Brian Cleary, Ph.D.

Year of Graduation: 



Prof. Aviv Regev and Prof. Eric Lander

Current Position: 

Assistant Professor, Boston University

Cleary Lab Website

The Cleary Lab studies tissue physiology, cellular pathways, and human genetics using a combination of algorithmic insights, new experimental methods, and advanced computational tools.

Doctoral Thesis Title: Leveraging latent patterns in the study of living systems


Publications while at MIT: 

1. Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming.

Schiebinger G, Shu J, Tabaka M, Cleary B, Subramanian V, Solomon A, Gould J, Liu S, Lin S, Berube P, Lee L, Chen J, Brumbaugh J, Rigollet P, Hochedlinger K, Jaenisch R, Regev A, Lander ES.

Cell. 2019 Feb 7;176(4):928-943.e22. doi: 10.1016/j.cell.2019.01.006. Epub 2019 Jan 31. Erratum in: Cell. 2019 Mar 7;176(6):1517



2. High resolution time series reveals cohesive but short-lived communities in coastal plankton.

Martin-Platero AM, Cleary B, Kauffman K, Preheim SP, McGillicuddy DJ, Alm EJ, Polz MF.

Nat Commun. 2018 Jan 18;9(1):266. doi: 10.1038/s41467-017-02571-4.

PMID:29348571  Free PMC Article


3. Efficient Generation of Transcriptomic Profiles by Random Composite Measurements.

Cleary B, Cong L, Cheung A, Lander ES, Regev A.

Cell. 2017 Nov 30;171(6):1424-1436.e18. doi: 10.1016/j.cell.2017.10.023. Epub 2017 Nov 16.

PMID:29153835  Free PMC Article


4. Systematic mapping of functional enhancer-promoter connections with CRISPR interference.

Fulco CP, Munschauer M, Anyoha R, Munson G, Grossman SR, Perez EM, Kane M, Cleary B, Lander ES, Engreitz JM.

Science. 2016 Nov 11;354(6313):769-773. Epub 2016 Sep 29.

PMID:27708057  Free PMC Article


5. Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning.

Cleary B,Brito IL, Huang K, Gevers D, Shea T, Young S, Alm EJ.

Nat Biotechnol. 2015 Oct;33(10):1053-60. doi: 10.1038/nbt.3329. Epub 2015 Sep 14.

PMID:26368049 Free PMC Article