TitleAssistant Professor
InstitutionBaylor College of Medicine
DepartmentDepartment of Integrative Physiology
AddressOne Baylor Plaza
Houston, TX 77030
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Yafi MA, Hisham MHH, Grisanti F, Martin JF, Rahman A, Samee MAH. scGIST: gene panel design for spatial transcriptomics with prioritized gene sets. Genome Biol. 2024 Feb 26; 25(1):57. PMID: 38408997; PMCID: PMC10895727.
      Citations:    Fields:    Translation:Cells
    2. Li 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 JF. YAP induces a neonatal-like pro-renewal niche in the adult heart. Nat Cardiovasc Res. 2024 Mar; 3(3):283-300. PMID: 38510108; PMCID: PMC10954255.
    3. Tseng YJ, Kageyama Y, Murdaugh RL, Kitano A, Kim JH, Hoegenauer KA, Tiessen J, Smith MH, Uryu H, Takahashi K, Martin JF, Samee MAH, Nakada D. Increased iron uptake by splenic hematopoietic stem cells promotes TET2-dependent erythroid regeneration. Nat Commun. 2024 Jan 15; 15(1):538. PMID: 38225226; PMCID: PMC10789814.
      Citations:    Fields:    Translation:HumansCells
    4. Long H, Steimle JD, Grisanti Canozo FJ, Kim JH, Li X, Morikawa Y, Park M, Turaga D, Adachi I, Wythe JD, Samee MAH, Martin JF. Endothelial cells adopt a pro-reparative immune responsive signature during cardiac injury. Life Sci Alliance. 2024 Feb; 7(2). PMID: 38012001; PMCID: PMC10681909.
      Citations:    Fields:    Translation:HumansAnimalsCells
    5. Rahman MN, Noman AA, Turza AM, Abrar MA, Samee MAH, Rahman MS. ScribbleDom: using scribble-annotated histology images to identify domains in spatial transcriptomics data. Bioinformatics. 2023 Oct 03; 39(10). PMID: 37756699; PMCID: PMC10564617.
      Citations: 1     Fields:    
    6. Tsai CR, Kim J, Li X, Czarnewski P, Li R, Meng F, Zheng M, Zhao X, Steimle J, Grisanti F, Wang J, Samee MAH, Martin J. Hippo-deficient cardiac fibroblasts differentiate into osteochondroprogenitors. bioRxiv. 2023 Sep 08. PMID: 38529510; PMCID: PMC10962739.
    7. Liu Z, Samee MAH. Structural underpinnings of mutation rate variations in the human genome. Nucleic Acids Res. 2023 08 11; 51(14):7184-7197. PMID: 37395403; PMCID: PMC10415140.
      Citations: 4     Fields:    Translation:Humans
    8. Samee MAH. Noncanonical binding of transcription factors: time to revisit specificity? Mol Biol Cell. 2023 08 01; 34(9). PMID: 37486893; PMCID: PMC10398899.
      Citations:    Fields:    Translation:HumansCells
    9. Abrar MA, Kaykobad M, Rahman MS, Samee MAH. NoVaTeST: identifying genes with location-dependent noise variance in spatial transcriptomics data. Bioinformatics. 2023 06 01; 39(6). PMID: 37285319; PMCID: PMC10283152.
      Citations: 1     Fields:    Translation:Cells
    10. Ortiz CJ, Romero J, Pedersen SE, Samee MAH, Pautler RG, Lutter JC, Batchev AL, Sertage AG, Subasinghe SAAS, Allen MJ. Outersphere 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. PMID: 36906514; PMCID: PMC10440236.
      Citations:    Fields:    Translation:Humans
    11. Xu W, Graves A, Weisz-Hubshman M, Hegazy L, Magyar C, Liu Z, Nasiotis E, Samee MAH, Burris T, Lalani S, Zhang L. Assigning 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. PMID: 36229919; PMCID: PMC9990987.
      Citations:    Fields:    Translation:Humans
    12. Khan SR, Sakib S, Rahman MS, Samee MAH. DeepBend: An interpretable model of DNA bendability. iScience. 2023 Feb 17; 26(2):105945. PMID: 36866046; PMCID: PMC9971889.
    13. Park M, Singh S, Khan SR, Abrar MA, Grisanti F, Rahman MS, Samee MAH. Multinomial Convolutions for Joint Modeling of Regulatory Motifs and Sequence Activity Readouts. Genes (Basel). 2022 09 08; 13(9). PMID: 36140783; PMCID: PMC9498894.
