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 submitted

  • Kreimer A, Zeng H, Edwards M, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong N, Li Y, Eraslan G, Amin T, Goke J, Mueller N, Kellis M, Kundaje A, Beer M, Keles S, Gifford D, and Yosef N. 2016. Predicting gene expression in massively parallel reporter assays: a comparative study. Under review at Human Mutation
  • Beer M. 2016. Predicting Enhancer Activity and Variant Impact using gkm-SVM. Under review at Hum Mutation
  • 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. 2016. Matching Phenotypes to Whole Genomes: Lessons Learned from Three Iterations of the Personal Genome Project Community Challenges. Under review at Human Mutation
  • Capriotti E, Martelli PL, Fariselli P, and Casadio R. 2016. Blind prediction of deleterious variants with SNPs&GO. Under review at Human Mutation
  • Edwards M, Zeng H, Guo Y, and Gifford D. 2016. Predicting gene expression from DNA sequence in a massively parallel reporter assay: a comparative study.
  • Under review at Human Mutation
  • Giollo M, Jones D, Carraro M, Leonardi E, Ferrari C, and Tosatto S. 2016. Crohn’s disease risk prediction – best practices and pitfalls with exome data. Under review at Human Mutation
  • Katsonis P and Lichtarge O. 2016. Objective Assessment of the Evolutionary Action Equation for the Fitness Effect of Missense Mutations Across CAGI Blinded Contests. Under review at Human Mutation
  • Niroula and M. Vihinen, Improving prediction performance. 2016. Lessons learned from cagi challenges. Under review at Human Mutation
  • Sundaram L, Li X & Rana R. 2016. DeepBipolar: Identifying Genomic Mutations for Bipolar Disorder via Deep Learning. Under review at Human Mutation
  • Wang MH, Chang B, Sun R, Hu I, Chong MKC, and Zee BCY. 2016. A Stratified Polygenic Risk Prediction Model with Application on CAGI Bipolar Disorder Sequencing Data. Under review at Human Mutation

Papers in preparation

  • Carraro M, G. Minervini, Giollo M, Scaini MC, Menin C, De Nicolo A, Ferrari C, Bromberg Y, Capriotti E, Casadio R, Dunbrack R, Fariselli P, Gough J, Katsonis P, Lichtarge P, Martelli PL, Niroula A, Pal LR, Vihinen M, Wei Q, Xu Q, Yang Y, Yin Y, Zhao H, Zhou Y, Brenner SE, Hoskins RA, Repo S, Moult J, and Tosatto SCE. 2016. Performance of in silico tools for the evaluation of CDKN2A missense variants in CAGI. 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. 2016. Predicting disease and drug phenotypes from exome data. Human Mutation
  • Kundu K, Pal LR, Yin Y, and Moult J. 2016. 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. 2016. 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. 2016. CAGI4 SickKids clinical genomes challenge: a pipeline for identifying pathogenic variants. Human Mutation
  • Pejaver V, Li B, Mooney SD, and Radivojac P. 2016. Variant pathogenicity predictors generalize well across a range of function-specific challenges. Human Mutation
  • Üstünkar G, Döm HA, Yılmaz A, and Son YA. 2016. 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.2016. Development and evaluation of consensus methods for interpreting missense mutations in the NAGLU and SUMO-ligase CAGI4 challenges. Human Mutation
  • Chandonia JM, Adhikari A, Buckley AB, Marco C, Chhibber A, Cutting GR, Fu Y, Gasparini A, Jones DT, Kramer A, Kundu K, Lam YKL, Leonardi E, Moult J, Pal LR, Searls DB, Shah S, Tosatto S, Yin Y, and Sunyaev S. 2016. Lessons from the CAGI-4 Hopkins clinical panel challenge. Human Mutation
  • LeBowitz J, Yu KG, Hengl L, Aoyagi-Scharber M, and Wyatt TC. 2016. N-acetyl-glucosaminidase (NAGLU): predict the effect of naturally occurring missense mutations on cellular enzymatic activity. Human Mutation
  • Marshall C, Stavropoulos DJ, Bowdin S, Monfarad N, and Meyn S. 2016. Predict patients’ clinical descriptions and pathogenic variants from their genome sequences. Human Mutation
  • Grishin N. 2016. Human SUMO ligase (UBE2l): predict the effects of missense mutations on competitive growth in a high-throughput yeast complementation assay. Human Mutation