MOsAIciSM

Our Work

Publications

31 peer-reviewed publications

Selected Publications

Transgenerational transmission of post-zygotic mutations suggests symmetric contribution of first two blastomeres to human germline.

Jang Y, Tomasini L, Bae T, Szekely A, Vaccarino FM, Abyzov A.

Nat Commun 2024 Oct 23;15(1):9117.

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Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability.

Bae T*, Fasching L*, Wang Y*, Shin JH*, et al.

Science 2022 Jul 29;377(6605):511-517.

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Comprehensive identification of somatic nucleotide variants in human brain tissue.

Wang Y*, Bae T*, Thorpe J*, Sherman MA*, Jones AG*, et al.

Genome Biol 2021 Mar 29;22(1):92.

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Early developmental asymmetries in cell lineage trees in living individuals.

Fasching L, Jang Y, Tomasi S, Schreiner J, Tomasini L, Brady M, Bae T, Sarangi V, Vasmatzis N, Wang Y, Szekely A, Fernandez TV, Leckman JF, Abyzov A, Vaccarino FM.

Science 2021 Mar 19;371(6535):1245-1248.

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Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis.

Bae T, Tomasini L, Mariani J, Zhou B, Roychowdhury T, Franjic D, Pletikos M, Pattni R, Chen BJ, Venturini E, Riley-Gillis B, Sestan N, Urban AE, Abyzov A, Vaccarino FM.

Science 2018 Feb 2;359(6375):550.

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Publications

2024

2
Key Publication

Transgenerational transmission of post-zygotic mutations suggests symmetric contribution of first two blastomeres to human germline.

Jang Y, Tomasini L, Bae T, Szekely A, Vaccarino FM, Abyzov A.

Nat Commun 2024 Oct 23;15(1):9117.

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Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes.

Maury EA, Jones A, Seplyarskiy V, Nguyen TTL, Rosenbluh C, Bae T, et al.

Science 2024 Oct 11;386(6718):217-224.

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2023

5

Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases.

Garrison MA, Jang Y, Bae T, et al.

Sci Data 2023 Nov 20;10(1):813.

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Clonally Selected Lines After CRISPR-Cas Editing Are Not Isogenic.

Panda A, Suvakov M, Mariani J, Drucker KL, Park Y, Jang Y, Kollmeyer TM, Sarkar G, Bae T, et al.

CRISPR J 2023 Apr;6(2):176-182.

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Efficient reconstruction of cell lineage trees for cell ancestry and cancer.

Jang Y, Fasching L, Bae T, Tomasini L, Schreiner J, Szekely A, Fernandez TV, Leckman JF, Vaccarino FM, Abyzov A.

Nucleic Acids Res 2023 Apr 7:gkad254.

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Comprehensive multi-omic profiling of somatic mutations in malformations of cortical development.

Chung C, Yang X, Bae T, et al.

Nat Genet 2023 Feb;55(2):209-220.

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Control-independent mosaic single nucleotide variant detection with DeepMosaic.

Yang X, Xu X, Breuss MW, Antaki D, Ball LL, Chung C, Shen J, Li C, George RD, Wang Y, Bae T, Cheng Y, Abyzov A, Wei L, Alexandrov L, Sebat J, NIMH Brain Somatic Mosaicism Network, Gleeson JG.

Nat Biotechnol 2023 Jan 2.

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2022

3

Somatic genomic mosaicism in the brain during aging: Scratching the surface.

Bae T, Wang Y, Vaccarino FM, Abyzov A.

Clin Transl Med 2022 Dec;12(12):e1138.

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Key Publication

Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability.

Bae T*, Fasching L*, Wang Y*, Shin JH*, et al.

Science 2022 Jul 29;377(6605):511-517.

Google Scholar

All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons.

Sarangi V, Jang Y, Suvakov M, Bae T, et al.

PLoS Comput Biol 2022 Apr 20;18(4):e1009487.

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2021

3
Key Publication

Comprehensive identification of somatic nucleotide variants in human brain tissue.

Wang Y*, Bae T*, Thorpe J*, Sherman MA*, Jones AG*, et al.

Genome Biol 2021 Mar 29;22(1):92.

Google Scholar
Key Publication

Early developmental asymmetries in cell lineage trees in living individuals.

Fasching L, Jang Y, Tomasi S, Schreiner J, Tomasini L, Brady M, Bae T, Sarangi V, Vasmatzis N, Wang Y, Szekely A, Fernandez TV, Leckman JF, Abyzov A, Vaccarino FM.

Science 2021 Mar 19;371(6535):1245-1248.

