Literature DB >> 35132262

A Python library for probabilistic analysis of single-cell omics data.

Adam Gayoso1, Romain Lopez2, Galen Xing1,3, Pierre Boyeau2,4, Valeh Valiollah Pour Amiri1,2, Justin Hong1,2, Katherine Wu2, Michael Jayasuriya2, Edouard Mehlman4,5, Maxime Langevin5,6,7, Yining Liu2,8, Jules Samaran9, Gabriel Misrachi5,10, Achille Nazaret5,8, Oscar Clivio4,11, Chenling Xu1, Tal Ashuach1, Mariano Gabitto1,2, Mohammad Lotfollahi12,13, Valentine Svensson14, Eduardo da Veiga Beltrame15, Vitalii Kleshchevnikov16, Carlos Talavera-López16,17, Lior Pachter15,18, Fabian J Theis12,13, Aaron Streets1,3,19, Michael I Jordan1,2,20, Jeffrey Regier21, Nir Yosef22,23,24,25.   

Abstract

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Year:  2022        PMID: 35132262     DOI: 10.1038/s41587-021-01206-w

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   54.908


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  19 in total

1.  Benchmarking spatial and single-cell transcriptomics integration methods.

Authors: 
Journal:  Nat Methods       Date:  2022-06       Impact factor: 28.547

2.  Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies.

Authors:  Daniel Reichart; Eric L Lindberg; Henrike Maatz; Hendrik Milting; Michela Noseda; Gavin Y Oudit; Matthias Heinig; Jonathan G Seidman; Norbert Hubner; Christine E Seidman; Antonio M A Miranda; Anissa Viveiros; Nikolay Shvetsov; Anna Gärtner; Emily R Nadelmann; Michael Lee; Kazumasa Kanemaru; Jorge Ruiz-Orera; Viktoria Strohmenger; Daniel M DeLaughter; Giannino Patone; Hao Zhang; Andrew Woehler; Christoph Lippert; Yuri Kim; Eleonora Adami; Joshua M Gorham; Sam N Barnett; Kemar Brown; Rachel J Buchan; Rasheda A Chowdhury; Chrystalla Constantinou; James Cranley; Leanne E Felkin; Henrik Fox; Ahla Ghauri; Jan Gummert; Masatoshi Kanda; Ruoyan Li; Lukas Mach; Barbara McDonough; Sara Samari; Farnoush Shahriaran; Clarence Yapp; Caroline Stanasiuk; Pantazis I Theotokis; Fabian J Theis; Antoon van den Bogaerdt; Hiroko Wakimoto; James S Ware; Catherine L Worth; Paul J R Barton; Young-Ae Lee; Sarah A Teichmann
Journal:  Science       Date:  2022-08-05       Impact factor: 63.714

3.  RNA velocity unraveled.

Authors:  Gennady Gorin; Meichen Fang; Tara Chari; Lior Pachter
Journal:  PLoS Comput Biol       Date:  2022-09-12       Impact factor: 4.779

4.  MIRA: joint regulatory modeling of multimodal expression and chromatin accessibility in single cells.

Authors:  Allen W Lynch; Christina V Theodoris; Henry W Long; Myles Brown; X Shirley Liu; Clifford A Meyer
Journal:  Nat Methods       Date:  2022-09-06       Impact factor: 47.990

5.  Inference of cell state transitions and cell fate plasticity from single-cell with MARGARET.

Authors:  Kushagra Pandey; Hamim Zafar
Journal:  Nucleic Acids Res       Date:  2022-08-26       Impact factor: 19.160

6.  Single-cell transcriptomics of adult macaque hippocampus reveals neural precursor cell populations.

Authors:  Zhao-Zhe Hao; Jia-Ru Wei; Dongchang Xiao; Ruifeng Liu; Nana Xu; Lei Tang; Mengyao Huang; Yuhui Shen; Changsheng Xing; Wanjing Huang; Xialin Liu; Mengqing Xiang; Yizhi Liu; Zhichao Miao; Sheng Liu
Journal:  Nat Neurosci       Date:  2022-05-30       Impact factor: 28.771

7.  PyLiger: scalable single-cell multi-omic data integration in Python.

Authors:  Lu Lu; Joshua D Welch
Journal:  Bioinformatics       Date:  2022-05-13       Impact factor: 6.931

8.  WormBase single-cell tools.

Authors:  Eduardo da Veiga Beltrame; Valerio Arnaboldi; Paul W Sternberg
Journal:  Bioinform Adv       Date:  2022-03-28

9.  Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution.

Authors:  Dian Yang; Matthew G Jones; Santiago Naranjo; William M Rideout; Kyung Hoi Joseph Min; Raymond Ho; Wei Wu; Joseph M Replogle; Jennifer L Page; Jeffrey J Quinn; Felix Horns; Xiaojie Qiu; Michael Z Chen; William A Freed-Pastor; Christopher S McGinnis; David M Patterson; Zev J Gartner; Eric D Chow; Trever G Bivona; Michelle M Chan; Nir Yosef; Tyler Jacks; Jonathan S Weissman
Journal:  Cell       Date:  2022-05-05       Impact factor: 66.850

10.  PeakVI: A deep generative model for single-cell chromatin accessibility analysis.

Authors:  Tal Ashuach; Daniel A Reidenbach; Adam Gayoso; Nir Yosef
Journal:  Cell Rep Methods       Date:  2022-03-15
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