Vaishnav ED*, de Boer CG*, Yassour M, Molinet J, Fan L, Adiconis X, Thompson DA, Cubillos FA, Levin JZ, Regev A§. 2021. A comprehensive fitness landscape model reveals the evolutionary history and future evolvability of eukaryotic cis-regulatory DNA sequences. https://doi.org/10.1101/2021.02.17.430503. bioRxiv. GitHub. Zenodo. GEO (and here).

de Boer CG*, Ray JP*, Hacohen N, Regev R. MAUDE: Inferring expression changes in sorting-based CRISPR screens. Genome Biol. 2020 Jun 3;21(1):134. doi: 10.1186/s13059-020-02046-8. PubMed. Journal. bioRxiv. GitHub.

Ray JP*, de Boer CG*, Fulco CP, Lareau CA, Kanai M, Ulirsch JC, Tewhey R, Ludwig LS, Reilly SK, Bergman DT, Engreitz JM, Issner R, Finucane HK, Lander ES, Regev A, Hacohen N. Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features. Nat Commun. 2020 Mar 6;11(1):1237. doi: 10.1038/s41467-020-15022-4. PubMed. Journal. GitHub (and here and here). GEO.

de Boer CG, Vaishnav ED, Sadeh R, Abeyta EL, Friedman N, Regev A. Deciphering gene-regulatory logic with 100 million random promoters. Nat Biotechnol. 2020 Jan;38(1):56-65. doi: 10.1038/s41587-019-0315-8. Epub 2019 Dec 2. PubMed. Journal. GitHub. bioRxiv. GEO (and here).

Mann M*, Mehta A*, de Boer C*, Kowalczyk MS*, Lee K, Rogel N, Knecht AR, Farouq D, Regev A, Baltimore D. Heterogeneous Responses of Hematopoietic Stem Cells to Inflammatory Stimuli are Altered with Age. Cell Rep. 2018 Dec 11;25(11):2992-3005.e5. PubMed. Journal.

Sade-Feldman M*, Yizhak K*, Bjorgaard SL, Ray JP, de Boer CG, Lieb DJ, Chen JH, Frederick DT, Barzily-Rokni M, Freeman SS, Reuben A, Hoover PJ, Villani A-C, Eliane J-P, Hammond MR, Vitzthum H, Blackmon SM, Li B, Gopalakrishnan V, Reddy SM, Zachary A, Cooper ZA, Stemmer-Rachamimov A, Flaherty KT, Wargo JA, Boland GM, Sullivan RJ, Getz G, and Hacohen N.  Defining T cell states associated with response to checkpoint immunotherapy in melanoma. Cell. 2018 Nov 1;175(4):998-1013.e20. PubMed. Journal.

de Boer CG, Regev A. BROCKMAN: Deciphering variance in epigenomic regulators by k-mer factorization. BMC Bioinformatics. 2018 Jul 3;19(1):253. PubMed. Journal. GitHub.

Puram RV, Kowalczyk MS, de Boer CG, Schneider RK, Miller PG, McConkey M, Tothova Z, Tejero H, Heckl D, Järås M, Chen MC, Li H, Tamayo A, Cowley GS, Rozenblatt-Rosen O, Al-Shahrour F, Regev A, Ebert BL. Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML. Cell. 2016 Apr 7;165(2):303-16. PubMed. Journal.

Salinas F*, de Boer CG*, Abarca V, García V, Cuevas M, Araos S, Larrondo LF, Martínez C, Cubillos FA. Natural variation in non-coding regions underlying phenotypic diversity in budding yeast. Sci Rep. 2016 Feb 22;6:21849. doi: 10.1038/srep21849. PubMed. Journal.

de Boer CG, van Bakel H, Tsui K, Li J, Morris QD, Nislow C, Greenblatt JF, Hughes TR. 2014. A Unified Model for Yeast Transcript Definition. Genome Res. 24(1): 154-166. PubMed. Journal.

For the complete listing, please see my Google Scholar page.