Literature DB >> 36064595

Big data in basic and translational cancer research.

Peng Jiang1, Sanju Sinha2, Kenneth Aldape3, Sridhar Hannenhalli2, Cenk Sahinalp2, Eytan Ruppin4.   

Abstract

Historically, the primary focus of cancer research has been molecular and clinical studies of a few essential pathways and genes. Recent years have seen the rapid accumulation of large-scale cancer omics data catalysed by breakthroughs in high-throughput technologies. This fast data growth has given rise to an evolving concept of 'big data' in cancer, whose analysis demands large computational resources and can potentially bring novel insights into essential questions. Indeed, the combination of big data, bioinformatics and artificial intelligence has led to notable advances in our basic understanding of cancer biology and to translational advancements. Further advances will require a concerted effort among data scientists, clinicians, biologists and policymakers. Here, we review the current state of the art and future challenges for harnessing big data to advance cancer research and treatment.
© 2022. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.

Entities:  

Year:  2022        PMID: 36064595      PMCID: PMC9443637          DOI: 10.1038/s41568-022-00502-0

Source DB:  PubMed          Journal:  Nat Rev Cancer        ISSN: 1474-175X            Impact factor:   69.800


  172 in total

Review 1.  Cancer transcriptome profiling at the juncture of clinical translation.

Authors:  Marcin Cieślik; Arul M Chinnaiyan
Journal:  Nat Rev Genet       Date:  2017-12-27       Impact factor: 53.242

Review 2.  Tackling the widespread and critical impact of batch effects in high-throughput data.

Authors:  Jeffrey T Leek; Robert B Scharpf; Héctor Corrada Bravo; David Simcha; Benjamin Langmead; W Evan Johnson; Donald Geman; Keith Baggerly; Rafael A Irizarry
Journal:  Nat Rev Genet       Date:  2010-09-14       Impact factor: 53.242

3.  Genomic and transcriptomic profiling expands precision cancer medicine: the WINTHER trial.

Authors:  Jordi Rodon; Jean-Charles Soria; Raanan Berger; Wilson H Miller; Eitan Rubin; Aleksandra Kugel; Apostolia Tsimberidou; Pierre Saintigny; Aliza Ackerstein; Irene Braña; Yohann Loriot; Mohammad Afshar; Vincent Miller; Fanny Wunder; Catherine Bresson; Jean-François Martini; Jacques Raynaud; John Mendelsohn; Gerald Batist; Amir Onn; Josep Tabernero; Richard L Schilsky; Vladimir Lazar; J Jack Lee; Razelle Kurzrock
Journal:  Nat Med       Date:  2019-04-22       Impact factor: 53.440

4.  Next-generation characterization of the Cancer Cell Line Encyclopedia.

Authors:  Mahmoud Ghandi; Franklin W Huang; Judit Jané-Valbuena; Gregory V Kryukov; Christopher C Lo; E Robert McDonald; Jordi Barretina; Ellen T Gelfand; Craig M Bielski; Haoxin Li; Kevin Hu; Alexander Y Andreev-Drakhlin; Jaegil Kim; Julian M Hess; Brian J Haas; François Aguet; Barbara A Weir; Michael V Rothberg; Brenton R Paolella; Michael S Lawrence; Rehan Akbani; Yiling Lu; Hong L Tiv; Prafulla C Gokhale; Antoine de Weck; Ali Amin Mansour; Coyin Oh; Juliann Shih; Kevin Hadi; Yanay Rosen; Jonathan Bistline; Kavitha Venkatesan; Anupama Reddy; Dmitriy Sonkin; Manway Liu; Joseph Lehar; Joshua M Korn; Dale A Porter; Michael D Jones; Javad Golji; Giordano Caponigro; Jordan E Taylor; Caitlin M Dunning; Amanda L Creech; Allison C Warren; James M McFarland; Mahdi Zamanighomi; Audrey Kauffmann; Nicolas Stransky; Marcin Imielinski; Yosef E Maruvka; Andrew D Cherniack; Aviad Tsherniak; Francisca Vazquez; Jacob D Jaffe; Andrew A Lane; David M Weinstock; Cory M Johannessen; Michael P Morrissey; Frank Stegmeier; Robert Schlegel; William C Hahn; Gad Getz; Gordon B Mills; Jesse S Boehm; Todd R Golub; Levi A Garraway; William R Sellers
Journal:  Nature       Date:  2019-05-08       Impact factor: 49.962

