Publications

CAGI flagship paper

Adebali O, Adhikari A, Adzhubey I, Altman R, Amin T, Andreoletti G, Arkin AP, Azaria JR, Babbi G, Babbitt P, Bachar E, Bachman B, Baek M, Ball MP, Barsky D, Beer M, Beleva-Guthrie V, Berger B, Bernard B, Bhat R, Bhattacharya R, Bobe J, Bonvini P, Bovo S, Breese M, Brenner SE, Brodie AS, Bromberg Y, Buckley B, Butte A, Cai B, Campbell C, Cao C, Capriotti E, Carraro M, Casadio R, Chandonia JM, Chang BHW, Chellappan A, Chen CY, Chen F, Chen R, Chen SC, Chen YC, Church G, Clark WT, Cline M, Corredor A, Cutting GR, D’Andrea E, Dabbiru N, Daneshjou R, Davis C, De Baets G, Di Lena P, Diekhans M, Dogan RI, Douville C, Driver I, Dunbrack R, van Durme J, Eakin A, Edwards M, L. Elefanti, L. Elnitski, Eraslan G, H. Fang, Fenton AW, Ferrari C, Flynn A, L. Folkman, Ford CT, Franke A, Frankish A, Franklin Z, Friedberg I, Fu Y, Gasparini A, Gaunt T, Getz G, Gifford D, Giollo M, Gonzaludo N, Gotea V, Gough J, Gray JW, Grishin N, Guo Y, Harrow J, Hart R, Hasenahuer M, Heo L, Hernandez R, Homayouni R, Hoskins RA, Hosur R, Huang CLV, Hubbard T, Huwe P, Hwang S, Imanishi T, Jacobsen J, Jannson L, Jeong CS, Y. Jiang, Jones DT, Jordan D, Kahn S, Kane JP, B. Kang, Karchin R, Katsonis P, Keles S, Kellis M, Kiga N, Kim D, Kim E, Kirsch JF, Kleyman M, Kraemer A, Kreimer A, Kundaje A, Kundu K, Kwok PY, Lam E, Lathrop R, LeBowitz JH, Lee D, Lee G, Lee I, Leonardi E, Li A, Li B, Li J, Li Y, Lichtarge O, Lin CF, Lovisa F, Lua RC, Ly MK, Mak ACY, Mak A, Malloy MJ, Martelli PL, Masica D, McCombie R, Medoff Z, Menin C, Meyn MS, Meyn S, Mezlini AM, Mohan R, Monzon AM, Mooney SD, Morgan AA, Mort M, Moult J, Mount S, Mucaki E, Mudge J, Mueller N, Mungall C, Murakami K, Nagai Y, Neumann AJ, Ng P, Niknafs N, Niroula A, Nodzak CML, Nussbaum R, Ofran Y, Olatubosun A, Organization NY, Pagel K, Pal LR, Pandey G, Park T, Pearson N, Pejaver V, Peng J, Petersen BS, Pirooznia M, Piryatinska A, Plotts C, Potash JB, Pullinger CR, Radivojac P, Rana S, Rao AR, Rao A, Repo S, Rine J, Ritchie G, Rogan P, Roth F, Rousseau F, Sabeti P, Sanford J, Scaini MC, Schmitt N, Schwarz JM, Schymkowitz J, Searls DB, Seok C, Shackelford G, Shah S, Shatsky M, Shendure J, Sheridan M, Shigeta R, Shihab HA, Shim JE, Shin J, Shin S, Shmulevich I, Shon J, Silver BR, Sinnott-Armstrong N, Smithers B, Snyder M, Sokolov A, Son YA, Srinivasan R, Stanke M, Sterne-Weiler T, Stitziel N, Stuart J, Su A, Sundaram L, Sunyaev S, Tang PLF, Tang P, Tavtigian S, Teerakulkittipong N, Tewhey R, Thurlby N, Thusberg J, Tian K, Tokheim C, Tosatto SCE, Tuncel Y, Turner T, Unger RS, Uppal A, Ustunkar G, Valiaho J, Veltman J, Vihinen M, Wahl M, Wainberg M, Wang LS, Wang M, Wang M, Wang X, Wang Y, Wei L, Wei Q, Wei L, Weile J, Welch R, Wilson S, Wu C, Xu L, Xu Q, Yang Y, Yates C, Yee S, Yeleswarapu SJ, Yin Y, Yu CH, Yu GK, Yuan D, Zandi P, Zaucha J, Zeng H, and Zuhl M. 2016. Findings from the Critical Assessment of Genome Interpretation (CAGI): community experiments to evaluate predictions of phenotype from genomic variation. In preparation.

