Doctoral Thesis Title: Gene-regulatory circuitry of disease risk and progression

Publications while at MIT:

Neurons burdened by DNA double-strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration.

Welch GM, Boix CA, Schmauch E, Davila-Velderrain J, Victor MB, Dileep V, Bozzelli PL, Su Q, Cheng JD, Lee A, Leary NS, Pfenning AR, Kellis M, Tsai LH.Sci Adv. 2022 Sep 30;8(39):eabo4662. doi: 10.1126/sciadv.abo4662. Epub 2022 Sep 28.PMID: 36170369 Free PMC article.

Regulatory genomic circuitry of human disease loci by integrative epigenomics.

Boix CA, James BT, Park YP, Meuleman W, Kellis M.Nature. 2021 Feb;590(7845):300-307. doi: 10.1038/s41586-020-03145-z. Epub 2021 Feb 3.PMID: 33536621 Free PMC article.

GENCODE 2021.

Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I, Berry A, Bignell A, Boix C, Carbonell Sala S, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Howe KL, Hunt T, Izuogu OG, Johnson R, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Riera FC, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Wolf MY, Xu J, Yang YT, Yates A, Zerbino D, Zhang Y, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Tress ML, Flicek P.Nucleic Acids Res. 2021 Jan 8;49(D1):D916-D923. doi: 10.1093/nar/gkaa1087.PMID: 33270111 Free PMC article.

Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity.

Shim WJ, Sinniah E, Xu J, Vitrinel B, Alexanian M, Andreoletti G, Shen S, Sun Y, Balderson B, Boix C, Peng G, Jing N, Wang Y, Kellis M, Tam PPL, Smith A, Piper M, Christiaen L, Nguyen Q, Bodén M, Palpant NJ.Cell Syst. 2020 Dec 16;11(6):625-639.e13. doi: 10.1016/j.cels.2020.11.001. Epub 2020 Dec 4.PMID: 33278344 Free PMC article.

Expanded encyclopaedias of DNA elements in the human and mouse genomes.

ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z.Nature. 2020 Jul;583(7818):699-710. doi: 10.1038/s41586-020-2493-4. Epub 2020 Jul 29.PMID: 32728249 Free PMC article.

Perspectives on ENCODE.

ENCODE Project Consortium, Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM.Nature. 2020 Jul;583(7818):693-698. doi: 10.1038/s41586-020-2449-8. Epub 2020 Jul 29.PMID: 32728248 Free PMC article.

Strain-level diversity drives alternative community types in millimetre-scale granular biofilms.

Leventhal GE, Boix C, Kuechler U, Enke TN, Sliwerska E, Holliger C, Cordero OX.Nat Microbiol. 2018 Nov;3(11):1295-1303. doi: 10.1038/s41564-018-0242-3. Epub 2018 Sep 24.PMID: 30250246