Literature DB >> 31471617

Data denoising with transfer learning in single-cell transcriptomics.

Jingshu Wang1, Divyansh Agarwal2, Mo Huang1, Gang Hu3, Zilu Zhou2, Chengzhong Ye4, Nancy R Zhang5.   

Abstract

Single-cell RNA sequencing (scRNA-seq) data are noisy and sparse. Here, we show that transfer learning across datasets remarkably improves data quality. By coupling a deep autoencoder with a Bayesian model, SAVER-X extracts transferable gene-gene relationships across data from different labs, varying conditions and divergent species, to denoise new target datasets.

Entities:  

Mesh：

Year:  2019        PMID： 31471617      PMCID： PMC7781045          DOI： 10.1038/s41592-019-0537-1

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  15 in total

1.  Reducing the dimensionality of data with neural networks.

Authors:  G E Hinton; R R Salakhutdinov
Journal:  Science       Date:  2006-07-28       Impact factor: 47.728

2.  An accurate and robust imputation method scImpute for single-cell RNA-seq data.

Authors:  Wei Vivian Li; Jingyi Jessica Li
Journal:  Nat Commun       Date:  2018-03-08       Impact factor: 14.919

3.  Mapping the Mouse Cell Atlas by Microwell-Seq.

Authors:  Xiaoping Han; Renying Wang; Yincong Zhou; Lijiang Fei; Huiyu Sun; Shujing Lai; Assieh Saadatpour; Ziming Zhou; Haide Chen; Fang Ye; Daosheng Huang; Yang Xu; Wentao Huang; Mengmeng Jiang; Xinyi Jiang; Jie Mao; Yao Chen; Chenyu Lu; Jin Xie; Qun Fang; Yibin Wang; Rui Yue; Tiefeng Li; He Huang; Stuart H Orkin; Guo-Cheng Yuan; Ming Chen; Guoji Guo
Journal:  Cell       Date:  2018-02-22       Impact factor: 41.582

4.  Recovering Gene Interactions from Single-Cell Data Using Data Diffusion.

Authors:  David van Dijk; Roshan Sharma; Juozas Nainys; Kristina Yim; Pooja Kathail; Ambrose J Carr; Cassandra Burdziak; Kevin R Moon; Christine L Chaffer; Diwakar Pattabiraman; Brian Bierie; Linas Mazutis; Guy Wolf; Smita Krishnaswamy; Dana Pe'er
Journal:  Cell       Date:  2018-06-28       Impact factor: 41.582

5.  Deep generative modeling for single-cell transcriptomics.

Authors:  Romain Lopez; Jeffrey Regier; Michael B Cole; Michael I Jordan; Nir Yosef
Journal:  Nat Methods       Date:  2018-11-30       Impact factor: 28.547

6.  SAVER: gene expression recovery for single-cell RNA sequencing.

Authors:  Mo Huang; Jingshu Wang; Eduardo Torre; Hannah Dueck; Sydney Shaffer; Roberto Bonasio; John I Murray; Arjun Raj; Mingyao Li; Nancy R Zhang
Journal:  Nat Methods       Date:  2018-06-25       Impact factor: 28.547

7.  False signals induced by single-cell imputation.

Authors:  Tallulah S Andrews; Martin Hemberg
Journal:  F1000Res       Date:  2018-11-02

8.  Single-cell RNA-seq denoising using a deep count autoencoder.

Authors:  Gökcen Eraslan; Lukas M Simon; Maria Mircea; Nikola S Mueller; Fabian J Theis
Journal:  Nat Commun       Date:  2019-01-23       Impact factor: 14.919

9.  Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex.

Authors:  Alex A Pollen; Tomasz J Nowakowski; Joe Shuga; Xiaohui Wang; Anne A Leyrat; Jan H Lui; Nianzhen Li; Lukasz Szpankowski; Brian Fowler; Peilin Chen; Naveen Ramalingam; Gang Sun; Myo Thu; Michael Norris; Ronald Lebofsky; Dominique Toppani; Darnell W Kemp; Michael Wong; Barry Clerkson; Brittnee N Jones; Shiquan Wu; Lawrence Knutsson; Beatriz Alvarado; Jing Wang; Lesley S Weaver; Andrew P May; Robert C Jones; Marc A Unger; Arnold R Kriegstein; Jay A A West
Journal:  Nat Biotechnol       Date:  2014-08-03       Impact factor: 54.908

10.  Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris.

