Publications

1. Capauto D, Wang Y, Wu F, Norton S, Mariani J, Inoue F, Crawford GE, Ahituv N, Abyzov A, Vaccarino FM. Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids. Sci Rep. 2024 Feb 16; 14 (1):3936
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2. Garrison MA, Jang Y, Bae T, Cherskov A, Emery SB, Fasching L, Jones A, Moldovan JB, Molitor C, Pochareddy S, Peters MA, Shin JH, Wang Y, Yang X, Akbarian S, Chess A, Gage FH, Gleeson JG, Kidd JM, McConnell M, Mills RE, Moran JV, Park PJ, Sestan N, Urban AE, Vaccarino FM, Walsh CA, Weinberger DR, Wheelan SJ, Abyzov A, BSMN Consortium. Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases. Sci Data. 2023 Nov 20; 10 (1):813
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3. Jourdon A, Wu F, Mariani J, Capauto D, Norton S, Tomasini L, Amiri A, Suvakov M, Schreiner JD, Jang Y, Panda A, Nguyen CK, Cummings EM, Han G, Powell K, Szekely A, McPartland JC, Pelphrey K, Chawarska K, Ventola P, Abyzov A, Vaccarino FM. Author Correction: Modeling idiopathic autism in forebrain organoids reveals an imbalance of excitatory cortical neuron subtypes during early neurogenesis. Nat Neurosci. 2023 Nov; 26 (11):2035
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4. Zhu X, Zhou B, Pattni R, Gleason K, Tan C, Kalinowski A, Sloan S, Fiston-Lavier AS, Mariani J, Petrov D, Barres BA, Duncan L, Abyzov A, Vogel H, Moran JV, Vaccarino FM, Tamminga CA, Levinson DF, Urban AE, Brain Somatic Mosaicism Network. Author Correction: Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia. Nat Neurosci. 2023 Oct; 26 (10):1833
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5. Jourdon A, Wu F, Mariani J, Capauto D, Norton S, Tomasini L, Amiri A, Suvakov M, Schreiner JD, Jang Y, Panda A, Nguyen CK, Cummings EM, Han G, Powell K, Szekely A, McPartland JC, Pelphrey K, Chawarska K, Ventola P, Abyzov A, Vaccarino FM. Modeling idiopathic autism in forebrain organoids reveals an imbalance of excitatory cortical neuron subtypes during early neurogenesis. Nat Neurosci. 2023 Sep; 26 (9):1505-1515 Epub 2023 Aug 10
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6. 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 Jun 9; 51 (10):e57
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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 LB, Sebat JL, Gleeson JG, NIMH Brain Somatic Mosaicism Network. Control-independent mosaic single nucleotide variant detection with DeepMosaic. Nat Biotechnol. 2023 Jun; 41 (6):870-877 Epub 2023 Jan 02
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8. Panda A, Suvakov M, Mariani J, Drucker KL, Park Y, Jang Y, Kollmeyer TM, Sarkar G, Bae T, Kim JJ, Yoon WH, Jenkins RB, Vaccarino FM, Abyzov A. Clonally Selected Lines After CRISPR-Cas Editing Are Not Isogenic. CRISPR J. 2023 Apr; 6 (2):176-182
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9. Chung C, Yang X, Bae T, Vong KI, Mittal S, Donkels C, Westley Phillips H, Li Z, Marsh APL, Breuss MW, Ball LL, Garcia CAB, George RD, Gu J, Xu M, Barrows C, James KN, Stanley V, Nidhiry AS, Khoury S, Howe G, Riley E, Xu X, Copeland B, Wang Y, Kim SH, Kang HC, Schulze-Bonhage A, Haas CA, Urbach H, Prinz M, Limbrick DD Jr, Gurnett CA, Smyth MD, Sattar S, Nespeca M, Gonda DD, Imai K, Takahashi Y, Chen HH, Tsai JW, Conti V, Guerrini R, Devinsky O, Silva WA Jr, Machado HR, Mathern GW, Abyzov A, Baldassari S, Baulac S, Gleeson JG, Focal Cortical Dysplasia Neurogenetics Consortium//Brain Somatic Mosaicism Network. Comprehensive multi-omic profiling of somatic mutations in malformations of cortical development. Nat Genet. 2023 Feb; 55 (2):209-220 Epub 2023 Jan 12
