MD. ABUL HASSANSAMEEMD. ABUL HASSAN SAMEE14899SAMEE, MD. ABUL HASSANAssistant Professorplugins:TwitterTwitterprns:coAuthorOfcoauthor ofprns:emailEncryptedemail addressFaculty 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:pluginSearchableDataProfilesRNS Plugin Searchable Dataprns:positionInDepartmentposition in departmentprns:positionInDivisionposition in divisionprns:predicateNodepredicate nodeprns:publicationDatepublication dateprns:similarTosimilar toprns:sortOrdersort orderprns:uniquenessWeightuniqueness weightprns:yearyearAcademic ArticleArticleDocumentbibo:pmidPubMed IdentifierAddressvivo:address1address line 1vivo:addressCitycityvivo:addressPostalCodepostal codevivo:addressStatestate or provincevivo:authorInAuthorshipselected publicationsvivo:authorRankauthor rank in publicationAuthorshipDepartmentDivisionvivo:hasResearchArearesearch areasvivo:hrJobTitleHR job titleInformation Resourcevivo:linkAnchorTextlink anchor textvivo:linkedAuthorlinked authorvivo:linkedInformationResourcelinked information resourcevivo:mailingAddressmailing addressvivo:personInPositionpositionsPositionvivo:positionInOrganizationposition in organizationvivo:preferredTitlepreferred titleURLLinkvivo:webpagewebpagerdf:predicatepredicaterdf:typetyperdfs:labellabelConceptAgentfoaf:firstNamefirst namefoaf:lastNamelast nameOrganizationPersonMolecular & Cellular OncologyMD Anderson74Professor10Assistant Professor14Associate Professor47Distinguished Service ProfessorJOHNTAINERJOHN TAINER11926TAINER, JOHNProfessorMedicine-Epidemiology & Populat Sci53Graduate StudentCHRISAMOSCHRIS AMOS13498AMOS, CHRISProfessortrue1ProfessorProfessortrue1ProfessorProfessorD004247Chemicals & Drugs86226890.536389DNAD001665Chemicals & Drugs74421670.708734Binding SitesD014157Chemicals & Drugs126452670.358125Transcription FactorsDepartment of MedicineDepartment of Molecular & Human GeneticsMolecular & Human GeneticsMolecular Physiology & BiophysicsBaylor College of MedicineJAMESMARTINJAMES MARTIN0.000000000000000.000000000000001889MARTIN, JAMESProfessorJAMESLUPSKIJAMES LUPSKI29.71073630000000-95.396604500000003140LUPSKI, JAMESProfessorHUGOBELLENHUGO BELLEN29.71010310000000-95.397396100000003292BELLEN, HUGODistinguished Service ProfessorDAISUKENAKADAOKo74GHGQIn2S8Ho5G4=DAISUKE NAKADA29.71073630000000-95.396604500000004024NAKADA, DAISUKEProfessorD059467Concepts & IdeasGenes & Molecular Sequences76218630.524004TranscriptomeD059645Concepts & Ideas1542230.900031Mutation RateCHAOCHENGCHAO CHENG14626CHENG, CHAOAssociate ProfessorOne Baylor PlazaHouston, 77030TXtrue1Postdoc Fellows and AssociatesPostdoc Fellows and Associatestrue1Graduate StudentGraduate Studenttrue1Postdoc Fellows and AssociatesPostdoc Fellows and AssociatesQuantitative & Computational Biosciences1.91870.013459599research areas1.015740.055404517coauthor of21.10555.2057360similar to1126selected publicationsWeiyiXuWeiyi Xu14947Xu, WeiyiPostdoc Fellows and AssociatesZianLiuZian Liu15039Liu, ZianGraduate StudentJeffreySteimleJeffrey David Steimle15195Steimle, JeffreyPostdoc Fellows and AssociatesAuthorship 9587532Authorship 9589412Authorship 9590151Authorship 9590543Authorship 9592377Authorship 9592531Authorship 9592665Authorship 9597881Authorship 960350128978476Samee MAH, Lydiard-Martin T, Biette KM, Vincent BJ, Bragdon MD, Eckenrode KB, Wunderlich