Literature DB >> 28817245

Reports from CAGI: The Critical Assessment of Genome Interpretation.

Roger A Hoskins1, Susanna Repo1, Daniel Barsky1, Gaia Andreoletti1, John Moult2,3, Steven E Brenner1.   

Abstract

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Year:  2017        PMID： 28817245      PMCID： PMC5606199          DOI： 10.1002/humu.23290

Source DB:  PubMed          Journal:  Hum Mutat        ISSN： 1059-7794            Impact factor:   4.878


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  23 in total

1.  Whole-protein alanine-scanning mutagenesis of allostery: A large percentage of a protein can contribute to mechanism.

Authors:  Qingling Tang; Aron W Fenton
Journal:  Hum Mutat       Date:  2017-06-16       Impact factor: 4.878

2.  Predicting gene expression in massively parallel reporter assays: A comparative study.

Authors:  Anat Kreimer; Haoyang Zeng; Matthew D Edwards; Yuchun Guo; Kevin Tian; Sunyoung Shin; Rene Welch; Michael Wainberg; Rahul Mohan; Nicholas A Sinnott-Armstrong; Yue Li; Gökcen Eraslan; Talal Bin Amin; Ryan Tewhey; Pardis C Sabeti; Jonathan Goke; Nikola S Mueller; Manolis Kellis; Anshul Kundaje; Michael A Beer; Sunduz Keles; David K Gifford; Nir Yosef
Journal:  Hum Mutat       Date:  2017-03-09       Impact factor: 4.878

3.  Accurate eQTL prioritization with an ensemble-based framework.

Authors:  Haoyang Zeng; Matthew D Edwards; Yuchun Guo; David K Gifford
Journal:  Hum Mutat       Date:  2017-04-19       Impact factor: 4.878

4.  PON-P and PON-P2 predictor performance in CAGI challenges: Lessons learned.

Authors:  Abhishek Niroula; Mauno Vihinen
Journal:  Hum Mutat       Date:  2017-05-02       Impact factor: 4.878

Review 5.  Objective assessment of the evolutionary action equation for the fitness effect of missense mutations across CAGI-blinded contests.

Authors:  Panagiotis Katsonis; Olivier Lichtarge
Journal:  Hum Mutat       Date:  2017-06-21       Impact factor: 4.878

6.  Predicting enhancer activity and variant impact using gkm-SVM.

Authors:  Michael A Beer
Journal:  Hum Mutat       Date:  2017-03-15       Impact factor: 4.878

7.  Stratified polygenic risk prediction model with application to CAGI bipolar disorder sequencing data.

Authors:  Maggie Haitian Wang; Billy Chang; Rui Sun; Inchi Hu; Xiaoxuan Xia; William Ka Kei Wu; Ka Chun Chong; Benny Chung-Ying Zee
Journal:  Hum Mutat       Date:  2017-06-13       Impact factor: 4.878

8.  CAGI4 Crohn's exome challenge: Marker SNP versus exome variant models for assigning risk of Crohn disease.

Authors:  Lipika R Pal; Kunal Kundu; Yizhou Yin; John Moult
Journal:  Hum Mutat       Date:  2017-06-28       Impact factor: 4.878

9.  Genetic variant in folate homeostasis is associated with lower warfarin dose in African Americans.

Authors:  Roxana Daneshjou; Eric R Gamazon; Ben Burkley; Larisa H Cavallari; Julie A Johnson; Teri E Klein; Nita Limdi; Sara Hillenmeyer; Bethany Percha; Konrad J Karczewski; Taimour Langaee; Shitalben R Patel; Carlos D Bustamante; Russ B Altman; Minoli A Perera
Journal:  Blood       Date:  2014-07-30       Impact factor: 22.113

10.  Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.

Authors:  Binghuang Cai; Biao Li; Nikki Kiga; Janita Thusberg; Timothy Bergquist; Yun-Ching Chen; Noushin Niknafs; Hannah Carter; Collin Tokheim; Violeta Beleva-Guthrie; Christopher Douville; Rohit Bhattacharya; Hui Ting Grace Yeo; Jean Fan; Sohini Sengupta; Dewey Kim; Melissa Cline; Tychele Turner; Mark Diekhans; Jan Zaucha; Lipika R Pal; Chen Cao; Chen-Hsin Yu; Yizhou Yin; Marco Carraro; Manuel Giollo; Carlo Ferrari; Emanuela Leonardi; Silvio C E Tosatto; Jason Bobe; Madeleine Ball; Roger A Hoskins; Susanna Repo; George Church; Steven E Brenner; John Moult; Julian Gough; Mario Stanke; Rachel Karchin; Sean D Mooney
Journal:  Hum Mutat       Date:  2017-06-19       Impact factor: 4.878
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  23 in total

