Literature DB >> 36064802

Smart software untangles gene regulation in cells.

Jeffrey M Perkel.   

Abstract

Entities:  

Keywords:  Computational biology and bioinformatics; Computer science; Genetics; Genomics

Mesh：

Year:  2022        PMID： 36064802     DOI： 10.1038/d41586-022-02826-1

Source DB:  PubMed          Journal:  Nature        ISSN： 0028-0836            Impact factor:   69.504


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  11 in total

1.  Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq.

Authors:  Joseph M Replogle; Reuben A Saunders; Angela N Pogson; Jeffrey A Hussmann; Alexander Lenail; Alina Guna; Lauren Mascibroda; Eric J Wagner; Karen Adelman; Gila Lithwick-Yanai; Nika Iremadze; Florian Oberstrass; Doron Lipson; Jessica L Bonnar; Marco Jost; Thomas M Norman; Jonathan S Weissman
Journal:  Cell       Date:  2022-06-09       Impact factor: 66.850

2.  Network inference with Granger causality ensembles on single-cell transcriptomics.

Authors:  Atul Deshpande; Li-Fang Chu; Ron Stewart; Anthony Gitter
Journal:  Cell Rep       Date:  2022-02-08       Impact factor: 9.995

3.  A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.

Authors:  Britt Adamson; Thomas M Norman; Marco Jost; Min Y Cho; James K Nuñez; Yuwen Chen; Jacqueline E Villalta; Luke A Gilbert; Max A Horlbeck; Marco Y Hein; Ryan A Pak; Andrew N Gray; Carol A Gross; Atray Dixit; Oren Parnas; Aviv Regev; Jonathan S Weissman
Journal:  Cell       Date:  2016-12-15       Impact factor: 41.582

4.  Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.

Authors:  Atray Dixit; Oren Parnas; Biyu Li; Jenny Chen; Charles P Fulco; Livnat Jerby-Arnon; Nemanja D Marjanovic; Danielle Dionne; Tyler Burks; Raktima Raychowdhury; Britt Adamson; Thomas M Norman; Eric S Lander; Jonathan S Weissman; Nir Friedman; Aviv Regev
Journal:  Cell       Date:  2016-12-15       Impact factor: 41.582

5.  The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo.

Authors:  Richard Bonneau; David J Reiss; Paul Shannon; Marc Facciotti; Leroy Hood; Nitin S Baliga; Vesteinn Thorsson
Journal:  Genome Biol       Date:  2006-05-10       Impact factor: 13.583

6.  Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells.

Authors:  Emily R Miraldi; Maria Pokrovskii; Aaron Watters; Dayanne M Castro; Nicholas De Veaux; Jason A Hall; June-Yong Lee; Maria Ciofani; Aviv Madar; Nick Carriero; Dan R Littman; Richard Bonneau
Journal:  Genome Res       Date:  2019-01-29       Impact factor: 9.043

7.  Data-driven modeling predicts gene regulatory network dynamics during the differentiation of multipotential hematopoietic progenitors.

Authors:  Joanna E Handzlik
Journal:  PLoS Comput Biol       Date:  2022-01-14       Impact factor: 4.475

8.  Predicting genotype-specific gene regulatory networks.

Authors:  Deborah Weighill; Marouen Ben Guebila; Kimberly Glass; John Quackenbush; John Platig
Journal:  Genome Res       Date:  2022-02-22       Impact factor: 9.043

9.  Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.

Authors:  Alex K Shalek; Rahul Satija; Xian Adiconis; Rona S Gertner; Jellert T Gaublomme; Raktima Raychowdhury; Schraga Schwartz; Nir Yosef; Christine Malboeuf; Diana Lu; John J Trombetta; Dave Gennert; Andreas Gnirke; Alon Goren; Nir Hacohen; Joshua Z Levin; Hongkun Park; Aviv Regev
Journal:  Nature       Date:  2013-05-19       Impact factor: 49.962

10.  Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data.

Authors:  Aditya Pratapa; Amogh P Jalihal; Jeffrey N Law; Aditya Bharadwaj; T M Murali
Journal:  Nat Methods       Date:  2020-01-06       Impact factor: 28.547
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