Papers accepted

  • Gallion J, Koire A, Katsonis P, Schoenegge AM, Bouvier M, Lichtarge O. Predicting phenotype from genotype: Improving accuracy through more robust experimental and computational modeling. Hum Mutat. 2017. PMID: 28230923.
  • Carraro M, Minervini G, Giollo M, Bromberg Y, Capriotti E, Casadio R, Dunbrack R, Elefanti L, Fariselli P, Ferrari C, Gough J, Katsonis P, Leonardi E, Lichtarge O, Menin C, Martelli PL, Niroula A, Pal LR, Repo S, Scaini MC, Vihinen M, Wei Q, Xu Q, Yang Y, Yin Y, Zaucha J, Zhao H, Zhou Y, Brenner SE, Moult J, Tosatto SCE. Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI. Hum Mutat. 2017. PMID: 28440912.
  • Wang MH, Chang B, Sun R, Hu I, Xia X, Wu WKK, Chong KC, Zee BC. Stratified polygenic risk prediction model with application to CAGI bipolar disorder sequencing data. Hum Mutat. 2017. PMID: 28419606.
  • Chandonia JM, Adhikari A, Carraro M, Chhibber A, Cutting GR, Fu Y, Gasparini A, Jones DT, Kramer A, Kundu K, Lam HY, Leonardi E, Moult J, Pal LR, Searls DB, Shah S, Sunyaev S, Tosatto SC, Yin Y, Buckley BA. 3Lessons from the CAGI-4 Hopkins clinical panel challenge. Hum Mutat. 2017 Apr 11. doi: 10.1002/humu.23225. [Epub ahead of print] PubMed PMID: 28397312.
  • Xu Q, Tang Q, Katsonis P, Lichtarge O, Jones D, Bovo S, Babbi G, Martelli PL, Casadio R, Lee GR, Seok C, Fenton AW, Dunbrack RL Jr. Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4. Hum Mutat. 2017. PMID: 28370845.
  • Niroula A, Vihinen M. PON-P and PON-P2 predictor performance in CAGI challenges: Lessons learned. Hum Mutat. 2017. PMID: 28224672.
  • Zeng H, Edwards MD, Guo Y, Gifford DK. Accurate eQTL prioritization with an ensemble-based framework. Hum Mutat. 2017. PMID: 28224684.
  • Kreimer A, Zeng H, Edwards MD, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong NA, Li Y, Eraslan G, Amin TB, Tewhey R, Sabeti PC, Goke J, Mueller NS, Kellis M, Kundaje A, Beer MA, Keles S, Gifford DK, Yosef N. Predicting gene expression in massively parallel reporter assays: A comparative study. Hum Mutat. 2017. PMID: 28220625.
  • Beer MA. Predicting enhancer activity and variant impact using gkm-SVM. Hum Mutat. PubMed PMID: 28120510.
  • Capriotti E, Martelli PL, Fariselli P, Casadio R. Blind Prediction of Deleterious Amino Acid Variations with SNPs&GO. Hum Mutat. 2017. PMID: 28102005.
  • Giollo M, Jones DT, Carraro M, Leonardi E, Ferrari C, Tosatto SC. Crohn disease risk prediction-Best practices and pitfalls with exome data. Hum Mutat. 2017. PMID: 28087895.