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10. Argouarch AR, Schultz N, Yang AC, Jang Y, Garcia K, Cosme CG, Corrales CI, Nana AL, Karydas AM, Spina S, Grinberg LT, Miller B, Wyss-Coray T, Abyzov A, Goodarzi H, Seeley WW, Kao AW. Postmortem Human Dura Mater Cells Exhibit Phenotypic, Transcriptomic and Genetic Abnormalities that Impact their Use for Disease Modeling. Stem Cell Rev Rep. 2022 Dec; 18 (8):3050-3065 Epub 2022 July 09
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11. Yanchus C, Drucker KL, Kollmeyer TM, Tsai R, Winick-Ng W, Liang M, Malik A, Pawling J, De Lorenzo SB, Ali A, Decker PA, Kosel ML, Panda A, Al-Zahrani KN, Jiang L, Browning JWL, Lowden C, Geuenich M, Hernandez JJ, Gosio JT, Ahmed M, Loganathan SK, Berman J, Trcka D, Michealraj KA, Fortin J, Carson B, Hollingsworth EW, Jacinto S, Mazrooei P, Zhou L, Elia A, Lupien M, He HH, Murphy DJ, Wang L, Abyzov A, Dennis JW, Maass PG, Campbell K, Wilson MD, Lachance DH, Wrensch M, Wiencke J, Mak T, Pennacchio LA, Dickel DE, Visel A, Wrana J, Taylor MD, Zadeh G, Dirks P, Eckel-Passow JE, Attisano L, Pombo A, Ida CM, Kvon EZ, Jenkins RB, Schramek D. A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation. Science. 2022 Oct 7; 378 (6615):68-78 Epub 2022 Oct 06
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12. Bae T, Fasching L, Wang Y, Shin JH, Suvakov M, Jang Y, Norton S, Dias C, Mariani J, Jourdon A, Wu F, Panda A, Pattni R, Chahine Y, Yeh R, Roberts RC, Huttner A, Kleinman JE, Hyde TM, Straub RE, Walsh CA, Urban AE, Leckman JF, Weinberger DR, Vaccarino FM, Abyzov A, Brain Somatic Mosaicism Network section sign. Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability. Science. 2022 Jul 29; 377 (6605):511-517 Epub 2022 July 28
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13. Sarangi V, Jang Y, Suvakov M, Bae T, Fasching L, Sekar S, Tomasini L, Mariani J, Vaccarino FM, Abyzov A. All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons. PLoS Comput Biol. 2022 Apr; 18 (4):e1009487 Epub 2022 Apr 20
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14. Suvakov M, Panda A, Diesh C, Holmes I, Abyzov A. CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing. Gigascience. 2021 Nov 18; 10 (11)
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15. Tran Q, Abyzov A. LongAGE: defining breakpoints of genomic structural variants through optimal and memory efficient alignments of long reads. Bioinformatics. 2021 May 17; 37 (7):1015-1017
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16. Wang Y, Bae T, Thorpe J, Sherman MA, Jones AG, Cho S, Daily K, Dou Y, Ganz J, Galor A, Lobon I, Pattni R, Rosenbluh C, Tomasi S, Tomasini L, Yang X, Zhou B, Akbarian S, Ball LL, Bizzotto S, Emery SB, Doan R, Fasching L, Jang Y, Juan D, Lizano E, Luquette LJ, Moldovan JB, Narurkar R, Oetjens MT, Rodin RE, Sekar S, Shin JH, Soriano E, Straub RE, Zhou W, Chess A, Gleeson JG, Marques-Bonet T, Park PJ, Peters MA, Pevsner J, Walsh CA, Weinberger DR, Vaccarino FM, Moran JV, Urban AE, Kidd JM, Mills RE, Abyzov A, Brain Somatic Mosaicism Network. Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biol. 2021 Mar 29; 22 (1):92
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17. Fasching L, Jang Y, Tomasi S, Schreiner J, Tomasini L, Brady MV, 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
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18. Bizzotto S, Dou Y, Ganz J, Doan RN, Kwon M, Bohrson CL, Kim SN, Bae T, Abyzov A, Park PJ, Walsh CA, NIMH Brain Somatic Mosaicism Network. Landmarks of human embryonic development inscribed in somatic mutations. Science. 2021 Mar 19; 371 (6535):1249-1253
