Doctoral Thesis Title: Modeling structured biological processes with machine learning

Publications while at MIT: 

 Generating experimentally unrelated target molecule-binding highly functionalized nucleic-acid polymers using machine learning.

Chen JC, Chen JP, Shen MW, Wornow M, Bae M, Yeh WH, Hsu A, Liu DR.Nat Commun. 2022 Aug 4;13(1):4541. doi: 10.1038/s41467-022-31955-4.PMID: 35927274 Free PMC article.

Reconstruction of evolving gene variants and fitness from short sequencing reads.

Shen MW, Zhao KT, Liu DR.Nat Chem Biol. 2021 Nov;17(11):1188-1198. doi: 10.1038/s41589-021-00876-6. Epub 2021 Oct 11.PMID: 34635842 Free PMC article.

Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning.

Koblan LW, Arbab M, Shen MW, Hussmann JA, Anzalone AV, Doman JL, Newby GA, Yang D, Mok B, Replogle JM, Xu A, Sisley TA, Weissman JS, Adamson B, Liu DR.Nat Biotechnol. 2021 Nov;39(11):1414-1425. doi: 10.1038/s41587-021-00938-z. Epub 2021 Jun 28.PMID: 34183861 Free PMC article.

Small molecule inhibition of ATM kinase increases CRISPR-Cas9 1-bp insertion frequency.

Bermudez-Cabrera HC, Culbertson S, Barkal S, Holmes B, Shen MW, Zhang S, Gifford DK, Sherwood RI.Nat Commun. 2021 Aug 25;12(1):5111. doi: 10.1038/s41467-021-25415-8.PMID: 34433825 Free PMC article.

Detection of gene cis-regulatory element perturbations in single-cell transcriptomes.

Yeo GHT, Juez O, Chen Q, Banerjee B, Chu L, Shen MW, Sabry M, Logister I, Sherwood RI, Gifford DK.PLoS Comput Biol. 2021 Mar 12;17(3):e1008789. doi: 10.1371/journal.pcbi.1008789. eCollection 2021 Mar.PMID: 33711017 Free PMC article.

PrimeDesign software for rapid and simplified design of prime editing guide RNAs.

Hsu JY, Grünewald J, Szalay R, Shih J, Anzalone AV, Lam KC, Shen MW, Petri K, Liu DR, Joung JK, Pinello L.Nat Commun. 2021 Feb 15;12(1):1034. doi: 10.1038/s41467-021-21337-7.PMID: 33589617 Free PMC article.

Machine learning based CRISPR gRNA design for therapeutic exon skipping.

Louie W, Shen MW, Tahiry Z, Zhang S, Worstell D, Cassa CA, Sherwood RI, Gifford DK.PLoS Comput Biol. 2021 Jan 8;17(1):e1008605. doi: 10.1371/journal.pcbi.1008605. eCollection 2021 Jan.PMID: 33417623 Free PMC article.

Comprehensive Mapping of Key Regulatory Networks that Drive Oncogene Expression.

Lin L, Holmes B, Shen MW, Kammeron D, Geijsen N, Gifford DK, Sherwood RI.Cell Rep. 2020 Nov 24;33(8):108426. doi: 10.1016/j.celrep.2020.108426.PMID: 33238122 Free PMC article.

Determinants of Base Editing Outcomes from Target Library Analysis and Machine Learning.

Arbab M, Shen MW, Mok B, Wilson C, Matuszek Ż, Cassa CA, Liu DR.Cell. 2020 Jul 23;182(2):463-480.e30. doi: 10.1016/j.cell.2020.05.037. Epub 2020 Jun 12.PMID: 32533916 Free PMC article.

Continuous evolution of SpCas9 variants compatible with non-G PAMs.

Miller SM, Wang T, Randolph PB, Arbab M, Shen MW, Huang TP, Matuszek Z, Newby GA, Rees HA, Liu DR.Nat Biotechnol. 2020 Apr;38(4):471-481. doi: 10.1038/s41587-020-0412-8. Epub 2020 Feb 10.PMID: 32042170 Free PMC article.

Predictable and precise template-free CRISPR editing of pathogenic variants.

Shen MW, Arbab M, Hsu JY, Worstell D, Culbertson SJ, Krabbe O, Cassa CA, Liu DR, Gifford DK, Sherwood RI.Nature. 2018 Nov;563(7733):646-651. doi: 10.1038/s41586-018-0686-x. Epub 2018 Nov 7.PMID: 30405244 Free PMC article.