Papers submitted

  • Cai B, Kiga N, Thusberg J, Bergquist T, Chen Y, Niknafs N, Carter H, Tokheim C, Beleva-Guthrie V, Douville C, Bhattacharya R, Yeo HTG, Fan J, Sengupta S, Kim D, Cline M, Turner T, Diekhans M, Zaucha J, Pal LR, Cao C, Yu CH, Yin Y, Carraro M, Giollo M, Ferrari C, Leonardi E, Tosatto S, Bobe J, Ball M, Hoskins RA, Repo S, Church G, Brenner S, Moult J, Gough J, Stanke M, Karchin R, and Mooney SD. 2017. Matching Phenotypes to Whole Genomes: Lessons Learned from Three Iterations of the Personal Genome Project Community Challenges. Human Mutation
  • Katsonis P and Lichtarge O. 2017. Objective Assessment of the Evolutionary Action Equation for the Fitness Effect of Missense Mutations Across CAGI Blinded Contests. Human Mutation
  • Sundaram L, Li X & Rana R. 2017. DeepBipolar: Identifying Genomic Mutations for Bipolar Disorder via Deep Learning. Human Mutation
  • Daneshjou R, Morgan AA, Tosatto S, Jones DT, Giollo M, Ferrari C, Carraro M, Gasparini A, Leonardi E, Wang Y, Bromberg Y, Pal LR, Kundu K, Yin Y, Bachar E, Azaria JR, Ofran Y, Unger R, Haitian MW, Chang B, Sundaram L, Bhat R, Li X, Niroula A, Vihinen M, Bovo S, Martelli PL, Babbi G, Casadio R, Hoskins R, Repo S, Edwards M, Zeng H, Gifford D, Altman R, Moult J, and Brenner S. 2017. Predicting disease and drug phenotypes from exome data. Human Mutation
  • Kundu K, Pal LR, Yin Y, and Moult J. 2017. Determination of disease phenotypes and pathogenic variants in the CAGI4 clinical gene panel challenge. Human Mutation
  • Pal LR, Kundu K, Yin Y, and Moult J. 2017. CAGI4 Crohn’s exome challenge: Marker SNP versus exome variant models for assigning risk of Crohn’s disease. Human Mutation
  • Pal LR, Kundu K, Yin Y, and Moult J. 2017. CAGI4 SickKids clinical genomes challenge: a pipeline for identifying pathogenic variants. Human Mutation
  • Pejaver V, Li B, Mooney SD, and Radivojac P. 2017. Variant pathogenicity predictors generalize well across a range of function-specific challenges. Human Mutation
  • Üstünkar G, Döm HA, Yılmaz A, and Son YA. 2017. Analytic Hierarchy Process Based Structured SNP Prioritization Scheme for Multi-hierarchical Filtering of Informative SNPs. Human Mutation
  • Yin Y, Kundu K, Pal LR, and Moult J.2017. Development and evaluation of consensus methods for interpreting missense mutations in the NAGLU and SUMO-ligase CAGI4 challenges. Human Mutation
  • Marshall C, Stavropoulos DJ, Bowdin S, Monfarad N, and Meyn S. 2017. CAGI4 SickKids clinical genomes challenge: a pipeline for identifying pathogenic variants. Human Mutation

Papers in preparation

  • LeBowitz J, Yu KG, Hengl L, Aoyagi-Scharber M, and Wyatt TC. 2017. N-acetyl-glucosaminidase (NAGLU): predict the effect of naturally occurring missense mutations on cellular enzymatic activity. Human Mutation
  • Grishin N. 2017. Human SUMO ligase (UBE2l): predict the effects of missense mutations on competitive growth in a high-throughput yeast complementation assay. Human Mutation