Literature DB >> 35459940

An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks.

Marouen Ben Guebila1, Deborah Weighill1,2, Camila M Lopes-Ramos1,3, Rebekka Burkholz1,4, Romana T Pop5, Kalyan Palepu6, Mia Shapoval7, Maud Fagny1,8, Daniel Schlauch1,9, Kimberly Glass1,3, Michael Altenbuchinger10, Marieke L Kuijjer5,11,12, John Platig3, John Quackenbush13,14,15.   

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Year:  2022        PMID: 35459940      PMCID: PMC9239854          DOI: 10.1038/s41592-022-01479-2

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   47.990


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  7 in total

1.  The GenePattern Notebook Environment.

Authors:  Michael Reich; Thorin Tabor; Ted Liefeld; Helga Thorvaldsdóttir; Barbara Hill; Pablo Tamayo; Jill P Mesirov
Journal:  Cell Syst       Date:  2017-08-16       Impact factor: 10.304

2.  BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud.

Authors:  Denis Torre; Alexander Lachmann; Avi Ma'ayan
Journal:  Cell Syst       Date:  2018-11-14       Impact factor: 10.304

3.  The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks.

Authors:  Aurélien Naldi; Céline Hernandez; Nicolas Levy; Gautier Stoll; Pedro T Monteiro; Claudine Chaouiya; Tomáš Helikar; Andrei Zinovyev; Laurence Calzone; Sarah Cohen-Boulakia; Denis Thieffry; Loïc Paulevé
Journal:  Front Physiol       Date:  2018-06-19       Impact factor: 4.566

4.  Regulatory Network of PD1 Signaling Is Associated with Prognosis in Glioblastoma Multiforme.

Authors:  Camila M Lopes-Ramos; Tatiana Belova; Tess H Brunner; Marouen Ben Guebila; Daniel Osorio; John Quackenbush; Marieke L Kuijjer
Journal:  Cancer Res       Date:  2021-09-07       Impact factor: 12.701

5.  Reproducibility standards for machine learning in the life sciences.

Authors:  Benjamin J Heil; Michael M Hoffman; Florian Markowetz; Su-In Lee; Casey S Greene; Stephanie C Hicks
Journal:  Nat Methods       Date:  2021-10       Impact factor: 47.990

6.  Appyters: Turning Jupyter Notebooks into data-driven web apps.

Authors:  Daniel J B Clarke; Minji Jeon; Daniel J Stein; Nicole Moiseyev; Eryk Kropiwnicki; Charles Dai; Zhuorui Xie; Megan L Wojciechowicz; Skylar Litz; Jason Hom; John Erol Evangelista; Lucas Goldman; Serena Zhang; Christine Yoon; Tahmid Ahamed; Samantha Bhuiyan; Minxuan Cheng; Julie Karam; Kathleen M Jagodnik; Ingrid Shu; Alexander Lachmann; Sam Ayling; Sherry L Jenkins; Avi Ma'ayan
Journal:  Patterns (N Y)       Date:  2021-03-04

7.  Reproducibility in systems biology modelling.

Authors:  Krishna Tiwari; Sarubini Kananathan; Matthew G Roberts; Johannes P Meyer; Mohammad Umer Sharif Shohan; Ashley Xavier; Matthieu Maire; Ahmad Zyoud; Jinghao Men; Szeyi Ng; Tung V N Nguyen; Mihai Glont; Henning Hermjakob; Rahuman S Malik-Sheriff
Journal:  Mol Syst Biol       Date:  2021-02       Impact factor: 11.429

  7 in total

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