Literature DB >> 34311752

Enabling reproducible re-analysis of single-cell data.

Jordan W Squair1,2, Grégoire Courtine3,4,5, Michael A Skinnider6.   

Abstract

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Year:  2021        PMID： 34311752      PMCID： PMC8311938          DOI： 10.1186/s13059-021-02422-y

Source DB:  PubMed          Journal:  Genome Biol        ISSN： 1474-7596            Impact factor:   13.583


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  11 in total

1.  Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Authors:  A Brazma; P Hingamp; J Quackenbush; G Sherlock; P Spellman; C Stoeckert; J Aach; W Ansorge; C A Ball; H C Causton; T Gaasterland; P Glenisson; F C Holstege; I F Kim; V Markowitz; J C Matese; H Parkinson; A Robinson; U Sarkans; S Schulze-Kremer; J Stewart; R Taylor; J Vilo; M Vingron
Journal:  Nat Genet       Date:  2001-12       Impact factor: 38.330

2.  A comparison of single-cell trajectory inference methods.

Authors:  Wouter Saelens; Robrecht Cannoodt; Helena Todorov; Yvan Saeys
Journal:  Nat Biotechnol       Date:  2019-04-01       Impact factor: 54.908

3.  Putative cell type discovery from single-cell gene expression data.

Authors:  Zhichao Miao; Pablo Moreno; Ni Huang; Irene Papatheodorou; Alvis Brazma; Sarah A Teichmann
Journal:  Nat Methods       Date:  2020-05-18       Impact factor: 28.547

4.  PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.

Authors:  Oscar Franzén; Li-Ming Gan; Johan L M Björkegren
Journal:  Database (Oxford)       Date:  2019-01-01       Impact factor: 3.451

5.  Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling.

Authors:  Allen W Zhang; Ciara O'Flanagan; Elizabeth A Chavez; Jamie L P Lim; Nicholas Ceglia; Andrew McPherson; Matt Wiens; Pascale Walters; Tim Chan; Brittany Hewitson; Daniel Lai; Anja Mottok; Clementine Sarkozy; Lauren Chong; Tomohiro Aoki; Xuehai Wang; Andrew P Weng; Jessica N McAlpine; Samuel Aparicio; Christian Steidl; Kieran R Campbell; Sohrab P Shah
Journal:  Nat Methods       Date:  2019-09-09       Impact factor: 28.547

6.  Guidelines for reporting single-cell RNA-seq experiments.

Authors:  Anja Füllgrabe; Nancy George; Matthew Green; Parisa Nejad; Bruce Aronow; Silvie Korena Fexova; Clay Fischer; Mallory Ann Freeberg; Laura Huerta; Norman Morrison; Richard H Scheuermann; Deanne Taylor; Nicole Vasilevsky; Laura Clarke; Nils Gehlenborg; Jim Kent; John Marioni; Sarah Teichmann; Alvis Brazma; Irene Papatheodorou
Journal:  Nat Biotechnol       Date:  2020-12       Impact factor: 68.164

7.  Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinson's disease.

Authors:  Julien Bryois; Nathan G Skene; Thomas Folkmann Hansen; Lisette J A Kogelman; Hunna J Watson; Zijing Liu; Leo Brueggeman; Gerome Breen; Cynthia M Bulik; Ernest Arenas; Jens Hjerling-Leffler; Patrick F Sullivan
Journal:  Nat Genet       Date:  2020-04-27       Impact factor: 38.330

8.  Supervised classification enables rapid annotation of cell atlases.

Authors:  Hannah A Pliner; Jay Shendure; Cole Trapnell
Journal:  Nat Methods       Date:  2019-09-09       Impact factor: 28.547

9.  Cell type prioritization in single-cell data.

Authors:  Michael A Skinnider; Jordan W Squair; Claudia Kathe; Mark A Anderson; Matthieu Gautier; Kaya J E Matson; Marco Milano; Thomas H Hutson; Quentin Barraud; Aaron A Phillips; Leonard J Foster; Gioele La Manno; Ariel J Levine; Grégoire Courtine
Journal:  Nat Biotechnol       Date:  2020-07-20       Impact factor: 54.908

10.  A curated database reveals trends in single-cell transcriptomics.

Authors:  Valentine Svensson; Eduardo da Veiga Beltrame; Lior Pachter
Journal:  Database (Oxford)       Date:  2020-11-28       Impact factor: 3.451
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  3 in total

1.  Enhanced single-cell RNA-seq workflow reveals coronary artery disease cellular cross-talk and candidate drug targets.

Authors:  Wei Feng Ma; Chani J Hodonsky; Adam W Turner; Doris Wong; Yipei Song; Jose Verdezoto Mosquera; Alexandra V Ligay; Lotte Slenders; Christina Gancayco; Huize Pan; Nelson B Barrientos; David Mai; Gabriel F Alencar; Katherine Owsiany; Gary K Owens; Muredach P Reilly; Mingyao Li; Gerard Pasterkamp; Michal Mokry; Sander W van der Laan; Bohdan B Khomtchouk; Clint L Miller
Journal:  Atherosclerosis       Date:  2021-11-26       Impact factor: 5.162

2.  Perspectives on rigor and reproducibility in single cell genomics.

Authors:  Greg Gibson
Journal:  PLoS Genet       Date:  2022-05-10       Impact factor: 6.020

3.  PlaqView 2.0: A comprehensive web portal for cardiovascular single-cell genomics.

Authors:  Wei Feng Ma; Adam W Turner; Christina Gancayco; Doris Wong; Yipei Song; Jose Verdezoto Mosquera; Gaëlle Auguste; Chani J Hodonsky; Ajay Prabhakar; H Atakan Ekiz; Sander W van der Laan; Clint L Miller
Journal:  Front Cardiovasc Med       Date:  2022-08-08
  3 in total

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