5.  The single-cell pathology landscape of breast cancer.

Authors:  Hartland W Jackson; Jana R Fischer; Vito R T Zanotelli; H Raza Ali; Robert Mechera; Savas D Soysal; Holger Moch; Simone Muenst; Zsuzsanna Varga; Walter P Weber; Bernd Bodenmiller
Journal:  Nature       Date:  2020-01-20       Impact factor: 49.962

6.  Evaluating eligibility criteria of oncology trials using real-world data and AI.

Authors:  Ruishan Liu; Shemra Rizzo; Samuel Whipple; Navdeep Pal; Arturo Lopez Pineda; Michael Lu; Brandon Arnieri; Ying Lu; William Capra; Ryan Copping; James Zou
Journal:  Nature       Date:  2021-04-07       Impact factor: 69.504

7.  Determining cell type abundance and expression from bulk tissues with digital cytometry.

Authors:  Aaron M Newman; Chloé B Steen; Chih Long Liu; Andrew J Gentles; Aadel A Chaudhuri; Florian Scherer; Michael S Khodadoust; Mohammad S Esfahani; Bogdan A Luca; David Steiner; Maximilian Diehn; Ash A Alizadeh
Journal:  Nat Biotechnol       Date:  2019-05-06       Impact factor: 54.908

8.  Breast tumours maintain a reservoir of subclonal diversity during expansion.

Authors:  Darlan C Minussi; Michael D Nicholson; Hanghui Ye; Alexander Davis; Kaile Wang; Toby Baker; Maxime Tarabichi; Emi Sei; Haowei Du; Mashiat Rabbani; Cheng Peng; Min Hu; Shanshan Bai; Yu-Wei Lin; Aislyn Schalck; Asha Multani; Jin Ma; Thomas O McDonald; Anna Casasent; Angelica Barrera; Hui Chen; Bora Lim; Banu Arun; Funda Meric-Bernstam; Peter Van Loo; Franziska Michor; Nicholas E Navin
Journal:  Nature       Date:  2021-03-24       Impact factor: 69.504

9.  NCI Imaging Data Commons.

Authors:  Andrey Fedorov; William J R Longabaugh; David Pot; David A Clunie; Steve Pieper; Hugo J W L Aerts; André Homeyer; Rob Lewis; Afshin Akbarzadeh; Dennis Bontempi; William Clifford; Markus D Herrmann; Henning Höfener; Igor Octaviano; Chad Osborne; Suzanne Paquette; James Petts; Davide Punzo; Madelyn Reyes; Daniela P Schacherer; Mi Tian; George White; Erik Ziegler; Ilya Shmulevich; Todd Pihl; Ulrike Wagner; Keyvan Farahani; Ron Kikinis
Journal:  Cancer Res       Date:  2021-06-15       Impact factor: 12.701

10.  Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients.

Authors:  Jianzhu Ma; Samson H Fong; Yunan Luo; Christopher J Bakkenist; John Paul Shen; Soufiane Mourragui; Lodewyk F A Wessels; Marc Hafner; Roded Sharan; Jian Peng; Trey Ideker
Journal:  Nat Cancer       Date:  2021-01-25
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  1 in total

1.  Artificial Intelligence in Public Health: Current Trends and Future Possibilities.

Authors:  Daniele Giansanti
Journal:  Int J Environ Res Public Health       Date:  2022-09-21       Impact factor: 4.614

  1 in total

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