Google Scholar

Landmarks of human embryonic and brain development inscribed in somatic mutations.

Bizzotto S, Dou Y, Ganz J, Doan RN, Kwon M, Bohrson CL, Kim SN, Bae T, Abyzov A, NIMH Brain Somatic Mosaicism Network, Park PJ, Walsh CA.

Science 2021 Mar 19;371(6535):1249-1253.

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2020

2

Complex mosaic structural variations in human fetal brains.

Sekar S, Tomasini L, Proukakis C, Bae T, Manlove L, Jang Y, Scuderi S, Zhou B, Kalyva M, Amiri A, Mariani J, Sedlazeck FJ, Urban AE, Vaccarino FM, Abyzov A.

Genome Res 2020 Dec 30;30(12):1695-1704.

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SCELLECTOR: ranking amplification bias in single cells using shallow sequencing.

Sarangi V, Jourdon A, Bae T, Panda A, Vaccarino F, Abyzov A.

BMC Bioinformatics 2020 Nov 12;21(1):521.

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2018

2

Molecular characterization of colorectal adenomas with and without malignancy reveals distinguishing genome, transcriptome and methylome alterations.

Druliner BR, Wang P, Bae T, et al.

Scientific Reports 2018 Feb 16;8(1):3161.

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Key Publication

Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis.

Bae T, Tomasini L, Mariani J, Zhou B, Roychowdhury T, Franjic D, Pletikos M, Pattni R, Chen BJ, Venturini E, Riley-Gillis B, Sestan N, Urban AE, Abyzov A, Vaccarino FM.

Science 2018 Feb 2;359(6375):550.

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2017

2

Inferring modes of evolution from colorectal cancer with residual polyp of origin.

Kim M, Druliner BR, Vasmatzis N, Bae T, Chia N, Abyzov A, & Boardman LA.

Oncotarget 2017 Dec 26;9(6):6780-6792.

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Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network.

McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, et al.

Science 2017 Apr 28;356(6336):395.

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2016

1

Colorectal Cancer with Residual Polyp of Origin: A Model of Malignant Transformation.

Druliner BR, Rashtak S, Ruan X, Bae T, Vasmatzis N, O'Brien D, Johnson R, Felmlee-Devine D, Washechek-Aletto J, Basu N, Liu H, Smyrk T, Abyzov A, Boardman LA.

Transl Oncol 2016 Aug;9(4):280-6.

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2015

4

The PsychENCODE project.

Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, et al.

Nat Neurosci 2015 Dec;18(12):1707-12.

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Restoration of paclitaxel resistance by CDK1 intervention in drug-resistant ovarian cancer.

Bae T*, Weon KY*, Lee JW, Eum KH, Kim S, Choi JW.

Carcinogenesis 2015 Dec;36(12):1561-71.

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Transcriptome analysis indicates TFEB1 and YEATS4 as regulatory transcription factors for drug resistance of ovarian cancer.

Kim YR, Park MS, Eum KH, Kim J, Lee JW, Bae T, Lee DH, Choi JW.

Oncotarget 2015 Oct 13;6(31):31030-8.

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An integrated map of structural variation in 2,504 human genomes.

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stutz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, et al.

Nature 2015 Oct 01;526(7571):75-81.

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2013

2

Identification of master regulator candidates in conjunction with network screening and inference.

Saito S, Zhou X, Bae T, Kim S, Horimoto K.

Int J Data Min Bioinform 2013;8(3):366.

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Identification of upstream regulators for prognostic expression signature genes in colorectal cancer.

Bae T*, Rho K*, Choi JW, Horimoto K, Kim W, Kim S.

BMC Syst Biol 2013;7:86.

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2012

3

CDA: combinatorial drug discovery using transcriptional response modules.

Lee J-H, Kim DG, Bae TJ, et al.

PloS One 2012;7(8):e42573.

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Rational drug repositioning guided by an integrated pharmacological network of protein, disease and drug.

Lee HS*, Bae T*, Lee J-H*, et al.

BMC Syst Biol 2012;6:80.

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Selecting SNPs for pharmacogenomic association study.

Ahn TJ, Park K, Son DS, Huh N, Oh S, Bae T, et al.

Int J Data Min Bioinform 2012;6(5):521.

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2011

1

GARNET--gene set analysis with exploration of annotation relations.

Rho K, Kim B, Jang Y, Lee S, Bae T, et al.

BMC Bioinformatics 2011;12(Suppl 1):S25.

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2004

1

Lipid raft proteome reveals ATP synthase complex in the cell surface.

Bae T-J*, Kim M-S*, Kim J-W*, et al.

Proteomics 2004;4(11):3536-48.

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