    14. Subasinghe SAAS, Pautler RG, Samee MAH, Yustein JT, Allen MJ. Dual-Mode Tumor Imaging Using Probes That Are Responsive to Hypoxia-Induced Pathological Conditions. Biosensors (Basel). 2022 Jun 30; 12(7). PMID: 35884281; PMCID: PMC9313010.
      Citations:    Fields:    Translation:Humans
    15. Steimle JD, Grisanti Canozo FJ, Park M, Kadow ZA, Samee MAH, Martin JF. Decoding the PITX2-controlled genetic network in atrial fibrillation. JCI Insight. 2022 06 08; 7(11). PMID: 35471998; PMCID: PMC9221021.
      Citations:    Fields:    Translation:Humans
    16. Samee MAH. Approaching deconvolution with Fermi's mindset. Cell Syst. 2022 05 18; 13(5):351-352. PMID: 35588698.
      Citations:    Fields:    Translation:Cells
    17. Grisanti Canozo FJ, Zuo Z, Martin JF, Samee MAH. Cell-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. PMID: 34626538; PMCID: PMC8776574.
      Citations: 1     Fields:    Translation:AnimalsCells
    18. Chumpitaz-Diaz L, Samee MAH, Pollard KS. Systematic identification of non-canonical transcription factor motifs. BMC Mol Cell Biol. 2021 Aug 31; 22(1):44. PMID: 34465294; PMCID: PMC8408965.
      Citations:    Fields:    Translation:HumansCells
    19. Samee MAH, Bruneau BG, Pollard KS. A 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. PMID: 30660610; PMCID: PMC6368855.
      Citations: 20     Fields:    Translation:HumansCells
    20. Samee MAH, Lydiard-Martin T, Biette KM, Vincent BJ, Bragdon MD, Eckenrode KB, Wunderlich Z, Estrada J, Sinha S, DePace AH. Quantitative 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. PMID: 28978476; PMCID: PMC5690553.
      Citations: 7     Fields:    Translation:AnimalsCells
    21. Luna-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, Bruneau BG, M?ller CW. Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis. Cell. 2016 Feb 25; 164(5):999-1014. PMID: 26875865; PMCID: PMC4769693.
      Citations: 85     Fields:    Translation:AnimalsCells
    22. Samee MA, Lu H, Rushlow CA, Sinha S, Lim B, Samper N, Jim?nez G, Shvartsman SY. A Systematic Ensemble Approach to Thermodynamic Modeling of Gene Expression from Sequence Data. Cell Syst. 2015 Dec 23; 1(6):396-407. PMID: 27136354; PMCID: PMC5094195.
      Citations: 18     Fields:    
    23. Kazemian M, Suryamohan K, Chen JY, Zhang Y, Samee MA, Halfon MS, Sinha S. Evidence for deep regulatory similarities in early developmental programs across highly diverged insects. Genome Biol Evol. 2014 Sep; 6(9):2301-20. PMID: 25173756; PMCID: PMC4217690.
      Citations: 21     Fields:    Translation:AnimalsCells
    24. Samee MA, Sinha S. Quantitative modeling of a gene's expression from its intergenic sequence. PLoS Comput Biol. 2014 Mar; 10(3):e1003467. PMID: 24604095; PMCID: PMC3945089.
      Citations: 18     Fields:    Translation:AnimalsCells
    25. Duque T, Samee MA, Kazemian M, Pham HN, Brodsky MH, Sinha S. Simulations of enhancer evolution provide mechanistic insights into gene regulation. Mol Biol Evol. 2014 Jan; 31(1):184-200. PMID: 24097306; PMCID: PMC3879441.
      Citations: 15     Fields:    Translation:AnimalsCells
    26. Suleimenov Y, Ay A, Samee MA, Dresch JM, Sinha S, Arnosti DN. Global parameter estimation for thermodynamic models of transcriptional regulation. Methods. 2013 Jul 15; 62(1):99-108. PMID: 23726942.
      Citations: 4     Fields:    Translation:HumansAnimalsCells
    27. He X, Samee MA, Blatti C, Sinha S. Thermodynamics-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). PMID: 20862354; PMCID: PMC2940721.
      Citations: 88     Fields:    Translation:AnimalsCells
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