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PNAS Nexus|June 30, 2025
GraphAge: Unleashing the power of graph neural network to decode epigenetic agingSaleh Sakib Ahmed, Nahian Shabab, Abul Hassan Samee, et al.Briefings in Bioinformatics|March 2, 2026
ORANGE: a machine learning approach for modeling tissue-specific aging from transcriptomic dataWasif Jalal, Mubasshira Musarrat, Md Abul Hassan Samee, et al.Iscience|March 3, 2023
DeepBend: An interpretable model of DNA bendabilitySamin Rahman Khan, Sadman Sakib, M Sohel Rahman, et al.Bioinformatics (Oxford, England)|June 7, 2023
NoVaTeST: identifying genes with location-dependent noise variance in spatial transcriptomics dataMohammed Abid Abrar, M Kaykobad, M Saifur Rahman, et al.Cell Systems|October 9, 2021
Cell-type modeling in spatial transcriptomics data elucidates spatially variable colocalization and communication between cell-types in mouse brainFrancisco Jose Grisanti Canozo, Zhen Zuo, James F Martin, et al.STAR Protocols|May 20, 2026
Protocol for spatially resolved pathology scores using optimal transport on spatial transcriptomics dataMohammad Nuwaisir Rahman, James F Martin, M Saifur Rahman, et al.Genome Research|January 14, 2026
Quantifying pathological progression from single-cell transcriptomic data with scPSSSamin Rahman Khan, M Saifur Rahman, M Sohel Rahman, et al.Molecular Biology and Evolution|October 8, 2013
Simulations of enhancer evolution provide mechanistic insights into gene regulationThyago Duque, Md Abul Hassan Samee, Majid Kazemian, et al.Methods (San Diego, Calif.)|June 4, 2013
Global parameter estimation for thermodynamic models of transcriptional regulationYerzhan Suleimenov, Ahmet Ay, Md Abul Hassan Samee, et al.Genome Biology and Evolution|September 1, 2014
Evidence for deep regulatory similarities in early developmental programs across highly diverged insectsMajid Kazemian, Kushal Suryamohan, Jia-Yu Chen, et al.Pageof 5