Literature DB >> 27905430

Safikhani et al. reply.

Zhaleh Safikhani1,2, Nehme El-Hachem3, Petr Smirnov1, Mark Freeman1, Anna Goldenberg4,5, Nicolai J Birkbak6, Andrew H Beck7,8, Hugo J W L Aerts8,9,10, John Quackenbush9,11, Benjamin Haibe-Kains1,2,5,12.   

Abstract

Year:  2016        PMID： 27905430     DOI： 10.1038/nature19839

Source DB:  PubMed          Journal:  Nature        ISSN： 0028-0836            Impact factor:   49.962


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  14 in total

1.  Comparison of the predicted and observed secondary structure of T4 phage lysozyme.

Authors:  B W Matthews
Journal:  Biochim Biophys Acta       Date:  1975-10-20

2.  Systematic assessment of analytical methods for drug sensitivity prediction from cancer cell line data.

Authors:  In Sock Jang; Elias Chaibub Neto; Juistin Guinney; Stephen H Friend; Adam A Margolin
Journal:  Pac Symp Biocomput       Date:  2014

3.  Reproducible pharmacogenomic profiling of cancer cell line panels.

Authors:  Peter M Haverty; Eva Lin; Jenille Tan; Yihong Yu; Billy Lam; Steve Lianoglou; Richard M Neve; Scott Martin; Jeff Settleman; Robert L Yauch; Richard Bourgon
Journal:  Nature       Date:  2016-05-19       Impact factor: 49.962

4.  Consistency in large pharmacogenomic studies.

Authors:  Paul Geeleher; Eric R Gamazon; Cathal Seoighe; Nancy J Cox; R Stephanie Huang
Journal:  Nature       Date:  2016-11-30       Impact factor: 49.962

5.  Inconsistency in large pharmacogenomic studies.

Authors:  Benjamin Haibe-Kains; Nehme El-Hachem; Nicolai Juul Birkbak; Andrew C Jin; Andrew H Beck; Hugo J W L Aerts; John Quackenbush
Journal:  Nature       Date:  2013-11-27       Impact factor: 49.962

6.  Pharmacogenomic agreement between two cancer cell line data sets.

Authors: 
Journal:  Nature       Date:  2015-11-16       Impact factor: 49.962

7.  Comparison and validation of genomic predictors for anticancer drug sensitivity.

Authors:  Simon Papillon-Cavanagh; Nicolas De Jay; Nehme Hachem; Catharina Olsen; Gianluca Bontempi; Hugo J W L Aerts; John Quackenbush; Benjamin Haibe-Kains
Journal:  J Am Med Inform Assoc       Date:  2013-01-26       Impact factor: 4.497

8.  Systematic identification of genomic markers of drug sensitivity in cancer cells.

Authors:  Mathew J Garnett; Elena J Edelman; Sonja J Heidorn; Chris D Greenman; Anahita Dastur; King Wai Lau; Patricia Greninger; I Richard Thompson; Xi Luo; Jorge Soares; Qingsong Liu; Francesco Iorio; Didier Surdez; Li Chen; Randy J Milano; Graham R Bignell; Ah T Tam; Helen Davies; Jesse A Stevenson; Syd Barthorpe; Stephen R Lutz; Fiona Kogera; Karl Lawrence; Anne McLaren-Douglas; Xeni Mitropoulos; Tatiana Mironenko; Helen Thi; Laura Richardson; Wenjun Zhou; Frances Jewitt; Tinghu Zhang; Patrick O'Brien; Jessica L Boisvert; Stacey Price; Wooyoung Hur; Wanjuan Yang; Xianming Deng; Adam Butler; Hwan Geun Choi; Jae Won Chang; Jose Baselga; Ivan Stamenkovic; Jeffrey A Engelman; Sreenath V Sharma; Olivier Delattre; Julio Saez-Rodriguez; Nathanael S Gray; Jeffrey Settleman; P Andrew Futreal; Daniel A Haber; Michael R Stratton; Sridhar Ramaswamy; Ultan McDermott; Cyril H Benes
Journal:  Nature       Date:  2012-03-28       Impact factor: 49.962

9.  Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel.