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19. Zhu X, Zhou B, Pattni R, Gleason K, Tan C, Kalinowski A, Sloan S, Fiston-Lavier AS, Mariani J, Petrov D, Barres BA, Duncan L, Abyzov A, Vogel H, Moran JV, Vaccarino FM, Tamminga CA, Levinson DF, Urban AE, Brain Somatic Mosaicism Network. Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia. Nat Neurosci. 2021 Feb; 24 (2):186-196 Epub 2021 Jan 11
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20. Jourdon A, Scuderi S, Capauto D, Abyzov A, Vaccarino FM. PsychENCODE and beyond: transcriptomics and epigenomics of brain development and organoids. Neuropsychopharmacology. 2021 Jan; 46 (1):70-85 Epub 2020 July 13
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21. Jourdon A, Fasching L, Scuderi S, Abyzov A, Vaccarino FM. The role of somatic mosaicism in brain disease. Curr Opin Genet Dev. 2020 Dec; 65:84-90 Epub 2020 July 01
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22. 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 (12):1695-1704 Epub 2020 Oct 29
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23. Eckel-Passow JE, Drucker KL, Kollmeyer TM, Kosel ML, Decker PA, Molinaro AM, Rice T, Praska CE, Clark L, Caron A, Abyzov A, Batzler A, Song JS, Pekmezci M, Hansen HM, McCoy LS, Bracci PM, Wiemels J, Wiencke JK, Francis S, Burns TC, Giannini C, Lachance DH, Wrensch M, Jenkins RB. Adult diffuse glioma GWAS by molecular subtype identifies variants in D2HGDH and FAM20C. Neuro Oncol. 2020 Nov 26; 22 (11):1602-1613
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24. 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
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25. Abyzov A, Vaccarino FM. Cell Lineage Tracing and Cellular Diversity in Humans. Annu Rev Genomics Hum Genet. 2020 Aug 31; 21:101-116 Epub 2020 May 15
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26. Le-Rademacher JG, Lopez CL, Kanwar R, Major-Elechi B, Abyzov A, Banck MS, Therneau TM, Sloan JA, Loprinzi CL, Beutler AS. Neurological safety of oxaliplatin in patients with uncommon variants in Charcot-Marie-tooth disease genes. J Neurol Sci. 2020 Apr 15; 411:116687 Epub 2020 Jan 14
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27. Sangtani A, Wang C, Weaver A, Hoppman NL, Kerr SE, Abyzov A, Shridhar V, Staub J, Kocher JA, Voss JS, Podratz KC, Wentzensen N, Kisiel JB, Sherman ME, Bakkum-Gamez JN. Combining copy number, methylation markers, and mutations as a panel for endometrial cancer detection via intravaginal tampon collection. Gynecol Oncol. 2020 Feb; 156 (2):387-392 Epub 2019 Nov 28
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28. Zhou B, Ho SS, Greer SU, Spies N, Bell JM, Zhang X, Zhu X, Arthur JG, Byeon S, Pattni R, Saha I, Huang Y, Song G, Perrin D, Wong WH, Ji HP, Abyzov A, Urban AE. Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2. Nucleic Acids Res. 2019 May 7; 47 (8):3846-3861
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29. Roychowdhury T, Abyzov A. Chromatin organization modulates the origin of heritable structural variations in human genome. Nucleic Acids Res. 2019 Apr 8; 47 (6):2766-2777
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30. Zhou B, Ho SS, Greer SU, Zhu X, Bell JM, Arthur JG, Spies N, Zhang X, Byeon S, Pattni R, Ben-Efraim N, Haney MS, Haraksingh RR, Song G, Ji HP, Perrin D, Wong WH, Abyzov A, Urban AE. Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562. Genome Res. 2019 Mar; 29 (3):472-484 Epub 2019 Feb 08
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31. Jang JS, Li Y, Mitra AK, Bi L, Abyzov A, van Wijnen AJ, Baughn LB, Van Ness B, Rajkumar V, Kumar S, Jen J. Molecular signatures of multiple myeloma progression through single cell RNA-Seq. Blood Cancer J. 2019 Jan 3; 9 (1):2 Epub 2019 Jan 03