Z, Estrada J, Sinha S, DePace AHCell reportsQuantitative Measurement and Thermodynamic Modeling of Fused Enhancers Support a Two-Tiered Mechanism for Interpreting Regulatory DNA. Cell Rep. 2017 Oct 03; 21(1):236-245.Cell Rep2017-10-03T00:00:002017Quantitative Measurement and Thermodynamic Modeling of Fused Enhancers Support a Two-Tiered Mechanism for Interpreting Regulatory DNA.24604095Samee MA, Sinha SPLoS computational biologyQuantitative modeling of a gene's expression from its intergenic sequence. PLoS Comput Biol. 2014 Mar; 10(3):e1003467.PLoS Comput Biol2014-03-06T00:00:002014Quantitative modeling of a gene's expression from its intergenic sequence.26875865Luna-Zurita L, Stirnimann CU, Glatt S, Kaynak BL, Thomas S, Baudin F, Samee MA, He D, Small EM, Mileikovsky M, Nagy A, Holloway AK, Pollard KS, M?ller CW, Bruneau BGCellComplex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis. Cell. 2016 Feb 25; 164(5):999-1014.Cell2016-02-11T00:00:002016Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis.27136354Samee MA, Lim B, Samper N, Lu H, Rushlow CA, Jim?nez G, Shvartsman SY, Sinha SCell systemsA Systematic Ensemble Approach to Thermodynamic Modeling of Gene Expression from Sequence Data. Cell Syst. 2015 Dec 23; 1(6):396-407.Cell Syst2015-12-23T00:00:002015A Systematic Ensemble Approach to Thermodynamic Modeling of Gene Expression from Sequence Data.25173756Kazemian M, Suryamohan K, Chen JY, Zhang Y, Samee MA, Halfon MS, Sinha SGenome biology and evolutionEvidence for deep regulatory similarities in early developmental programs across highly diverged insects. Genome Biol Evol. 2014 Sep; 6(9):2301-20.Genome Biol Evol2014-09-01T00:00:002014Evidence for deep regulatory similarities in early developmental programs across highly diverged insects.30660610Samee MAH, Bruneau BG, Pollard KSCell systemsA De Novo Shape Motif Discovery Algorithm Reveals Preferences of Transcription Factors for DNA Shape Beyond Sequence Motifs. Cell Syst. 2019 01 23; 8(1):27-42.e6.Cell Syst2019-01-16T00:00:002019A De Novo Shape Motif Discovery Algorithm Reveals Preferences of Transcription Factors for DNA Shape Beyond Sequence Motifs.20862354He X, Samee MA, Blatti C, Sinha SPLoS computational biologyThermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression. PLoS Comput Biol. 2010 Sep 16; 6(9).PLoS Comput Biol2010-09-16T00:00:002010Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression.24097306Duque T, Samee MA, Kazemian M, Pham HN, Brodsky MH, Sinha SMolecular biology and evolutionSimulations of enhancer evolution provide mechanistic insights into gene regulation. Mol Biol Evol. 2014 Jan; 31(1):184-200.Mol Biol Evol2013-10-04T00:00:002013Simulations of enhancer evolution provide mechanistic insights into gene regulation.23726942Suleimenov Y, Ay A, Samee MA, Dresch JM, Sinha S, Arnosti DNMethods (San Diego, Calif.)Global parameter estimation for thermodynamic models of transcriptional regulation. Methods. 