Muhammad S Shamim
Muhammad S Shamim
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Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments
NC Durand, MS Shamim, I Machol, SSP Rao, MH Huntley, ES Lander, ...
Cell systems 3 (1), 95-98, 2016
Cohesin loss eliminates all loop domains
SSP Rao, SC Huang, BG St Hilaire, JM Engreitz, EM Perez, ...
Cell 171 (2), 305-320. e24, 2017
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
O Dudchenko, SS Batra, AD Omer, SK Nyquist, M Hoeger, NC Durand, ...
Science 356 (6333), 92-95, 2017
Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom
NC Durand, JT Robinson, MS Shamim, I Machol, JP Mesirov, ES Lander, ...
Cell systems 3 (1), 99-101, 2016
The energetics and physiological impact of cohesin extrusion
L Vian, A Pękowska, SSP Rao, KR Kieffer-Kwon, S Jung, L Baranello, ...
Cell 173 (5), 1165-1178. e20, 2018
Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture
EM Darrow, MH Huntley, O Dudchenko, EK Stamenova, NC Durand, ...
Proceedings of the National Academy of Sciences 113 (31), E4504-E4512, 2016
Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development
DH Phanstiel, K Van Bortle, DV Spacek, GT Hess, MS Shamim, I Machol, ...
Molecular Cell 67 (6), 1037–1048, 2017
The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000
O Dudchenko, MS Shamim, SS Batra, NC Durand, NT Musial, R Mostofa, ...
BioRxiv, 254797, 2018
Genetic determinants of co-accessible chromatin regions in activated T cells across humans
RE Gate, CS Cheng, AP Aiden, A Siba, M Tabaka, D Lituiev, I Machol, ...
Nature genetics 50 (8), 1140-1150, 2018
The fundamental role of chromatin loop extrusion in physiological V (D) J recombination
Y Zhang, X Zhang, Z Ba, Z Liang, EW Dring, H Hu, J Lou, N Kyritsis, ...
Nature 573 (7775), 600-604, 2019
Large DNA methylation nadirs anchor chromatin loops maintaining hematopoietic stem cell identity
X Zhang, M Jeong, X Huang, XQ Wang, X Wang, W Zhou, MS Shamim, ...
Molecular cell 78 (3), 506-521. e6, 2020
Multiomic profiling identifies cis-regulatory networks underlying human pancreatic β cell identity and function
N Lawlor, EJ Marquez, P Orchard, N Narisu, MS Shamim, A Thibodeau, ...
Cell reports 26 (3), 788-801. e6, 2019
Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst 3: 95–98
NC Durand, MS Shamim, I Machol, SSP Rao, MH Huntley, ES Lander, ...
CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions
A Kaushal, G Mohana, J Dorier, I Özdemir, A Omer, P Cousin, ...
Nature communications 12 (1), 1011, 2021
Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus)
PA Larsen, RA Harris, Y Liu, SC Murali, CR Campbell, AD Brown, ...
BMC biology 15, 1-17, 2017
MCPH1 inhibits Condensin II during interphase by regulating its SMC2-Kleisin interface
M Houlard, EE Cutts, MS Shamim, J Godwin, D Weisz, AP Aiden, ...
Elife 10, e73348, 2021
The ENCODE uniform analysis pipelines
BC Hitz, JW Lee, O Jolanki, MS Kagda, K Graham, P Sud, I Gabdank, ...
bioRxiv, 2023.04. 04.535623, 2023
Hi-C yields chromosome-length scaffolds for a legume genome, Trifolium subterraneum
O Dudchenko, M Pham, C Lui, SS Batra, M Hoeger, SK Nyquist, ...
bioRxiv, 473553, 2018
Cooperation among an anonymous group protected Bitcoin during failures of decentralization
A Blackburn, C Huber, Y Eliaz, MS Shamim, D Weisz, G Seshadri, K Kim, ...
arXiv preprint arXiv:2206.02871, 2022
The Hi-Culfite assay reveals relationships between chromatin contacts and DNA methylation state
EK Stamenova, NC Durand, O Dudchenko, MS Shamim, SC Huang, ...
Biorxiv, 481283, 2018
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