IBBR Publications

Kasak L, Bakolitsa C, Hu Z, Yu C, Rine J, Dimster-Denk DF, Pandey G, De Baets G, Bromberg Y, Cao C, et al. Assessing Computational Predictions of the Phenotypic Effect of Cystathionine-beta-Synthase Variants. Hum Mutat. 2019 .

Pejaver V, Babbi G, Casadio R, Folkman L, Katsonis P, Kundu K, Lichtarge O, Martelli PLuigi, Miller M, Moult J, et al. Assessment of methods for predicting the effects of PTEN and TPMT protein variants. Hum Mutat. 2019 .

Carraro M, Monzon AMiguel, Chiricosta L, Reggiani F, Aspromonte MCristina, Bellini M, Pagel K, Jiang Y, Radivojac P, Kundu K, et al. Assessment of patient clinical descriptions and pathogenic variants from gene panel sequences in the CAGI-5 intellectual disability challenge. Hum Mutat. 2019 .

Clark WT, Kasak L, Bakolitsa C, Hu Z, Andreoletti G, Babbi G, Bromberg Y, Casadio R, Dunbrack R, Folkman L, et al. Assessment of predicted enzymatic activity of alpha-N-acetylglucosaminidase (NAGLU) variants of unknown significance for CAGI 2016. Hum Mutat. 2019 .

Kasak L, Hunter JM, Udani R, Bakolitsa C, Hu Z, Adhikari AN, Babbi G, Casadio R, Gough J, Guerrero RF, et al. CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases. Hum Mutat. 2019 .

Pal LR, Kundu K, Yin Y, Moult J. Matching whole genomes to rare genetic disorders: Identification of potential causative variants using phenotype-weighted knowledge in the CAGI SickKids5 clinical genomes challenge. Hum Mutat. 2019 .

McInnes G, Daneshjou R, Katsonis P, Lichtarge O, Srinivasan RG, Rana S, Radivojac P, Mooney SD, Pagel KA, Stamboulian M, et al. Predicting venous thromboembolism risk from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Hum Mutat. 2019 .

Andreoletti G, Pal LR, Moult J, Brenner SE. Reports from the fifth edition of CAGI: The Critical Assessment of Genome Interpretation. Hum Mutat. 2019 .

Darden L, Kundu K, Pal LR, Moult J. Harnessing formal concepts of biological mechanism to analyze human disease. PLoS Comput Biol. 2018 ;14(12):e1006540.

Chandonia J-M, Adhikari A, Carraro M, Chhibber A, Cutting GR, Fu Y, Gasparini A, Jones DT, Kramer A, Kundu K, et al. 3Lessons from the CAGI-4 Hopkins clinical panel challenge. Hum Mutat. 2017 .

Pal LR, Kundu K, Yin Y, Moult J. CAGI4 Crohn's exome challenge: Marker SNP versus exome variant models for assigning risk of Crohn disease. Hum Mutat. 2017 .

Pal LR, Kundu K, Yin Y, Moult J. CAGI4 SickKids clinical genomes challenge: A pipeline for identifying pathogenic variants. Hum Mutat. 2017 .

Kundu K, Pal LR, Yin Y, Moult J. Determination of disease phenotypes and pathogenic variants from exome sequence data in the CAGI 4 gene panel challenge. Hum Mutat. 2017 .

Yin Y, Kundu K, Pal LR, Moult J. Ensemble variant interpretation methods to predict enzyme activity and assign pathogenicity in the CAGI4 NAGLU (Human N-acetyl-glucosaminidase) and UBE2I (Human SUMO-ligase) challenges. Hum Mutat. 2017 .

Cai B, Li B, Kiga N, Thusberg J, Bergquist T, Chen Y-C, Niknafs N, Carter H, Tokheim C, Beleva-Guthrie V, et al. Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges. Hum Mutat. 2017 .

Carraro M, Minervini G, Giollo M, Bromberg Y, Capriotti E, Casadio R, Dunbrack R, Elefanti L, Fariselli P, Ferrari C, et al. Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI. Hum Mutat. 2017 .

Pal LR, Chao KL, Moult J, Herzberg O. Reply to HU et al.: On the interpretation of gasdermin-B expression quantitative trait loci data. Proc Natl Acad Sci U S A. 2017 ;114(38):E7863-E7864.

Daneshjou R, Wang Y, Bromberg Y, Bovo S, Martelli PL, Babbi G, Di Lena P, Casadio R, Edwards M, Gifford D, et al. Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Hum Mutat. 2017 .

Yu C-H, Pal LR, Moult J. Consensus Genome-Wide Expression Quantitative Trait Loci and Their Relationship with Human Complex Trait Disease. OMICS. 2016 ;20(7):400-14.

Pal LR, Moult J. Genetic Basis of Common Human Disease: Insight into the Role of Missense SNPs from Genome-Wide Association Studies. J Mol Biol. 2015 ;427(13):2271-89.

Pal LR, Yu C-H, Mount SM, Moult J. Insights from GWAS: emerging landscape of mechanisms underlying complex trait disease. BMC Genomics. 2015 ;16 Suppl 8:S4.

Gorlatova N, Chao K, Pal LR, Araj RHanna, Galkin A, Turko IV, Moult J, Herzberg O. Protein characterization of a candidate mechanism SNP for Crohn's disease: the macrophage stimulating protein R689C substitution. PLoS One. 2011 ;6(11):e27269.

Galkin A, Li Z, Li L, Kulakova L, Pal LR, Dunaway-Mariano D, Herzberg O. Structural insights into the substrate binding and stereoselectivity of giardia fructose-1,6-bisphosphate aldolase. Biochemistry. 2009 ;48(14):3186-96.