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Literature DB >> 28398314

Toil enables reproducible, open source, big biomedical data analyses.

John Vivian¹, Arjun Arkal Rao¹, Frank Austin Nothaft^2,3, Christopher Ketchum¹, Joel Armstrong¹, Adam Novak¹, Jacob Pfeil¹, Jake Narkizian¹, Alden D Deran¹, Audrey Musselman-Brown¹, Hannes Schmidt¹, Peter Amstutz⁴, Brian Craft¹, Mary Goldman¹, Kate Rosenbloom¹, Melissa Cline¹, Brian O'Connor¹, Megan Hanna⁵, Chet Birger⁵, W James Kent¹, David A Patterson^2,3, Anthony D Joseph^2,3, Jingchun Zhu¹, Sasha Zaranek⁴, Gad Getz⁵, David Haussler¹, Benedict Paten¹.

Abstract

Entities: Disease Species

Mesh：

Year: 2017 PMID： 28398314 PMCID： PMC5546205 DOI： 10.1038/nbt.3772

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

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11 in total

1. The human genome browser at UCSC.

Authors: W James Kent; Charles W Sugnet; Terrence S Furey; Krishna M Roskin; Tom H Pringle; Alan M Zahler; David Haussler
Journal: Genome Res Date: 2002-06 Impact factor: 9.043

2. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

Authors: Aaron McKenna; Matthew Hanna; Eric Banks; Andrey Sivachenko; Kristian Cibulskis; Andrew Kernytsky; Kiran Garimella; David Altshuler; Stacey Gabriel; Mark Daly; Mark A DePristo
Journal: Genome Res Date: 2010-07-19 Impact factor: 9.043

3. I-SPY 2: an adaptive breast cancer trial design in the setting of neoadjuvant chemotherapy.

Authors: A D Barker; C C Sigman; G J Kelloff; N M Hylton; D A Berry; L J Esserman
Journal: Clin Pharmacol Ther Date: 2009-05-13 Impact factor: 6.875

4. UK gears up to decode 100,000 genomes from NHS patients.

Authors: Nayanah Siva
Journal: Lancet Date: 2015-01-10 Impact factor: 79.321

5. STAR: ultrafast universal RNA-seq aligner.

Authors: Alexander Dobin; Carrie A Davis; Felix Schlesinger; Jorg Drenkow; Chris Zaleski; Sonali Jha; Philippe Batut; Mark Chaisson; Thomas R Gingeras
Journal: Bioinformatics Date: 2012-10-25 Impact factor: 6.937

6. Near-optimal probabilistic RNA-seq quantification.

Authors: Nicolas L Bray; Harold Pimentel; Páll Melsted; Lior Pachter
Journal: Nat Biotechnol Date: 2016-04-04 Impact factor: 54.908

7. The Cancer Genome Atlas Pan-Cancer analysis project.

Authors: John N Weinstein; Eric A Collisson; Gordon B Mills; Kenna R Mills Shaw; Brad A Ozenberger; Kyle Ellrott; Ilya Shmulevich; Chris Sander; Joshua M Stuart
Journal: Nat Genet Date: 2013-10 Impact factor: 38.330

8. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

Authors: Jeremy Goecks; Anton Nekrutenko; James Taylor
Journal: Genome Biol Date: 2010-08-25 Impact factor: 13.583

9. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.

Authors: Bo Li; Colin N Dewey
Journal: BMC Bioinformatics Date: 2011-08-04 Impact factor: 3.307

10. International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data.

Authors: Junjun Zhang; Joachim Baran; A Cros; Jonathan M Guberman; Syed Haider; Jack Hsu; Yong Liang; Elena Rivkin; Jianxin Wang; Brett Whitty; Marie Wong-Erasmus; Long Yao; Arek Kasprzyk
Journal: Database (Oxford) Date: 2011-09-19 Impact factor: 3.451

314 in total

1. OCTAD: an open workspace for virtually screening therapeutics targeting precise cancer patient groups using gene expression features.

Authors: Billy Zeng; Benjamin S Glicksberg; Patrick Newbury; Evgeny Chekalin; Jing Xing; Ke Liu; Anita Wen; Caven Chow; Bin Chen
Journal: Nat Protoc Date: 2020-12-23 Impact factor: 13.491

2. FTO-Dependent N ⁶-Methyladenosine Modifications Inhibit Ovarian Cancer Stem Cell Self-Renewal by Blocking cAMP Signaling.

Authors: Hao Huang; Yinu Wang; Manoj Kandpal; Guangyuan Zhao; Horacio Cardenas; Yanrong Ji; Anusha Chaparala; Edward J Tanner; Jianjun Chen; Ramana V Davuluri; Daniela Matei
Journal: Cancer Res Date: 2020-06-30 Impact factor: 12.701

3. Tibanna: software for scalable execution of portable pipelines on the cloud.

Authors: Soohyun Lee; Jeremy Johnson; Carl Vitzthum; Koray Kırlı; Burak H Alver; Peter J Park
Journal: Bioinformatics Date: 2019-11-01 Impact factor: 6.937

4. Expression of the Vesicular Monoamine Transporter Gene Solute Carrier Family 18 Member 1 (SLC18A1) in Lung Cancer.

Authors: Steven Lehrer; Peter H Rheinstein
Journal: Cancer Genomics Proteomics Date: 2018 Sep-Oct Impact factor: 4.069

5. 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

6. Tumor-Derived Thymic Stromal Lymphopoietin Expands Bone Marrow B-cell Precursors in Circulation to Support Metastasis.

Authors: Emeline Ragonnaud; Kanako Moritoh; Monica Bodogai; Fedor Gusev; Soizic Garaud; Chen Chen; Xin Wang; Tuvshintugs Baljinnyam; Kevin G Becker; Robert W Maul; Karen Willard-Gallo; Evgeny Rogaev; Arya Biragyn
Journal: Cancer Res Date: 2019-10-01 Impact factor: 12.701