Publications

Publications

Peer-reviewed work and preprints from the lab and our collaborations. Names in bold mark lab authorship.

2025

Beyond the gene: Decoding alternative isoforms

Mattioli K, Bulyk ML · Trends in Genetics

Read →
2025

Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms

Lambourne L, Mattioli K, Santoso C, Sheynkman G, Inukai S, Kaundal B, Berenson A, Spirohn-Fitzgerald K, Bhattacharjee A, Rothman E, Shrestha S, Laval F, Carroll BS, Plassmeyer SP, Emenecker RJ, Yang Z, Bisht D, Sewell JA, Li G, Prasad A, Phanor S, Lane R, Moyer DC, Hunt T, Balcha D, Gebbia M, Twizere J, Hao T, Holehouse AS, Frankish A, Riback JA, Salomonis N, Calderwood MA, Hill DE, Sahni N, Vidal M, Bulyk ML, Fuxman Bass JI · Molecular Cell

Read →
2024

AKT and EZH2 inhibitors kill TNBCs by hijacking mechanisms of involution

Schade AE, Perurena N, Yang Y, Rodriguez CL, Krishnan A, Gardner A, Loi P, Xu Y, Nguyen VTM, Mastellone GM, Pilla NF, Watanabe M, Ota K, Davis RA, Mattioli K, Xiang D, Zoeller JJ, Lin J-R, Morganti S, Garrido-Castro AC, Tolaney SM, Li Z, Barbie DA, Sorger PK, Helin K, Santagata S, Knott SRV, Cichowski K · Nature

Read →
2024

Epigenetic and oncogenic inhibitors cooperatively drive differentiation and kill KRAS-mutant colorectal cancers

Loi P, Schade AE, Rodriguez CL, Krishnan A, Perurena N, Nguyen VTM, Xu Y, Watanabe M, Davis RA, Gardner A, Pilla NF, Mattioli K, Popow O, Gunduz N, Lannagan TRM, Fitzgerald S, Sicinska ET, Lin JR, Tan W, Brais LK, Haigis KM, Giannakis M, Ng K, Santagata S, Helin K, Sansom OJ, Cichowski K · Cancer Discovery

Read →
2024

Determinants of gastric cancer immune escape identified from non-coding immune-landscape quantitative trait loci

Miliotis C, Ma Y, Katopodi X, Karagkouni D, Kanata E, Mattioli K, Kalavros N, Pita-Juárez YH, Batalini F, Ramnarine VR, Nanda S, Slack FJ, Vlachos IS · Nature Communications

Read →
2023

Systematic characterization of regulatory variants of blood pressure genes

Oliveros W, Delfosse K, Lato DF, Kiriakopulos K, Mokhtaridoost M, Said A, McMurray BJ, Browning JWL, Mattioli K, Meng G, Ellis J, Mital S, Melé M, Maass PG · Cell Genomics

Read →
2023

Combating castration-resistant prostate cancer by co-targeting the epigenetic regulators EZH2 and HDAC

Schade AE, Kuzmickas R, Rodriguez CL, Mattioli K, Enos M, Gardner A, Cichowski K · PLOS Biology

Read →
2022

Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy

Lesurf R, Said A, Akinrinade O, Breckpot J, Delfosse K, Liu T, Yao R, Persad G, McKenna F, Noche RR, Oliveros W, Mattioli K, Shah S, Miron A, Yang Q, Meng G, Et Al. · npj Genomic Medicine

Read →
2021

Genome-wide CRISPR interference screen identifies lncRNA loci required for pluripotency and differentiation

Haswell JR, Mattioli K, Gerhardinger C, Foster DJ, Fernandez PP, Maass PG, Rinn JL, Slack FJ · PLOS ONE

Read →
2020

Cis and trans effects differentially contribute to the evolution of promoters and enhancers

Mattioli K, Gerhardinger C, Andergassen D, Maass PG, Rinn JL, Melé M · Genome Biology

Read →
2020

Resolving mechanisms of immune-mediated disease in primary CD4 T cells

Bourges C, Groff AF, Burren OS, Gerhardinger C, Mattioli K, Hu T, Anand T, Epping MW, Smith KGC, Rinn JL, Lee JC · EMBO Molecular Medicine

Read →
2019

High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue-specificity

Mattioli K, Volders PJ, Gerhardinger C, Lee JC, Maass PG, Melé M, Rinn JL · Genome Research

Read →
2017

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs

Melé M, Mattioli K, Mallard W, Shechner DM, Gerhardinger C, Rinn JL · Genome Research

Read →