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32. Amiri A, Coppola G, Scuderi S, Wu F, Roychowdhury T, Liu F, Pochareddy S, Shin Y, Safi A, Song L, Zhu Y, Sousa AMM, Gerstein M, Crawford GE, Sestan N, Abyzov A, Vaccarino FM, PsychENCODE Consortium. Transcriptome and epigenome landscape of human cortical development modeled in organoids. Science. 2018 Dec 14; 362 (6420)
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33. Druliner BR, Wang P, Bae T, Baheti S, Slettedahl S, Mahoney D, Vasmatzis N, Xu H, Kim M, Bockol M, O'Brien D, Grill D, Warner N, Munoz-Gomez M, Kossick K, Johnson R, Mouchli M, Felmlee-Devine D, Washechek-Aletto J, Smyrk T, Oberg A, Wang J, Chia N, Abyzov A, Ahlquist D, Boardman LA. Molecular characterization of colorectal adenomas with and without malignancy reveals distinguishing genome, transcriptome and methylome alterations. Sci Rep. 2018 Feb 16; 8 (1):3161
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34. 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):550-555 Epub 2017 Dec 07
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35. 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. 2018 Jan 23; 9 (6):6780-6792 Epub 2017 Dec 26
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36. Zhou B, Haney MS, Zhu X, Pattni R, Abyzov A, Urban AE. Detection and Quantification of Mosaic Genomic DNA Variation in Primary Somatic Tissues Using ddPCR: Analysis of Mosaic Transposable-Element Insertions, Copy-Number Variants, and Single-Nucleotide Variants. Methods Mol Biol. 2018; 1768:173-190
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37. Le-Rademacher J, Kanwar R, Seisler D, Pachman DR, Qin R, Abyzov A, Ruddy KJ, Banck MS, Lavoie Smith EM, Dorsey SG, Aaronson NK, Sloan J, Loprinzi CL, Beutler AS. Patient-reported (EORTC QLQ-CIPN20) versus physician-reported (CTCAE) quantification of oxaliplatin- and paclitaxel/carboplatin-induced peripheral neuropathy in NCCTG/Alliance clinical trials. Support Care Cancer. 2017 Nov; 25 (11):3537-3544 Epub 2017 June 20
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38. Zhang Y, Li S, Abyzov A, Gerstein MB. Landscape and variation of novel retroduplications in 26 human populations. PLoS Comput Biol. 2017 Jun; 13 (6):e1005567 Epub 2017 June 29
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39. Ardhanareeswaran K, Mariani J, Coppola G, Abyzov A, Vaccarino FM. Human induced pluripotent stem cells for modelling neurodevelopmental disorders. Nat Rev Neurol. 2017 May; 13: (5)265-278.
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40. Haraksingh RR, Abyzov A, Urban AE. Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans. BMC Genomics. 2017 Apr 24; 18 (1):321
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41. Abyzov A, Tomasini L, Zhou B, Vasmatzis N, Coppola G, Amenduni M, Pattni R, Wilson M, Gerstein M, Weissman S, Urban AE, Vaccarino FM. One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin. Genome Res. 2017 Apr; 27 (4):512-523 Epub 2017 Feb 24
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42. McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, Cortes-Ciriano I, Erwin JA, Fasching L, Flasch DA, Freed D, Ganz J, Jaffe AE, Kwan KY, Kwon M, Lodato MA, Mills RE, Paquola ACM, Rodin RE, Rosenbluh C, Sestan N, Sherman MA, Shin JH, Song S, Straub RE, Thorpe J, Weinberger DR, Urban AE, Zhou B, Gage FH, Lehner T, Senthil G, Walsh CA, Chess A, Courchesne E, Gleeson JG, Kidd JM, Park PJ, Pevsner J, Vaccarino FM. Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network Science. 2017; 356: (6336)395.
