Publications

Paul E, He J, Mallick H.  2025.  Accelerated Bayesian Reciprocal LASSO. Communications in Statistics - Simulation and Computation.

Anceschi N, Ferrari F, Dunson DB, Mallick H.  2024.  Bayesian Joint Additive Factor Models for Multiview Learning. arXiv preprint arXiv:2406.00778.

Chatterjee S, Fadikar A, Hanumesh V, Meshram SSunil, Zoh RS, Ma S, Arunkumar G, Mallick H.  2024.  Group Heteroscedasticity - A Silent Saboteur of Power and False Discovery in RNA-Seq Differential Expression. bioRxiv, 2024.04. 01.587633.

Mallick H, Porwal A, Saha S, Basak P, Svetnik V, Paul E.  2024.  An integrated Bayesian framework for multi-omics prediction and classification. Stat Med. 43(5):983-1002.

Paul E, Afzal AM, Brown R, Cao S, Liu Y, Matejovicova T, Porwal A, Sun Z, Baumgartner R, Mallick H.  2024.  A survey of Bayesian statistical methods in biomarker discovery and early clinical development. Communications in Statistics: Case Studies, Data Analysis and Applications. 10(1):67-93.

Alhamzawi R, Alhamzawi A, Mallick H.  2023.  The reciprocal elastic net. Communications in Statistics: Case Studies, Data Analysis and Applications. 9(4):422-436.

Mallick H, Chatterjee S, Chowdhury S, Chatterjee S, Rahnavard A, Hicks SC.  2022.  Differential expression of single-cell RNA-seq data using Tweedie models. Stat Med. 41(18):3492-3510.

Mallick H, An L, Chen M, Wang P, Zhao N.  2022.  Editorial: Methods for Single-Cell and Microbiome Sequencing Data. Front Genet. 13:920191.

Ma S, Shungin D, Mallick H, Schirmer M, Nguyen LH, Kolde R, Franzosa E, Vlamakis H, Xavier R, Huttenhower C.  2022.  Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin. Genome Biol. 23(1):208.

Paul E, Mallick H.  2022.  Unified reciprocal LASSO estimation via least squares approximation. Communications in Statistics - Simulation and Computation.

Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH et al..  2021.  Multivariable association discovery in population-scale meta-omics studies. PLoS Comput Biol. 17(11):e1009442.

Rahnavard A, Chatterjee S, Sayoldin B, Crandall KA, Tekola-Ayele F, Mallick H.  2021.  Omics community detection using multi-resolution clustering. Bioinformatics. 37(20):3588-3594.

Mallick H, Alhamzawi R, Paul E, Svetnik V.  2021.  The reciprocal Bayesian LASSO. Stat Med. 40(22):4830-4849.

Ma S, Ren B, Mallick H, Moon YSup, Schwager E, Maharjan S, Tickle TL, Lu Y, Carmody RN, Franzosa EA et al..  2021.  A statistical model for describing and simulating microbial community profiles. PLoS Comput Biol. 17(9):e1008913.

Nguyen LH, Ma W, Wang DD, Cao Y, Mallick H, Gerbaba TK, Lloyd-Price J, Abu-Ali G, A Hall B, Sikavi D et al..  2020.  Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men. Gastroenterology. 158(5):1313-1325.

Alhamzawi R, Mallick H.  2020.  Bayesian reciprocal LASSO quantile regression. Communications in Statistics - Simulation and Computation. 51:11

Mallick H, Bucci V, An L.  2020.  Editorial: Statistical and Computational Methods for Microbiome Multi-Omics Data. Front Genet. 11:927.

Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK et al..  2020.  Global chemical effects of the microbiome include new bile-acid conjugations. Nature. 579(7797):123-129.

Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, A Hall B, Mallick H, McIver LJ et al..  2019.  Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol. 4(2):293-305.

Oulhote Y, C H, Valvi D, Mallick H, J L-P, G R.  2019.  Human microbiome and lifetime exposure to environmental chemicals in healthy young adults. Environmental Epidemiology. 3

Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ et al..  2019.  Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 569(7758):655-662.

Mallick H, Franzosa EA, Mclver LJ, Banerjee S, Sirota-Madi A, Kostic AD, Clish CB, Vlamakis H, Xavier RJ, Huttenhower C.  2019.  Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences. Nat Commun. 10(1):3136.

Alhamzawi R, Yu K, Mallick H.  2019.  Quantile Regression and Beyond in Statistical Analysis of Data. Journal of Probability and Statistics.

Mallick H, Yi N.  2018.  Bayesian Bridge Regression. J Appl Stat. 45(6):988-1008.

Borren NZ, Conway G, Garber JJ, Khalili H, Budree S, Mallick H, Yajnik V, Xavier RJ, Ananthakrishnan AN.  2018.  Differences in Clinical Course, Genetics, and the Microbiome Between Familial and Sporadic Inflammatory Bowel Diseases. J Crohns Colitis. 12(5):525-531.