Authors:  Isidro Cortés-Ciriano; Gerard J P van Westen; Guillaume Bouvier; Michael Nilges; John P Overington; Andreas Bender; Thérèse E Malliavin
Journal:  Bioinformatics       Date:  2015-09-08       Impact factor: 6.937

10.  Ten simple rules for reproducible computational research.

Authors:  Geir Kjetil Sandve; Anton Nekrutenko; James Taylor; Eivind Hovig
Journal:  PLoS Comput Biol       Date:  2013-10-24       Impact factor: 4.475
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  8 in total

1.  Evaluating the consistency of large-scale pharmacogenomic studies.

Authors:  Raziur Rahman; Saugato Rahman Dhruba; Kevin Matlock; Carlos De-Niz; Souparno Ghosh; Ranadip Pal
Journal:  Brief Bioinform       Date:  2019-09-27       Impact factor: 11.622

2.  Revisiting inconsistency in large pharmacogenomic studies.

Authors:  Zhaleh Safikhani; Petr Smirnov; Mark Freeman; Nehme El-Hachem; Adrian She; Quevedo Rene; Anna Goldenberg; Nicolai J Birkbak; Christos Hatzis; Leming Shi; Andrew H Beck; Hugo J W L Aerts; John Quackenbush; Benjamin Haibe-Kains
Journal:  F1000Res       Date:  2016-09-16

3.  Patient-Derived In Vitro and In Vivo Models of Cancer.

Authors:  Sally E Claridge; Julie-Ann Cavallo; Benjamin D Hopkins
Journal:  Adv Exp Med Biol       Date:  2022       Impact factor: 2.622

4.  PATRI, a Genomics Data Integration Tool for Biomarker Discovery.

Authors:  G Ukmar; G E M Melloni; L Raddrizzani; P Rossi; S Di Bella; M R Pirchio; M Vescovi; A Leone; M Callari; M Cesarini; A Somaschini; G Della Vedova; M G Daidone; M Pettenella; A Isacchi; R Bosotti
Journal:  Biomed Res Int       Date:  2018-06-28       Impact factor: 3.411

5.  Understanding of researcher behavior is required to improve data reliability.

Authors:  Mark N Wass; Larry Ray; Martin Michaelis
Journal:  Gigascience       Date:  2019-05-01       Impact factor: 6.524

6.  Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor.

Authors:  Alok Jaiswal; Prson Gautam; Elina A Pietilä; Sanna Timonen; Nora Nordström; Yevhen Akimov; Nina Sipari; Ziaurrehman Tanoli; Thomas Fleischer; Kaisa Lehti; Krister Wennerberg; Tero Aittokallio
Journal:  Mol Syst Biol       Date:  2021-03       Impact factor: 11.429

7.  Predicting Synergism of Cancer Drug Combinations Using NCI-ALMANAC Data.

Authors:  Pavel Sidorov; Stefan Naulaerts; Jérémy Ariey-Bonnet; Eddy Pasquier; Pedro J Ballester
Journal:  Front Chem       Date:  2019-07-16       Impact factor: 5.221

8.  Bayesian multi-source regression and monocyte-associated gene expression predict BCL-2 inhibitor resistance in acute myeloid leukemia.

Authors:  Brian S White; Suleiman A Khan; Mike J Mason; Muhammad Ammad-Ud-Din; Swapnil Potdar; Disha Malani; Heikki Kuusanmäki; Brian J Druker; Caroline Heckman; Olli Kallioniemi; Stephen E Kurtz; Kimmo Porkka; Cristina E Tognon; Jeffrey W Tyner; Tero Aittokallio; Krister Wennerberg; Justin Guinney
Journal:  NPJ Precis Oncol       Date:  2021-07-23
  8 in total

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