2013 Jul 15; 62(1):99-108.Methods2013-05-30T00:00:002013Global parameter estimation for thermodynamic models of transcriptional regulation.71Postdoc Fellows and AssociatesPostDochttp://flypush.imgen.bcm.tmc.eduBellen Lab Websitetrue1Distinguished Service ProfessorDistinguished Service ProfessorAuthorship 1028812234465294Chumpitaz-Diaz L, Samee MAH, Pollard KSBMC molecular and cell biologySystematic identification of non-canonical transcription factor motifs. BMC Mol Cell Biol. 2021 Aug 31; 22(1):44.BMC Mol Cell Biol2021-08-31T00:00:002021Systematic identification of non-canonical transcription factor motifs.Authorship 1031299434626538Grisanti Canozo FJ, Zuo Z, Martin JF, Samee MAHCell systemsCell-type modeling in spatial transcriptomics data elucidates spatially variable colocalization and communication between cell-types in mouse brain. Cell Syst. 2022 01 19; 13(1):58-70.e5.Cell Syst2021-10-08T00:00:002021Cell-type modeling in spatial transcriptomics data elucidates spatially variable colocalization and communication between cell-types in mouse brain.https://www.bcm.edu/research/faculty-labs/daisuke-nakada-labNakada labTwitter Tweets Harvard Tweetstrue1Associate ProfessorAssociate ProfessorAuthorship 1044515535471998Steimle JD, Grisanti Canozo FJ, Park M, Kadow ZA, Samee MAH, Martin JFJCI insightDecoding the PITX2-controlled genetic network in atrial fibrillation. JCI Insight. 2022 06 08; 7(11).JCI Insight2022-06-08T00:00:002022Decoding the PITX2-controlled genetic network in atrial fibrillation.Authorship 1046218135588698Samee MAHCell systemsApproaching deconvolution with Fermi's mindset. Cell Syst. 2022 05 18; 13(5):351-352.Cell Syst2022-05-18T00:00:002022Approaching deconvolution with Fermi's mindset.Authorship 1051457335884281Subasinghe SAAS, Pautler RG, Samee MAH, Yustein JT, Allen MJBiosensorsDual-Mode Tumor Imaging Using Probes That Are Responsive to Hypoxia-Induced Pathological Conditions. Biosensors (Basel). 2022 Jun 30; 12(7).Biosensors (Basel)2022-06-30T00:00:002022Dual-Mode Tumor Imaging Using Probes That Are Responsive to Hypoxia-Induced Pathological Conditions.true1Assistant ProfessorAssistant Professortrue1ProfessorProfessorDepartment of Integrative PhysiologyAuthorship 10568318Authorship 1058073736229919Xu W, Graves A, Weisz-Hubshman M, Hegazy L, Magyar C, Liu Z, Nasiotis E, Samee MAH, Burris T, Lalani S, Zhang LHuman molecular geneticsAssigning pathogenicity for TAB2 variants using a novel scalable functional assay and expanding TAB2 disease spectrum. Hum Mol Genet. 2023 03 06; 32(6):959-970.Hum Mol Genet2023-03-06T00:00:002023Assigning pathogenicity for TAB2 variants using a novel scalable functional assay and expanding TAB2 disease spectrum.36140783Park M, Singh S, Khan SR, Abrar MA, Grisanti F, Rahman MS, Samee MAHGenesMultinomial Convolutions for Joint Modeling of Regulatory Motifs and Sequence Activity Readouts. Genes (Basel). 2022 09 08; 13(9).Genes (Basel)2022-09-08T00:00:002022Multinomial Convolutions for Joint Modeling of Regulatory Motifs and Sequence Activity Readouts.Authorship 1064996436866046Khan SR, Sakib S, Rahman MS, Samee MAHiScienceDeepBend: An interpretable model of DNA bendability. iScience. 2023 Feb 17; 26(2):105945.iScience2023-01-07T00:00:002023DeepBend: An interpretable model of DNA bendability.Authorship 1065860436906514Lutter JC, Batchev AL, Ortiz CJ, Sertage AG, Romero J, Subasinghe SAAS, Pedersen SE, Samee MAH, Pautler RG, Allen MJAdvanced healthcare materialsOutersphere Approach to Increasing the Persistance of Oxygen-Sensitive Europium(II)-Containing Contrast Agents for Magnetic Resonance Imaging with Perfluorocarbon Nanoemulsions toward Imaging of Hypoxia. Adv Healthc Mater. 