Qian J, Rafi AM, Cazottes E, de Boer CG. Evaluation of Active Learning Selection Strategies and Characterization of Informative Sequences for Sequence-to-Expression Models. bioRxiv. 2026 May 26:10.64898/2026.05.21.727038. doi: 10.64898/2026.05.21.727038. BioRxiv.
Rafi AM, Kiyota B, Yachie N, de Boer CG. Characterizing homology-induced data leakage and memorization in genome-trained sequence models.bioRxiv. 2026 May 25:10.1101/2025.01.22.634321. doi: 10.1101/2025.01.22.634321. BioRxiv.
Aninta SI, Tewhey R, de Boer CG. Position-dependent variant effect reveal importance of context in genomic regulation. bioRxiv. 2026 March 18:10.64898/2026.03.17.712488. doi: 10.64898/2026.03.17.712488. BioRxiv.
Chapel M, Dennis J, de Boer CG. Variant Effect Depend on Polygenic Background: Experimental, Clinical, and Evolutionary Implications. Cell Genom. 2026 Feb 11;6(2):101131. doi: 10.1016/j.xgen.2025.101131. Epub 2026 Jan 26. PMID: 41592569; PMCID: PMC12903375. BioRxiv. Pubmed.
Salaudeen AL, Mateyko N, de Boer CG. RAPID-DASH: Fast and Efficient Assembly of Guide RNA Arrays for Multiplexed CRISPR-Cas9 Applications. Synth Biol (Oxf). 2025 Dec 18;11(1):ysaf020. doi: 10.1093/synbio/ysaf020. PMID: 40291718; PMCID: PMC12027327. BioRxiv. GitHub.
Chapel M, de Boer CG. Evolutionary Simulations Reveal Role for Genomic Recombination in the Evolution of Gene Regulatory Network Complexity and Robustness. bioRxiv [Preprint]. 2025 Aug 28:10.1101/2025.08.28.672878. doi: 10.1101/2025.08.28.672878. BioRxiv. GitHub.
Luthra I, Priyadarshi S, Guo R, Mahieu L, Kempynck N, Dooley D, Penzar D, Vorontsov I, Sheng Y, Tu X, Klie A, Drusinsky S, Floren A, Armand E, Alasoo K, Seelig G, Tewhey R, Koo P, Agarwal V, Gosai S, Pinello L, White MA, Lal A, Zeitlinger J, Pollard KS, Libbrecht M, Carter H, Mostafavi S, Kulakovskiy I, Hsiao W, Aerts S, Zhou J, de Boer CG. GAME: Genomic API for Model Evaluation. bioRxiv. 2025 Jul 8:2025.07.04.663250. doi: 10.1101/2025.07.04.663250. PMID: 40672207; PMCID: PMC12265512. BioRxiv. Github (here and here).
Mateyko N, de Boer CG. Culture Wars: Empirically Determining the Best Approach for Plasmid Library Amplification. ACS Synth Biol. 2024 Aug 16;13(8):2328-2334. doi: 10.1021/acssynbio.4c00377. Epub 2024 Jul 22. PMID: 39038190. BioRxiv. Pubmed. GitHub.
Rafi AM, Nogina D, Penzar D, Lee D, Lee D, Kim N, Kim S, Kim D, Shin Y, Kwak IY, Meshcheryakov G, Lando A, Zinkevich A, Kim BC, Lee J, Kang T, Vaishnav ED, Yadollahpour P; Random Promoter DREAM Challenge Consortium; Kim S, Albrecht J, Regev A, Gong W, Kulakovskiy IV, Meyer P, de Boer CG. A community effort to optimize sequence-based deep learning models of gene regulation. Nat Biotechnol. 2025 Aug;43(8):1373-1383. doi: 10.1038/s41587-024-02414-w. Epub 2024 Oct 11. PMID: 39394483; PMCID: PMC12339383. BioRxiv. Pubmed. Zenodo.
de Boer CG, Taipale J. Hold out the genome: a roadmap to solving the cis-regulatory code. Nature. 2024 Jan;625(7993):41-50. doi: 10.1038/s41586-023-06661-w. Epub 2023 Dec 13. PMID: 38093018. BioRxiv. Pubmed.
