Zobrazeno 1 - 9
of 9
pro vyhledávání: '"Ammar Tareen"'
Autor:
Ammar Tareen, Mahdi Kooshkbaghi, Anna Posfai, William T. Ireland, David M. McCandlish, Justin B. Kinney
Publikováno v:
Genome Biology, Vol 23, Iss 1, Pp 1-27 (2022)
Abstract Multiplex assays of variant effect (MAVEs) are a family of methods that includes deep mutational scanning experiments on proteins and massively parallel reporter assays on gene regulatory sequences. Despite their increasing popularity, a gen
Externí odkaz:
https://doaj.org/article/d828facebaf94f6cbf3c37f56bf4cdb6
Autor:
Chirangini Pukhrambam, Vadim Molodtsov, Mahdi Kooshkbaghi, Ammar Tareen, Hoa Vu, Kyle S. Skalenko, Min Su, Zhou Yin, Jared T. Winkelman, Justin B. Kinney, Richard H. Ebright, Bryce E. Nickels
Publikováno v:
Proceedings of the National Academy of Sciences of the United States of America. 119(23)
In σ-dependent transcriptional pausing, the transcription initiation factor σ, translocating with RNA polymerase (RNAP), makes sequence-specific protein-DNA interactions with a promoter-like sequence element in the transcribed region, inducing paus
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9a9ce08beed7340bc479f97b438c74d1
https://pubmed.ncbi.nlm.nih.gov/35653571
https://pubmed.ncbi.nlm.nih.gov/35653571
Autor:
Ammar Tareen, Justin B. Kinney
Publikováno v:
Bioinformatics
Sequence logos are visually compelling ways of illustrating the biological properties of DNA, RNA, and protein sequences, yet it is currently difficult to generate such logos within the Python programming environment. Here we introduce Logomaker, a P
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f2c8a40195d7123883a61675b5ff2e32
https://doi.org/10.1093/bioinformatics/btz921
https://doi.org/10.1093/bioinformatics/btz921
Autor:
Ammar Tareen, Bruce Stillman, Huilin Li, Christian Speck, William T. Ireland, Yi-Jun Sheu, Yixin Hu, Leemor Joshua-Tor, Justin B. Kinney
Publikováno v:
Nature Communications
Nature Communications, Vol 11, Iss 1, Pp 1-12 (2020)
Nature Communications, Vol 11, Iss 1, Pp 1-12 (2020)
DNA replication in eukaryotic cells initiates from replication origins that bind the Origin Recognition Complex (ORC). Origin establishment requires well-defined DNA sequence motifs in Saccharomyces cerevisiae and some other budding yeasts, but most
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3a93f3394324e2d60f66a92c50013ed5
https://pubmed.ncbi.nlm.nih.gov/33056978
https://pubmed.ncbi.nlm.nih.gov/33056978
Publikováno v:
Scientific Reports, Vol 10, Iss 1, Pp 1-9 (2020)
Scientific Reports
Scientific Reports
Are "turn-on" and "turn-off" functions in protein-protein interaction networks exact opposites of each other? To answer this question, we implement a minimal model for the evolution of functional protein-interaction networks using a sequence-based mu
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c1e0028473a908011f39e048cb0a58cd
https://doi.org/10.1038/s41598-020-66699-y
https://doi.org/10.1038/s41598-020-66699-y
Autor:
Ammar Tareen, Justin B. Kinney
The adoption of deep learning techniques in genomics has been hindered by the difficulty of mechanistically interpreting the models that these techniques produce. In recent years, a variety of post-hoc attribution methods have been proposed for addre
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5022f69e9ac3bbd41fcb8d77ee851375
https://doi.org/10.1101/835942
https://doi.org/10.1101/835942
Publikováno v:
Physical Review E. 97
Signal transduction networks can form highly interconnected systems within cells due to network crosstalk, the sharing of input signals between multiple downstream responses. To better understand the evolutionary design principles underlying such net
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::553905d074ddd6a6ad847708c0f9afe7
https://doi.org/10.1103/physreve.97.020402
https://doi.org/10.1103/physreve.97.020402
How might a smooth probability distribution be estimated, with accurately quantified uncertainty, from a limited amount of sampled data? Here we describe a field-theoretic approach that addresses this problem remarkably well in one dimension, providi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::08d3d0ac7a68226fdf2274f57d5599bd
Autor:
Sean Corbett, Lee Rudolph, Jake Simon Kramer, Ammar Tareen, Christopher Pietras, Li Han, Michael Chou, Dylan Glotzer, Emily Eagle, Jonathan Moran, Matthew Valko
Publikováno v:
Springer Tracts in Advanced Robotics ISBN: 9783642362781
WAFR
WAFR
Polygonal loops are interesting both as classical geometric objects and in modeling practical engineering systems, e.g., grasping systems with fingers having planar revolute joints. Convex loop configurations and path planning between them are import
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::aee63338fe086a3e2a84631855a9593c
https://doi.org/10.1007/978-3-642-36279-8_4
https://doi.org/10.1007/978-3-642-36279-8_4