2023 07; 12(19):e2203209.Adv Healthc Mater2023-03-24T00:00:002023Outersphere Approach to Increasing the Persistance of Oxygen-Sensitive Europium(II)-Containing Contrast Agents for Magnetic Resonance Imaging with Perfluorocarbon Nanoemulsions toward Imaging of Hypoxia.true1ProfessorProfessorAuthorship 10720944Authorship 1073343237285319Abrar MA, Kaykobad M, Rahman MS, Samee MAHBioinformatics (Oxford, England)NoVaTeST: identifying genes with location-dependent noise variance in spatial transcriptomics data. Bioinformatics. 2023 06 01; 39(6).Bioinformatics2023-06-01T00:00:002023NoVaTeST: identifying genes with location-dependent noise variance in spatial transcriptomics data.37395403Liu Z, Samee MAHNucleic acids researchStructural underpinnings of mutation rate variations in the human genome. Nucleic Acids Res. 2023 08 11; 51(14):7184-7197.Nucleic Acids Res2023-08-11T00:00:002023Structural underpinnings of mutation rate variations in the human genome.Authorship 1075666137486893Samee MAHMolecular biology of the cellNoncanonical binding of transcription factors: time to revisit specificity? Mol Biol Cell. 2023 08 01; 34(9).Mol Biol Cell2023-08-01T00:00:002023Noncanonical binding of transcription factors: time to revisit specificity?Authorship 1079798537756699Rahman MN, Noman AA, Turza AM, Abrar MA, Samee MAH, Rahman MSBioinformatics (Oxford, England)ScribbleDom: using scribble-annotated histology images to identify domains in spatial transcriptomics data. Bioinformatics. 2023 Oct 03; 39(10).Bioinformatics2023-10-03T00:00:002023ScribbleDom: using scribble-annotated histology images to identify domains in spatial transcriptomics data.Authorship 10838561138012001Long H, Steimle JD, Grisanti Canozo FJ, Kim JH, Li X, Morikawa Y, Park M, Turaga D, Adachi I, Wythe JD, Samee MAH, Martin JFLife science allianceEndothelial cells adopt a pro-reparative immune responsive signature during cardiac injury. Life Sci Alliance. 2024 Feb; 7(2).Life Sci Alliance2023-11-27T00:00:002023Endothelial cells adopt a pro-reparative immune responsive signature during cardiac injury.Authorship 10872761238225226Tseng YJ, Kageyama Y, Murdaugh RL, Kitano A, Kim JH, Hoegenauer KA, Tiessen J, Smith MH, Uryu H, Takahashi K, Martin JF, Samee MAH, Nakada DNature communicationsIncreased iron uptake by splenic hematopoietic stem cells promotes TET2-dependent erythroid regeneration. Nat Commun. 2024 Jan 15; 15(1):538.Nat Commun2024-01-15T00:00:002024Increased iron uptake by splenic hematopoietic stem cells promotes TET2-dependent erythroid regeneration.Authorship 1089587638408997Yafi MA, Hisham MHH, Grisanti F, Martin JF, Rahman A, Samee MAHGenome biologyscGIST: gene panel design for spatial transcriptomics with prioritized gene sets. Genome Biol. 2024 Feb 26; 25(1):57.Genome Biol2024-02-26T00:00:002024scGIST: gene panel design for spatial transcriptomics with prioritized gene sets.Authorship 10914141338510108Li RG, Li X, Morikawa Y, Grisanti-Canozo FJ, Meng F, Tsai CR, Zhao Y, Liu L, Kim J, Xie B, Klysik E, Liu S, Samee MAH, Martin JFNature cardiovascular researchYAP induces a neonatal-like pro-renewal niche in the adult heart. Nat Cardiovasc Res. 2024 Mar; 3(3):283-300.Nat Cardiovasc Res2024-02-14T00:00:002024YAP induces a neonatal-like pro-renewal niche in the adult heart.true1ProfessorProfessor