Zobrazeno 1 - 10
of 49
pro vyhledávání: '"Manu Setty"'
Autor:
Andrew A. Smith, Yee Nip, Sean R. Bennett, Danielle C. Hamm, Richard J.L.F. Lemmers, Patrick J. van der Vliet, Manu Setty, Silvère M. van der Maarel, Stephen J. Tapscott
Publikováno v:
Cell Reports, Vol 42, Iss 9, Pp 113114- (2023)
Summary: The transcription factor DUX4 regulates a portion of the zygotic gene activation (ZGA) program in the early embryo. Many cancers express DUX4 but it is unknown whether this generates cells similar to early embryonic stem cells. Here we ident
Externí odkaz:
https://doaj.org/article/70fb10c8f7de409fa807c206d67c1199
Autor:
Derek H. Janssens, Dominik J. Otto, Michael P. Meers, Manu Setty, Kami Ahmad, Steven Henikoff
Publikováno v:
Genome Biology, Vol 23, Iss 1, Pp 1-19 (2022)
Abstract Cleavage Under Targets and Tagmentation (CUT&Tag) is an antibody-directed transposase tethering strategy for in situ chromatin profiling in small samples and single cells. We describe a modified CUT&Tag protocol using a mixture of an antibod
Externí odkaz:
https://doaj.org/article/2363434c279348e18326a59aafb527f7
Autor:
Alexandre A Germanos, Sonali Arora, Ye Zheng, Erica T Goddard, Ilsa M Coleman, Anson T Ku, Scott Wilkinson, Hanbing Song, Nicholas J Brady, Robert A Amezquita, Michael Zager, Annalysa Long, Yu Chi Yang, Jason H Bielas, Raphael Gottardo, David S Rickman, Franklin W Huang, Cyrus M Ghajar, Peter S Nelson, Adam G Sowalsky, Manu Setty, Andrew C Hsieh
Publikováno v:
eLife, Vol 11 (2022)
Advanced prostate malignancies are a leading cause of cancer-related deaths in men, in large part due to our incomplete understanding of cellular drivers of disease progression. We investigate prostate cancer cell dynamics at single-cell resolution f
Externí odkaz:
https://doaj.org/article/df92bed0fdd1409a988b59a78b4ffbca
Autor:
Manu Setty, Karim Helmy, Aly A Khan, Joachim Silber, Aaron Arvey, Frank Neezen, Phaedra Agius, Jason T Huse, Eric C Holland, Christina S Leslie
Publikováno v:
Molecular Systems Biology, Vol 8, Iss 1, Pp 1-16 (2012)
Abstract Large‐scale cancer genomics projects are profiling hundreds of tumors at multiple molecular layers, including copy number, mRNA and miRNA expression, but the mechanistic relationships between these layers are often excluded from computatio
Externí odkaz:
https://doaj.org/article/78aa18a9a4874fceac1d6c85c18a2495
Autor:
Manu Setty, Christina S Leslie
Publikováno v:
PLoS Computational Biology, Vol 11, Iss 5, p e1004271 (2015)
Genome-wide maps of transcription factor (TF) occupancy and regions of open chromatin implicitly contain DNA sequence signals for multiple factors. We present SeqGL, a novel de novo motif discovery algorithm to identify multiple TF sequence signals f
Externí odkaz:
https://doaj.org/article/2c4706293abf4d019c72bc5dba4188c4
Autor:
Karim Helmy, John Halliday, Elena Fomchenko, Manu Setty, Ken Pitter, Christoph Hafemeister, Eric C Holland
Publikováno v:
PLoS ONE, Vol 7, Iss 10, p e46965 (2012)
Post-transcriptional regulation of gene expression contributes to the protein output of a cell, however, methods for measuring translational regulation in complex in vivo systems are lacking. Here, we describe a sensitive method for measuring transla
Externí odkaz:
https://doaj.org/article/fc4b138a9f534f58b18df35f48da5a12
Autor:
Joseph M. Chan, Samir Zaidi, Jillian R. Love, Jimmy L. Zhao, Manu Setty, Kristine M. Wadosky, Anuradha Gopalan, Zi-Ning Choo, Sitara Persad, Jungmin Choi, Justin LaClair, Kayla E. Lawrence, Ojasvi Chaudhary, Tianhao Xu, Ignas Masilionis, Irina Linkov, Shangqian Wang, Cindy Lee, Afsar Barlas, Michael J. Morris, Linas Mazutis, Ronan Chaligne, Yu Chen, David W. Goodrich, Wouter R. Karthaus, Dana Pe’er, Charles L. Sawyers
Publikováno v:
Science
Drug resistance in cancer is often linked to changes in tumor cell state or lineage, but the molecular mechanisms driving this plasticity remain unclear. Using murine organoid and genetically engineered mouse models, we investigated the causes of lin
Autor:
Vidur Garg, Yang Yang, Sonja Nowotschin, Manu Setty, Ying-Yi Kuo, Roshan Sharma, Alexander Polyzos, Eralda Salataj, Dylan Murphy, Amy Jang, Dana Pe’er, Effie Apostolou, Anna-Katerina Hadjantonakis
Publikováno v:
bioRxiv
SUMMARYTwo distinct fates, pluripotent epiblast (EPI) and primitive (extra-embryonic) endoderm (PrE), arise from common progenitor cells, the inner cell mass (ICM), in mammalian embryos. To study how these sister identities are forged, we leveraged e
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::37cf4ed600e290e5a885121db877f73d
https://europepmc.org/articles/PMC10081288/
https://europepmc.org/articles/PMC10081288/
Autor:
Sitara Persad, Zi-Ning Choo, Christine Dien, Noor Sohail, Ignas Masilionis, Ronan Chaligné, Tal Nawy, Chrysothemis C. Brown, Roshan Sharma, Itsik Pe’er, Manu Setty, Dana Pe’er
Publikováno v:
Nature Biotechnology.
Metacells are cell groupings derived from single-cell sequencing data that represent highly granular, distinct cell states. Here we present single-cell aggregation of cell states (SEACells), an algorithm for identifying metacells that overcome the sp
Autor:
Marius Lange, Volker Bergen, Michal Klein, Manu Setty, Bernhard Reuter, Mostafa Bakhti, Heiko Lickert, Meshal Ansari, Janine Schniering, Herbert B. Schiller, Dana Pe’er, Fabian J. Theis
Publikováno v:
Nature Methods. 19:159-170
Computational trajectory inference enables the reconstruction of cell state dynamics from single-cell RNA sequencing experiments. However, trajectory inference requires that the direction of a biological process is known, largely limiting its applica