Literature DB >> 33188371

Guidelines for reporting single-cell RNA-seq experiments.

Anja Füllgrabe1, Nancy George2, Matthew Green2, Parisa Nejad3, Bruce Aronow4, Silvie Korena Fexova2, Clay Fischer3, Mallory Ann Freeberg2, Laura Huerta2,5, Norman Morrison2, Richard H Scheuermann6, Deanne Taylor7,8, Nicole Vasilevsky9, Laura Clarke2, Nils Gehlenborg10, Jim Kent3, John Marioni2, Sarah Teichmann11,12, Alvis Brazma2, Irene Papatheodorou13.   

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Year:  2020        PMID: 33188371      PMCID: PMC9302581          DOI: 10.1038/s41587-020-00744-z

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   68.164


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  17 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.  Comparative Analysis of Single-Cell RNA Sequencing Methods.

Authors:  Christoph Ziegenhain; Beate Vieth; Swati Parekh; Björn Reinius; Amy Guillaumet-Adkins; Martha Smets; Heinrich Leonhardt; Holger Heyn; Ines Hellmann; Wolfgang Enard
Journal:  Mol Cell       Date:  2017-02-16       Impact factor: 17.970

Review 3.  Reuse of public genome-wide gene expression data.

Authors:  Johan Rung; Alvis Brazma
Journal:  Nat Rev Genet       Date:  2012-12-27       Impact factor: 53.242

4.  Efficient integration of heterogeneous single-cell transcriptomes using Scanorama.

Authors:  Brian Hie; Bryan Bryson; Bonnie Berger
Journal:  Nat Biotechnol       Date:  2019-05-06       Impact factor: 54.908

5.  NCBI GEO: archive for functional genomics data sets--update.

Authors:  Tanya Barrett; Stephen E Wilhite; Pierre Ledoux; Carlos Evangelista; Irene F Kim; Maxim Tomashevsky; Kimberly A Marshall; Katherine H Phillippy; Patti M Sherman; Michelle Holko; Andrey Yefanov; Hyeseung Lee; Naigong Zhang; Cynthia L Robertson; Nadezhda Serova; Sean Davis; Alexandra Soboleva
Journal:  Nucleic Acids Res       Date:  2012-11-27       Impact factor: 16.971

6.  Simultaneous epitope and transcriptome measurement in single cells.

Authors:  Marlon Stoeckius; Christoph Hafemeister; William Stephenson; Brian Houck-Loomis; Pratip K Chattopadhyay; Harold Swerdlow; Rahul Satija; Peter Smibert
Journal:  Nat Methods       Date:  2017-07-31       Impact factor: 28.547

7.  Joint analysis of heterogeneous single-cell RNA-seq dataset collections.

Authors:  Nikolas Barkas; Viktor Petukhov; Daria Nikolaeva; Yaroslav Lozinsky; Samuel Demharter; Konstantin Khodosevich; Peter V Kharchenko
Journal:  Nat Methods       Date:  2019-07-15       Impact factor: 28.547

8.  A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain.

Authors:  Kristofer Davie; Jasper Janssens; Duygu Koldere; Maxime De Waegeneer; Uli Pech; Łukasz Kreft; Sara Aibar; Samira Makhzami; Valerie Christiaens; Carmen Bravo González-Blas; Suresh Poovathingal; Gert Hulselmans; Katina I Spanier; Thomas Moerman; Bram Vanspauwen; Sarah Geurs; Thierry Voet; Jeroen Lammertyn; Bernard Thienpont; Sha Liu; Nikos Konstantinides; Mark Fiers; Patrik Verstreken; Stein Aerts
Journal:  Cell       Date:  2018-06-18       Impact factor: 41.582

9.  ArrayExpress update - from bulk to single-cell expression data.

Authors:  Awais Athar; Anja Füllgrabe; Nancy George; Haider Iqbal; Laura Huerta; Ahmed Ali; Catherine Snow; Nuno A Fonseca; Robert Petryszak; Irene Papatheodorou; Ugis Sarkans; Alvis Brazma
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

10.  Expression Atlas update: from tissues to single cells.

Authors:  Irene Papatheodorou; Pablo Moreno; Jonathan Manning; Alfonso Muñoz-Pomer Fuentes; Nancy George; Silvie Fexova; Nuno A Fonseca; Anja Füllgrabe; Matthew Green; Ni Huang; Laura Huerta; Haider Iqbal; Monica Jianu; Suhaib Mohammed; Lingyun Zhao; Andrew F Jarnuczak; Simon Jupp; John Marioni; Kerstin Meyer; Robert Petryszak; Cesar Augusto Prada Medina; Carlos Talavera-López; Sarah Teichmann; Juan Antonio Vizcaino; Alvis Brazma
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