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43. 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 Epub 2016 July 09
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44. Dhokarh D, Abyzov A. Elevated variant density around SV breakpoints in germline lineage lends support to error-prone replication hypothesis. Genome Res. 2016 Jul; 26 (7):874-81 Epub 2016 May 23
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45. Mitra AK, Mukherjee UK, Harding T, Jang JS, Stessman H, Li Y, Abyzov A, Jen J, Kumar S, Rajkumar V, Van Ness B. Single-cell analysis of targeted transcriptome predicts drug sensitivity of single cells within human myeloma tumors. Leukemia. 2016 May; 30 (5):1094-102 Epub 2015 Dec 29
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46. Boora GK, Kanwar R, Kulkarni AA, Abyzov A, Sloan J, Ruddy KJ, Banck MS, Loprinzi CL, Beutler AS. Testing of candidate single nucleotide variants associated with paclitaxel neuropathy in the trial NCCTG N08C1 (Alliance). Cancer Med. 2016 Apr; 5 (4):631-9 Epub 2016 Jan 14
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47. Chen J, Rozowsky J, Galeev TR, Harmanci A, Kitchen R, Bedford J, Abyzov A, Kong Y, Regan L, Gerstein M. A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals. Nat Commun. 2016; 7:11101.
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48. 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, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N, PsychENCODE Consortium. The PsychENCODE project. Nat Neurosci. 2015 Dec; 18 (12):1707-12
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49. 1000 Genomes Project Consortium , Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. A global reference for human genetic variation. Nature. 2015 Oct 1; 526(7571):68-74.
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50. Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stutz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO, 1000 Genomes Project Consortium. An integrated map of structural variation in 2,504 human genomes. Nature. 2015 Oct 1; 526 (7571):75-81
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51. Mohiyuddin M, Mu JC, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY. MetaSV: an accurate and integrative structural-variant caller for next generation sequencing. Bioinformatics. 2015 Aug 15; 31 (16):2741-4 Epub 2015 Apr 10
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52. Abyzov A, Li S, Kim DR, Mohiyuddin M, Stutz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB. Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms. Nat Commun. 2015 Jun 1; 6:7256 Epub 2015 June 01
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53. Mu JC, Mohiyuddin M, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY. VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications. Bioinformatics. 2015 May 1; 31: (9)1469-71.
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54. Mariani J, Coppola G, Zhang P, Abyzov A, Provini L, Tomasini L, Amenduni M, Szekely A, Palejev D, Wilson M, Gerstein M, Grigorenko EL, Chawarska K, Pelphrey KA, Howe JR, Vaccarino FM. FOXG1-dependent dysregulation of GABA/glutamate neuron differentiation in autism spectrum disorders. Cell. 2015; 162(2):375-90.
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55. Abyzov A, Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, Habegger L, Lee C, Gerstein M, 1000 Genomes Project Consortium. Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division. Genome Res. 2013 Dec; 23: (12)2042-52.
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56. Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gumus ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GR, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M, 1000 Genomes Project Consortium. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science. 2013 Oct 04; 342: (6154)1235587.
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57. Zhang Y, Haraksingh R, Grubert F, Abyzov A, Gerstein M, Weissman S, Urban AE. Child development and structural variation in the human genome. Child Dev. 2013 Jan-Feb; 84(1):34-48. Epub 2013 Jan 13.
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58. Abyzov A, Mariani J, Palejev D, Zhang Y, Haney MS, Tomasini L, Ferrandino AF, Rosenberg Belmaker LA, Szekely A, Wilson M, Kocabas A, Calixto NE, Grigorenko EL, Huttner A, Chawarska K, Weissman S, Urban AE, Gerstein M, Vaccarino FM. Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells. Nature. 2012 Dec 20; 492: (7429)438-42.
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59. 1000 Genomes Project Consortium , Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov 1; 491(7422):56-65.
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60. Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng J, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M. Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Sep 06; 489: (7414)91-100.
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61. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6; 489 (7414):57-74
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62. Iskow RC, Gokcumen O, Abyzov A, Malukiewicz J, Zhu Q, Sukumar AT, Pai AA, Mills RE, Habegger L, Cusanovich DA, Rubel MA, Perry GH, Gerstein M, Stone AC, Gilad Y, Lee C. Regulatory element copy number differences shape primate expression profiles. Proc Natl Acad Sci U S A. 2012 Jul 31; 109: (31)12656-61.
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63. Bhardwaj N, Abyzov A, Clarke D, Shou C, Gerstein MB. Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions. Protein Sci. 2011 Oct; 20: (10)1745-54.
