1. Jang Y, Tomasini L, Bae T, Szekely A, Vaccarino FM, Abyzov A. Transgenerational transmission of post-zygotic mutations suggests symmetric contribution of first two blastomeres to human germline. Nat Commun 2024 Oct 23;15(1):9117.
2. Maury EA, Jones A, Seplyarskiy V, Nguyen TTL, Rosenbluh C, Bae T, et al. Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes. Science 2024 Oct 11;386(6718):217-224.
3. Garrison MA, Jang Y, Bae T, et al. Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases. Sci Data 2023 Nov 20;10(1):813.
4. Panda A, Suvakov M, Mariani J, Drucker KL, Park Y, Jang Y, Kollmeyer TM, Sarkar G, Bae T, et al. Clonally Selected Lines After CRISPR-Cas Editing Are Not Isogenic. CRISPR J 2023 Apr;6(2):176-182.
5. Jang Y, Fasching L, Bae T, Tomasini L, Schreiner J, Szekely A, Fernandez TV, Leckman JF, Vaccarino FM, Abyzov A. Efficient reconstruction of cell lineage trees for cell ancestry and cancer. Nucleic Acids Res 2023 Apr 7:gkad254. Online ahead of print.
6. Chung C, Yang X, Bae T, et al. Comprehensive multi-omic profiling of somatic mutations in malformations of cortical development. Nat Genet 2023 Feb;55(2):209-220.
7. 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. Control-independent mosaic single nucleotide variant detection with DeepMosaic. Nat Biotechnol 2023 Jan 2. Online ahead of print
8. Bae T, Wang Y, Vaccarino FM, Abyzov A. Somatic genomic mosaicism in the brain during aging: Scratching the surface. Clin Transl Med 2022 Dec;12(12):e1138..
9. Bae T*, Fasching L*, Wang Y*, Shin JH*, et al. Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability. Science 2022 Jul 29;377(6605):511-517. *Equal contribution authors
10. Sarangi V, Jang Y, Suvakov M, Bae T, et al. All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons. PLoS Comput Biol 2022 Apr 20;18(4):e1009487.
11. Wang Y*, Bae T*, Thorpe J*, Sherman MA*, Jones AG*, et al. Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biol 2021 Mar 29; 22(1):92. *Equal contribution authors
12. 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. Early developmental asymmetries in cell lineage trees in living individuals. Science 2021 Mar 19; 371(6535):1245-1248.
13. 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. Landmarks of human embryonic and brain development inscribed in somatic mutations.Science 2021 Mar 19; 371(6535):1249-1253.
14. 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. Complex mosaic structural variations in human fetal brains. Genome Res 2020 Dec 30;30(12):1695-1704.
15. Sarangi V, Jourdon A, Bae T, Panda A, Vaccarino F, Abyzov A. SCELLECTOR: ranking amplification bias in single cells using shallow sequencing. BMC Bioinformatics 2020 Nov 12;21(1):521.
16. Druliner BR, Wang P, Bae T, et al. Molecular characterization of colorectal adenomas with and without malignancy reveals distinguishing genome, transcriptome and methylome alterations. Scientific Reports 2018 Feb 16; 8(1), 3161.
17. 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. Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis. Science 2018 Feb 2; 359 (6375):550.
18. Kim M, Druliner BR, Vasmatzis N, Bae T, Chia N, Abyzov A, & Boardman LA. Inferring modes of evolution from colorectal cancer with residual polyp of origin. Oncotarget 2017 Dec 26; 9(6), 6780–6792.
19. McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, et al. Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network Science 2017 Apr 28; 356 (6336):395.
20. 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. Colorectal Cancer with Residual Polyp of Origin: A Model of Malignant Transformation. Transl Oncol 2016 Aug; 9 (4):280-6.
21. 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. The PsychENCODE project. Nat Neurosci 2015 Dec; 18 (12):1707-12.
22. Bae T*, Weon KY*, Lee JW, Eum KH, Kim S, Choi JW. Restoration of paclitaxel resistance by CDK1 intervention in drug-resistant ovarian cancer. Carcinogenesis 2015 Dec; 36 (12):1561-71.
23. Kim YR, Park MS, Eum KH, Kim J, Lee JW, Bae T, Lee DH, Choi JW. Transcriptome analysis indicates TFEB1 and YEATS4 as regulatory transcription factors for drug resistance of ovarian cancer. Oncotarget 2015 Oct 13; 6 (31):31030-8.
24. 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. An integrated map of structural variation in 2,504 human genomes. Nature 2015 Oct 01; 526 (7571):75-81.
25. Saito S, Zhou X, Bae T, Kim S, Horimoto K. Identification of master regulator candidates in conjunction with network screening and inference. Int J Data Min Bioinform 2013, 8(3), 366.
26. Bae T*, Rho K*, Choi JW, Horimoto K, Kim W, Kim S. Identification of upstream regulators for prognostic expression signature genes in colorectal cancer. BMC Syst Biol 2013, 7:86.
27. Lee J-H, Kim DG, Bae TJ, et al. CDA: combinatorial drug discovery using transcriptional response modules. PloS One 2012, 7(8), e42573.
28. Lee HS*, Bae T*, Lee J-H*, et al. Rational drug repositioning guided by an integrated pharmacological network of protein, disease and drug. BMC Syst Biol 2012, 6:80. *Equal contribution authors
29. Ahn TJ, Park K, Son DS, Huh N, Oh S, Bae T, et al. Selecting SNPs for pharmacogenomic association study. Int J Data Min Bioinform 2012, 6(5), 521.
30. Rho K, Kim B, Jang Y, Lee S, Bae T, et al. GARNET--gene set analysis with exploration of annotation relations. BMC Bioinformatics 2011, 12(Suppl 1), S25.
31. Bae T-J*, Kim M-S*, Kim, J-W*, et al. Lipid raft proteome reveals ATP synthase complex in the cell surface. Proteomics2004, 4(11), 3536–48. *Equal contribution authors