1.  Gene-specific features enhance interpretation of mutational impact on acid α-glucosidase enzyme activity.

Authors:  Aashish N Adhikari
Journal:  Hum Mutat       Date:  2019-08-07       Impact factor: 4.878

2.  Deep learning in biomedicine.

Authors:  Michael Wainberg; Daniele Merico; Andrew Delong; Brendan J Frey
Journal:  Nat Biotechnol       Date:  2018-09-06       Impact factor: 54.908

3.  BRCA1- and BRCA2-specific in silico tools for variant interpretation in the CAGI 5 ENIGMA challenge.

Authors:  Natàlia Padilla; Alejandro Moles-Fernández; Casandra Riera; Gemma Montalban; Selen Özkan; Lars Ootes; Sandra Bonache; Orland Díez; Sara Gutiérrez-Enríquez; Xavier de la Cruz
Journal:  Hum Mutat       Date:  2019-07-03       Impact factor: 4.878

Review 4.  Principles and methods of in-silico prioritization of non-coding regulatory variants.

Authors:  Phil H Lee; Christian Lee; Xihao Li; Brian Wee; Tushar Dwivedi; Mark Daly
Journal:  Hum Genet       Date:  2017-12-29       Impact factor: 4.132

5.  VIPdb, a genetic Variant Impact Predictor Database.

Authors:  Zhiqiang Hu; Changhua Yu; Mabel Furutsuki; Gaia Andreoletti; Melissa Ly; Roger Hoskins; Aashish N Adhikari; Steven E Brenner
Journal:  Hum Mutat       Date:  2019-08-17       Impact factor: 4.878

6.  Predicting pathogenicity of missense variants with weakly supervised regression.

Authors:  Yue Cao; Yuanfei Sun; Mostafa Karimi; Haoran Chen; Oluwaseyi Moronfoye; Yang Shen
Journal:  Hum Mutat       Date:  2019-08-07       Impact factor: 4.878

7.  Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction.

Authors:  Daniel K Wells; Marit M van Buuren; Kristen K Dang; Vanessa M Hubbard-Lucey; Kathleen C F Sheehan; Katie M Campbell; Andrew Lamb; Jeffrey P Ward; John Sidney; Ana B Blazquez; Andrew J Rech; Jesse M Zaretsky; Begonya Comin-Anduix; Alphonsus H C Ng; William Chour; Thomas V Yu; Hira Rizvi; Jia M Chen; Patrice Manning; Gabriela M Steiner; Xengie C Doan; Taha Merghoub; Justin Guinney; Adam Kolom; Cheryl Selinsky; Antoni Ribas; Matthew D Hellmann; Nir Hacohen; Alessandro Sette; James R Heath; Nina Bhardwaj; Fred Ramsdell; Robert D Schreiber; Ton N Schumacher; Pia Kvistborg; Nadine A Defranoux
Journal:  Cell       Date:  2020-10-09       Impact factor: 41.582

8.  Assessment of predicted enzymatic activity of α-N-acetylglucosaminidase variants of unknown significance for CAGI 2016.

Authors:  Wyatt T Clark; Laura Kasak; Constantina Bakolitsa; Zhiqiang Hu; Gaia Andreoletti; Giulia Babbi; Yana Bromberg; Rita Casadio; Roland Dunbrack; Lukas Folkman; Colby T Ford; David Jones; Panagiotis Katsonis; Kunal Kundu; Olivier Lichtarge; Pier L Martelli; Sean D Mooney; Conor Nodzak; Lipika R Pal; Predrag Radivojac; Castrense Savojardo; Xinghua Shi; Yaoqi Zhou; Aneeta Uppal; Qifang Xu; Yizhou Yin; Vikas Pejaver; Meng Wang; Liping Wei; John Moult; Guoying Karen Yu; Steven E Brenner; Jonathan H LeBowitz
Journal:  Hum Mutat       Date:  2019-09       Impact factor: 4.878

9.  Matching whole genomes to rare genetic disorders: Identification of potential causative variants using phenotype-weighted knowledge in the CAGI SickKids5 clinical genomes challenge.

Authors:  Lipika R Pal; Kunal Kundu; Yizhou Yin; John Moult
Journal:  Hum Mutat       Date:  2019-11-15       Impact factor: 4.878

10.  Reports from the fifth edition of CAGI: The Critical Assessment of Genome Interpretation.

Authors:  Gaia Andreoletti; Lipika R Pal; John Moult; Steven E Brenner
Journal:  Hum Mutat       Date:  2019-08-26       Impact factor: 4.878
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