breast cancerPotential therapeutic optionPotential treatment optionTumor DNA sequencingWeb-based modules
2015
Customizing Laboratory Information Systems
Gershkovich P, Sinard JH. Customizing Laboratory Information Systems. Advances In Anatomic Pathology 2015, 22: 323-330. PMID: 26262515, DOI: 10.1097/pap.0000000000000088.Peer-Reviewed Original ResearchMutation-based treatment recommendations from next generation sequencing data: A comparison of web tools.
Patel J, Reiner E, Bossuyt V, Epstein L, Platt J, DiGiovanna M, Chung G, Silber A, Sanft T, Hofstatter E, Mougalian S, Abu-Khalaf M, Gershkovich P, Hatzis C, Pusztai L. Mutation-based treatment recommendations from next generation sequencing data: A comparison of web tools. Journal Of Clinical Oncology 2015, 33: e12564-e12564. DOI: 10.1200/jco.2015.33.15_suppl.e12564.Peer-Reviewed Original Research
2014
Are Amended Surgical Pathology Reports Getting to the Correct Responsible Care Provider?
Parkash V, Domfeh A, Cohen P, Fischbach N, Pronovost M, Haines GK, Gershkovich P. Are Amended Surgical Pathology Reports Getting to the Correct Responsible Care Provider? American Journal Of Clinical Pathology 2014, 142: 58-63. PMID: 24926086, DOI: 10.1309/ajcpy55evinjclgx.Peer-Reviewed Original ResearchConceptsCare providersTumor board discussionChart reviewPatient chartsPhysician chartsElectronic health record systemsPatient referralMalignant diagnosisErroneous managementSurgical pathologyHealth record systemsClinical teamOriginal diagnosisDiagnostic changesPhysiciansNew physiciansReport reviewPatientsRecord systemReferralDiagnosisEMR systemBoard discussionsDelivery systemReview
2013
A Retrospective Population-Based Comparison of HER2 Immunohistochemistry and Fluorescence In Situ Hybridization in Breast Carcinomas: Impact of 2007 American Society of Clinical Oncology/ College of American Pathologists Criteria
Schalper KA, Kumar S, Hui P, Rimm DL, Gershkovich P. A Retrospective Population-Based Comparison of HER2 Immunohistochemistry and Fluorescence In Situ Hybridization in Breast Carcinomas: Impact of 2007 American Society of Clinical Oncology/ College of American Pathologists Criteria. Archives Of Pathology & Laboratory Medicine 2013, 138: 213-9. PMID: 24164555, DOI: 10.5858/arpa.2012-0617-oa.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overBreast NeoplasmsCarcinomaCohort StudiesConnecticutFemaleHospitals, UniversityHumansImmunohistochemistryIn Situ Hybridization, FluorescenceMammary Glands, HumanMiddle AgedNeoplasm GradingNeoplasm InvasivenessNeoplasm ProteinsPractice Guidelines as TopicReceptor, ErbB-2Retrospective StudiesSocieties, MedicalUnited StatesUnited States Food and Drug Administration
2012
Custom software development for use in a clinical laboratory
Sinard JH, Gershkovich P. Custom software development for use in a clinical laboratory. Journal Of Pathology Informatics 2012, 3: 44. PMID: 23372985, PMCID: PMC3551490, DOI: 10.4103/2153-3539.104906.Peer-Reviewed Original ResearchSoftware developmentCustom software developmentSoftware development practicesHouse software developmentOpen source toolsLarge development teamsCustom developmentSingle programmerHouse solutionsDevelopment teamsFunctional specificationDepartmental workflowDevelopment processSignificant solutionCustom softwareDevelopment practicesDepartmental needsDecision balance sheetProgrammersDevelopment philosophyWorkflowSignificant advantagesDecisionsSoftwareSpecification
2011
Standardization of Estrogen Receptor Measurement in Breast Cancer Suggests False-Negative Results Are a Function of Threshold Intensity Rather Than Percentage of Positive Cells
Welsh AW, Moeder CB, Kumar S, Gershkovich P, Alarid ET, Harigopal M, Haffty BG, Rimm DL. Standardization of Estrogen Receptor Measurement in Breast Cancer Suggests False-Negative Results Are a Function of Threshold Intensity Rather Than Percentage of Positive Cells. Journal Of Clinical Oncology 2011, 29: 2978-2984. PMID: 21709197, PMCID: PMC3157961, DOI: 10.1200/jco.2010.32.9706.Peer-Reviewed Original ResearchConceptsER-positive patientsEstrogen receptorQuantitative immunofluorescenceBreast cancerTissue microarrayPositive cellsIndependent retrospective cohortsEstrogen receptor measurementsAssessment of survivalTMA cohortFalse-negative resultsRetrospective cohortER immunoreactivityTest discordancePrognostic outcomesIndependent cohortReceptor measurementsLimitations of immunohistochemistryPatientsDiscrepant casesCohortIHC methodPathologists' judgmentsDiscrepant resultsStandardized assays
2007
Dynamic Display of Turnaround Time Via Interactive 2D Images
Gershkovich P, Tselovalnikov A. Dynamic Display of Turnaround Time Via Interactive 2D Images. Lecture Notes In Computer Science 2007, 4370: 55-62. DOI: 10.1007/978-3-540-71027-1_6.Peer-Reviewed Original Research
2002
An approach to object-relational mapping in bioscience domains.
Tuck D, O'Connell R, Gershkovich P, Cowan J. An approach to object-relational mapping in bioscience domains. Proceedings / AMIA ... Annual Symposium. AMIA Symposium 2002, 820-4. PMID: 12463939, PMCID: PMC2244333.Peer-Reviewed Original Research
2001
An approach to guideline implementation with GEM.
Shiffman RN, Agrawal A, Deshpande AM, Gershkovich P. An approach to guideline implementation with GEM. 2001, 84: 271-5. PMID: 11604747.Peer-Reviewed Original ResearchConceptsGuideline Elements ModelInformation management servicesClinical domain expertsSystem programmersDocument markupDocument modelKnowledge extractionDomain expertsKnowledge engineersDesign databaseKnowledge customizationAudit trailKnowledge baseDesign goalsQuality assurance expertsKnowledge integrationManagement servicesConsistent knowledgeImplementationPatient dataCreation of strategiesProgrammersDevelopersExpertsCustomizationAn implementation framework for GEM encoded guidelines.
Gershkovich P, Shiffman RN. An implementation framework for GEM encoded guidelines. AMIA Annual Symposium Proceedings 2001, 204-8. PMID: 11825181, PMCID: PMC2243348.Peer-Reviewed Original ResearchConceptsGuideline Elements ModelDecision support informationPublishing frameworkEnd usersComputable formatSupport informationImplementation frameworkIntegration of knowledgeClinical systemsFormatImplementationPresentation formatGuideline knowledgeFeasibility of implementationFrameworkUsersGuideline contentProgrammingMain obstaclesMarkupLogicFunctionalityClinical knowledgeKnowledgeGuideline authors
Others
- Sinard J. H., Mutnick, N, Gershkovich, P (2011) Facilitating Feedback and Education on the Hot Seat Rotation. J. Pathol Inform 2011, 2:43 S12Peer-Reviewed Original Research
- Gershkovich, P., Sinard J. H. (2011) Duplicate Patients: Considering Clinical Priority in Resolving Patient Registration Errors. J. Pathol Inform 2011, 2:43 S5Peer-Reviewed Original Research