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  8 in total

1.  Detection of infiltrating fibroblasts by single-cell transcriptomics in human kidney allografts.

Authors:  Hemant Suryawanshi; Hua Yang; Michelle Lubetzky; Pavel Morozov; Mila Lagman; Gaurav Thareja; Alicia Alonso; Carol Li; Catherine Snopkowski; Aziz Belkadi; Franco B Mueller; John R Lee; Darshana M Dadhania; Steven P Salvatore; Surya V Seshan; Vijay K Sharma; Karsten Suhre; Manikkam Suthanthiran; Thomas Tuschl; Thangamani Muthukumar
Journal:  PLoS One       Date:  2022-06-03       Impact factor: 3.752

2.  Enabling reproducible re-analysis of single-cell data.

Authors:  Jordan W Squair; Grégoire Courtine; Michael A Skinnider
Journal:  Genome Biol       Date:  2021-07-26       Impact factor: 13.583

3.  Cell-level metadata are indispensable for documenting single-cell sequencing datasets.

Authors:  Sidhant Puntambekar; Jay R Hesselberth; Kent A Riemondy; Rui Fu
Journal:  PLoS Biol       Date:  2021-05-04       Impact factor: 8.029

4.  Avoiding a replication crisis in deep-learning-based bioimage analysis.

Authors:  Romain F Laine; Ignacio Arganda-Carreras; Ricardo Henriques; Guillaume Jacquemet
Journal:  Nat Methods       Date:  2021-10       Impact factor: 28.547

Review 5.  Ex uno, plures-From One Tissue to Many Cells: A Review of Single-Cell Transcriptomics in Cardiovascular Biology.

Authors:  Elvira Forte; Micheal A McLellan; Daniel A Skelly; Nadia A Rosenthal
Journal:  Int J Mol Sci       Date:  2021-02-19       Impact factor: 5.923

6.  Expression Atlas update: gene and protein expression in multiple species.

Authors:  Pablo Moreno; Silvie Fexova; Nancy George; Jonathan R Manning; Zhichiao Miao; Suhaib Mohammed; Alfonso Muñoz-Pomer; Anja Fullgrabe; Yalan Bi; Natassja Bush; Haider Iqbal; Upendra Kumbham; Andrey Solovyev; Lingyun Zhao; Ananth Prakash; David García-Seisdedos; Deepti J Kundu; Shengbo Wang; Mathias Walzer; Laura Clarke; David Osumi-Sutherland; Marcela Karey Tello-Ruiz; Sunita Kumari; Doreen Ware; Jana Eliasova; Mark J Arends; Martijn C Nawijn; Kerstin Meyer; Tony Burdett; John Marioni; Sarah Teichmann; Juan Antonio Vizcaíno; Alvis Brazma; Irene Papatheodorou
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 16.971

Review 7.  A proteomics sample metadata representation for multiomics integration and big data analysis.

Authors:  Chengxin Dai; Anja Füllgrabe; Julianus Pfeuffer; Elizaveta M Solovyeva; Jingwen Deng; Pablo Moreno; Selvakumar Kamatchinathan; Deepti Jaiswal Kundu; Nancy George; Silvie Fexova; Björn Grüning; Melanie Christine Föll; Johannes Griss; Marc Vaudel; Enrique Audain; Marie Locard-Paulet; Michael Turewicz; Martin Eisenacher; Julian Uszkoreit; Tim Van Den Bossche; Veit Schwämmle; Henry Webel; Stefan Schulze; David Bouyssié; Savita Jayaram; Vinay Kumar Duggineni; Patroklos Samaras; Mathias Wilhelm; Meena Choi; Mingxun Wang; Oliver Kohlbacher; Alvis Brazma; Irene Papatheodorou; Nuno Bandeira; Eric W Deutsch; Juan Antonio Vizcaíno; Mingze Bai; Timo Sachsenberg; Lev I Levitsky; Yasset Perez-Riverol
Journal:  Nat Commun       Date:  2021-10-06       Impact factor: 14.919

Review 8.  Data Integration Challenges for Machine Learning in Precision Medicine.

Authors:  Mireya Martínez-García; Enrique Hernández-Lemus
Journal:  Front Med (Lausanne)       Date:  2022-01-25
  8 in total

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