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Daniel E. Carlin
Researcher at University of California, San Diego
Publications - 25
Citations - 28069
Daniel E. Carlin is an academic researcher from University of California, San Diego. The author has contributed to research in topics: Cancer & Biological network. The author has an hindex of 15, co-authored 25 publications receiving 22707 citations. Previous affiliations of Daniel E. Carlin include University of California, Santa Cruz & Institute for Systems Biology.
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Journal ArticleDOI
A Fast and Flexible Framework for Network-Assisted Genomic Association.
Daniel E. Carlin,Samson Fong,Yue Qin,Tongqiu Jia,Justin K. Huang,Bokan Bao,Chao Zhang,Trey Ideker +7 more
TL;DR: It is shown that NAGA recovers many known disease genes from analysis of schizophrenia genetic data, and it substantially boosts associations with previously unappreciated genes such as amyloid beta precursor.
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A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines
Mehmet Gönen,Mehmet Gönen,Barbara A. Weir,Glenn S. Cowley,Glenn S. Cowley,Francisca Vazquez,Francisca Vazquez,Yuanfang Guan,Alok Jaiswal,Masayuki Karasuyama,Vladislav Uzunangelov,Tao Wang,Aviad Tsherniak,Sara Howell,Sara Howell,Daniel Marbach,Daniel Marbach,Bruce Hoff,Thea Norman,Antti Airola,Adrian Bivol,Kerstin Bunte,Kerstin Bunte,Daniel E. Carlin,Sahil Chopra,Sahil Chopra,Alden Deran,Kyle Ellrott,Kyle Ellrott,Peddinti Gopalacharyulu,Kiley Graim,Samuel Kaski,Samuel Kaski,Suleiman A. Khan,Yulia Newton,Sam Ng,Tapio Pahikkala,Evan O. Paull,Artem Sokolov,Hao Tang,Jing Tang,Krister Wennerberg,Yang Xie,Xiaowei Zhan,Zhu Fan,Bahman Afsari,Tero Aittokallio,Tero Aittokallio,Jesse S. Boehm,Yu Chuan Chang,Tenghui Chen,Zechen Chong,Haitham Elmarakeby,Elana J. Fertig,Emanuel Gonçalves,Pinghua Gong,Christoph Hafemeister,William C. Hahn,William C. Hahn,Lenwood S. Heath,Łukasz Kędziorski,Niraj Khemka,Erh kan King,Mario Lauria,Mark Liu,Daniel Machado,Hiroshi Mamitsuka,Adam A. Margolin,Mateusz Mazurkiewicz,Michael P. Menden,Szymon Migacz,Zhi Nie,Paurush Praveen,Corrado Priami,Simone Rizzetto,Miguel Rocha,David E. Root,Cameron Rudd,Witold R. Rudnicki,Julio Saez-Rodriguez,Lei Song,Gustavo Stolovitzky,Gustavo Stolovitzky,Joshua M. Stuart,Duanchen Sun,Bence Szalai,Difei Wang,Ling-Yun Wu,Guanghua Xiao,Jieping Ye,Yuting Ye,Wanding Zhou +91 more
TL;DR: This study establishes benchmarks for gene essentiality prediction, presents a community resource for future comparison with this benchmark, and provides insights into factors influencing the ability to predict gene essentiality from functional genetic screens.
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pyNBS: a Python implementation for network-based stratification of tumor mutations.
TL;DR: A modularized Python 2.7 implementation of the network-based stratification (NBS) algorithm for stratifying tumor somatic mutation profiles into molecularly and clinically relevant subtypes and provides a compact cancer reference network that increases the significance of tumor stratification using the NBS algorithm.
Journal ArticleDOI
Prophetic Granger Causality to infer gene regulatory networks.
Daniel E. Carlin,Evan O. Paull,Kiley Graim,Christopher K. Wong,Adrian Bivol,Peter Ryabinin,Kyle Ellrott,Artem Sokolov,Joshua M. Stuart +8 more
TL;DR: The investigations reveal that PGC provides complementary information to other approaches, raising the performance of ensemble learners, while on its own achieves moderate performance, and serves as a valuable new tool in the bioinformatics toolkit for analyzing temporal datasets.
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Modeling of RAS complexes supports roles in cancer for less studied partners
TL;DR: A RAS isoform-specific protein-protein interaction network is constructed and predicted 3D complexes involving RASisoforms and interaction partners to identify the most probable interaction interfaces and implicated residues in the allosteric and hyper-variable regions of RAS proteins as the predominant binding site for non-canonical effectors.