Authors: 
Journal:  Nature       Date:  2018-10-03       Impact factor: 49.962
View more
  36 in total

1.  IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq.

Authors:  Anjun Ma; Cankun Wang; Yuzhou Chang; Faith H Brennan; Adam McDermaid; Bingqiang Liu; Chi Zhang; Phillip G Popovich; Qin Ma
Journal:  Nucleic Acids Res       Date:  2020-07-02       Impact factor: 16.971

2.  Imputing missing RNA-sequencing data from DNA methylation by using a transfer learning-based neural network.

Authors:  Xiang Zhou; Hua Chai; Huiying Zhao; Ching-Hsing Luo; Yuedong Yang
Journal:  Gigascience       Date:  2020-07-01       Impact factor: 6.524

Review 3.  Single-Cell Techniques and Deep Learning in Predicting Drug Response.

Authors:  Zhenyu Wu; Patrick J Lawrence; Anjun Ma; Jian Zhu; Dong Xu; Qin Ma
Journal:  Trends Pharmacol Sci       Date:  2020-11-02       Impact factor: 14.819

4.  MARS: discovering novel cell types across heterogeneous single-cell experiments.

Authors:  Maria Brbić; Marinka Zitnik; Sheng Wang; Angela O Pisco; Russ B Altman; Spyros Darmanis; Jure Leskovec
Journal:  Nat Methods       Date:  2020-10-19       Impact factor: 28.547

Review 5.  Diagnostic accuracy and potential covariates of artificial intelligence for diagnosing orthopedic fractures: a systematic literature review and meta-analysis.

Authors:  Xiang Zhang; Yi Yang; Yi-Wei Shen; Ke-Rui Zhang; Ze-Kun Jiang; Li-Tai Ma; Chen Ding; Bei-Yu Wang; Yang Meng; Hao Liu
Journal:  Eur Radiol       Date:  2022-06-27       Impact factor: 7.034

Review 6.  Computational principles and challenges in single-cell data integration.

Authors:  Ricard Argelaguet; Anna S E Cuomo; Oliver Stegle; John C Marioni
Journal:  Nat Biotechnol       Date:  2021-05-03       Impact factor: 54.908

Review 7.  Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data.

Authors:  Tallulah S Andrews; Vladimir Yu Kiselev; Davis McCarthy; Martin Hemberg
Journal:  Nat Protoc       Date:  2020-12-07       Impact factor: 13.491

8.  Overcoming Immunological Challenges Limiting Capsid-Mediated Gene Therapy With Machine Learning.

Authors:  Anna Z Wec; Kathy S Lin; Jamie C Kwasnieski; Sam Sinai; Jeff Gerold; Eric D Kelsic
Journal:  Front Immunol       Date:  2021-04-27       Impact factor: 7.561

9.  SimiC enables the inference of complex gene regulatory dynamics across cell phenotypes.

Authors:  Jianhao Peng; Guillermo Serrano; Ian M Traniello; Maria E Calleja-Cervantes; Ullas V Chembazhi; Sushant Bangru; Teresa Ezponda; Juan Roberto Rodriguez-Madoz; Auinash Kalsotra; Felipe Prosper; Idoia Ochoa; Mikel Hernaez
Journal:  Commun Biol       Date:  2022-04-12

Review 10.  The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution.

Authors:  Orit Rozenblatt-Rosen; Aviv Regev; Philipp Oberdoerffer; Tal Nawy; Anna Hupalowska; Jennifer E Rood; Orr Ashenberg; Ethan Cerami; Robert J Coffey; Emek Demir; Li Ding; Edward D Esplin; James M Ford; Jeremy Goecks; Sharmistha Ghosh; Joe W Gray; Justin Guinney; Sean E Hanlon; Shannon K Hughes; E Shelley Hwang; Christine A Iacobuzio-Donahue; Judit Jané-Valbuena; Bruce E Johnson; Ken S Lau; Tracy Lively; Sarah A Mazzilli; Dana Pe'er; Sandro Santagata; Alex K Shalek; Denis Schapiro; Michael P Snyder; Peter K Sorger; Avrum E Spira; Sudhir Srivastava; Kai Tan; Robert B West; Elizabeth H Williams
Journal:  Cell       Date:  2020-04-16       Impact factor: 66.850
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.