Luthra I, Jensen C, Chen XE, Salaudeen AL, Rafi AM, de Boer CG. Regulatory activity is the default DNA state in eukaryotes. Nat Struct Mol Biol. 2024 Mar;31(3):559-567. doi: 10.1038/s41594-024-01235-4. Epub 2024 Mar 6. PMID: 38448573. BioRxiv. Pubmed. GEO.
Mateyko N, Tariq O, Chen XE, Cheney W, Salaudeen AL, Luthra I, Nikpour N, Rafi AM, Kamali Deghan H, Jensen C, de Boer C. GIL: a python package for designing custom indexing primers. Bioinformatics. 2023 Jun 1;39(6):btad328. doi: 10.1093/bioinformatics/btad328. Erratum in: Bioinformatics. 2023 Dec 1;39(12):btad735. doi: 10.1093/bioinformatics/btad735. PMID: 37208164; PMCID: PMC10246578.BioRxiv. Pubmed. GitHub.
Vaishnav ED, de Boer CG, Molinet J, Yassour M, Fan L, Adiconis X, Thompson DA, Levin JZ, Cubillos FA, Regev A. The evolution, evolvability and engineering of gene regulatory DNA. Nature. 2022 Mar;603(7901):455-463. doi: 10.1038/s41586-022-04506-6. Epub 2022 Mar 9. PMID: 35264797; PMCID: PMC8934302. Pubmed. Journal. GitHub. Zenodo. GEO (and here).
de Boer CG, Ray JP, Hacohen N, Regev A. MAUDE: inferring expression changes in sorting-based CRISPR screens. Genome Biol. 2020 Jun 3;21(1):134. doi: 10.1186/s13059-020-02046-8. PMID: 32493396; PMCID: PMC7268349. BioRxiv. Pubmed. Journal. 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. PMID: 32144282; PMCID: PMC7060350. PubMed. Journal. GitHub (and here and here). GEO.
de Boer CG, Vaishnav ED, Sadeh R, Abeyta EL, Friedman N, Regev A. Deciphering eukaryotic 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. Erratum in: Nat Biotechnol. 2020 Oct;38(10):1211. doi: 10.1038/s41587-020-0665-2. PMID: 31792407; PMCID: PMC6954276. PubMed. Journal. GitHub. bioRxiv. GEO (and here).
Mann M, Mehta A, de Boer CG, Kowalczyk MS, Lee K, Haldeman P, 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. doi: 10.1016/j.celrep.2018.11.056. PMID: 30540934; PMCID: PMC6424521. PubMed. Journal.
Sade-Feldman M, Yizhak K, Bjorgaard SL, Ray JP, de Boer CG, Jenkins RW, Lieb DJ, Chen JH, Frederick DT, Barzily-Rokni M, Freeman SS, Reuben A, Hoover PJ, Villani AC, Ivanova E, Portell A, Lizotte PH, Aref AR, Eliane JP, Hammond MR, Vitzthum H, Blackmon SM, Li B, Gopalakrishnan V, Reddy SM, Cooper ZA, Paweletz CP, Barbie DA, Stemmer-Rachamimov A, Flaherty KT, Wargo JA, Boland GM, Sullivan RJ, Getz G, Hacohen N. Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma. Cell. 2018 Nov 1;175(4):998-1013.e20. doi: 10.1016/j.cell.2018.10.038. Erratum in: Cell. 2019 Jan 10;176(1-2):404. doi: 10.1016/j.cell.2018.12.034. PMID: 30388456; PMCID: PMC6641984. 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. doi: 10.1186/s12859-018-2255-6. PMID: 29970004; PMCID: PMC6029352. 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. doi: 10.1016/j.cell.2016.03.015. PMID: 27058663; PMCID: PMC4826477. 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. PMID: 26898953; PMCID: PMC4761897. PubMed. Journal.
de Boer CG, van Bakel H, Tsui K, Li J, Morris QD, Nislow C, Greenblatt JF, Hughes TR. A unified model for yeast transcript definition. Genome Res. 2014 Jan;24(1):154-66. doi: 10.1101/gr.164327.113. Epub 2013 Oct 29. PMID: 24170600; PMCID: PMC3875857. PubMed. Journal.For the complete listing, please see Carl’s Google Scholar page.
For the complete listing, please see Carl’s Google Scholar page.