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64. Rozowsky J, Abyzov A, Wang J, Alves P, Raha D, Harmanci A, Leng J, Bjornson R, Kong Y, Kitabayashi N, Bhardwaj N, Rubin M, Snyder M, Gerstein M. AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol. 2011 Aug 02; 7:522.
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65. Zhang ZD, Du J, Lam H, Abyzov A, Urban AE, Snyder M, Gerstein M. Identification of genomic indels and structural variations using split reads. BMC Genomics. 2011 Jul 25; 12:375.
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66. Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 2011 Jun; 21: (6)974-84.
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67. Vaccarino FM, Urban AE, Stevens HE, Szekely A, Abyzov A, Grigorenko EL, Gerstein M, Weissman S. Annual Research Review: The promise of stem cell research for neuropsychiatric disorders. J Child Psychol Psychiatry. 2011 Apr; 52: (4)504-16.
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68. Abyzov A, Gerstein M. AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision. Bioinformatics. 2011 Mar 01; 27: (5)595-603.
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69. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stutz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Zhang Y, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO, 1000 Genomes Project. Mapping copy number variation by population-scale genome sequencing. Nature. 2011 Feb 3; 470 (7332):59-65
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70. Haraksingh RR, Abyzov A, Gerstein M, Urban AE, Snyder M. Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms. PLoS One. 2011; 6: (11)e27859.
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71. 1000 Genomes Project Consortium , Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28; 467(7319):1061-73.
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72. Bhardwaj N, Carson MB, Abyzov A, Yan KK, Lu H, Gerstein MB. Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets. PLoS Comput Biol. 2010 May 27; 6: (5)e1000755.
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73. Abyzov A, Bjornson R, Felipe M, Gerstein M. RigidFinder: a fast and sensitive method to detect rigid blocks in large macromolecular complexes. Proteins. 2010 Feb 01; 78: (2)309-24.
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74. Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB. PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol. 2009 Feb 23; 10: (2)R23.
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75. Wang LY, Abyzov A, Korbel JO, Snyder M, Gerstein M. MSB: a mean-shift-based approach for the analysis of structural variation in the genome. Genome Res. 2009 Jan; 19: (1)106-17.
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76. Abyzov A, Uzun A, Strauss PR, Ilyin VA. An AP endonuclease 1-DNA polymerase beta complex: theoretical prediction of interacting surfaces. PLoS Comput Biol. 2008 Apr 25; 4: (4)e1000066.
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77. Godoy VG, Jarosz DF, Simon SM, Abyzov A, Ilyin V, Walker GC. UmuD and RecA directly modulate the mutagenic potential of the Y family DNA polymerase DinB. Mol Cell. 2007 Dec 28; 28: (6)1058-70.
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78. Abyzov A, Ilyin VA. A comprehensive analysis of non-sequential alignments between all protein structures. BMC Struct Biol. 2007 Nov 16; 7:78.
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79. Uzun A, Leslin CM, Abyzov A, Ilyin V. Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. Nucleic Acids Res. 2007 Jul; 35: (Web Server issue)W384-92.
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80. Leslin CM, Abyzov A, Ilyin VA. TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. Nucleic Acids Res. 2007 Jan; 35: (Database issue)D317-21.
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81. Abyzov A, Errami M, Leslin CM, Ilyin VA. Friend, an integrated analytical front-end application for bioinformatics. Bioinformatics. 2005 Sep 15; 21: (18)3677-8.
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82. Shehadi IA, Abyzov A, Uzun A, Wei Y, Murga LF, Ilyin V, Ondrechen MJ. Active site prediction for comparative model structures with thematics. J Bioinform Comput Biol. 2005 Feb; 3: (1)127-43.
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83. Leslin CM, Abyzov A, Ilyin VA. Structural exon database, SEDB, mapping exon boundaries on multiple protein structures. Bioinformatics. 2004 Jul 22; 20: (11)1801-3.
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84. Ilyin VA, Abyzov A, Leslin CM. Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point. Protein Sci. 2004 Jul; 13: (7)1865-74.
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85. Abyzov A, Belkov A, Lanyov A, Spiridonov A, Walter M, Hulsbergen W. Efficiency Profile Method To Study The Hit Efficiency Of Drift Chambers. Part Nucl Lett. 2002; 5:40-52.