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Alexej Abyzov, PhD

Research & Publications
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Research Summary

I'm analyzing variation between humans on the genomic level.

Coauthors

Selected Publications

Modeling idiopathic autism in forebrain organoids reveals an imbalance of excitatory cortical neuron subtypes during early neurogenesisJourdon A, Wu F, Mariani J, Capauto D, Norton S, Tomasini L, Amiri A, Suvakov M, Schreiner J, Jang Y, Panda A, Nguyen C, Cummings E, Han G, Powell K, Szekely A, McPartland J, Pelphrey K, Chawarska K, Ventola P, Abyzov A, Vaccarino F. Modeling idiopathic autism in forebrain organoids reveals an imbalance of excitatory cortical neuron subtypes during early neurogenesis. Nature Neuroscience 2023, 26: 1505-1515. PMID: 37563294, PMCID: PMC10573709, DOI: 10.1038/s41593-023-01399-0.
Efficient reconstruction of cell lineage trees for cell ancestry and cancerJang Y, Fasching L, Bae T, Tomasini L, Schreiner J, Szekely A, Fernandez T, Leckman J, Vaccarino F, Abyzov A. Efficient reconstruction of cell lineage trees for cell ancestry and cancer. Nucleic Acids Research 2023, 51: e57-e57. PMID: 37026484, PMCID: PMC10250207, DOI: 10.1093/nar/gkad254.
Clonally Selected Lines After CRISPR-Cas Editing Are Not IsogenicPanda A, Suvakov M, Mariani J, Drucker K, Park Y, Jang Y, Kollmeyer T, Sarkar G, Bae T, Kim J, Yoon W, Jenkins R, Vaccarino F, Abyzov A. Clonally Selected Lines After CRISPR-Cas Editing Are Not Isogenic. The CRISPR Journal 2023, 6: 176-182. PMID: 37071670, PMCID: PMC10123805, DOI: 10.1089/crispr.2022.0050.
Comprehensive multi-omic profiling of somatic mutations in malformations of cortical developmentChung C, Yang X, Bae T, Vong K, Mittal S, Donkels C, Westley Phillips H, Li Z, Marsh A, Breuss M, Ball L, Garcia C, George R, Gu J, Xu M, Barrows C, James K, Stanley V, Nidhiry A, Khoury S, Howe G, Riley E, Xu X, Copeland B, Wang Y, Kim S, Kang H, Schulze-Bonhage A, Haas C, Urbach H, Prinz M, Limbrick D, Gurnett C, Smyth M, Sattar S, Nespeca M, Gonda D, Imai K, Takahashi Y, Chen H, Tsai J, Conti V, Guerrini R, Devinsky O, Silva W, Machado H, Mathern G, Abyzov A, Baldassari S, Baulac S, Gleeson J. Comprehensive multi-omic profiling of somatic mutations in malformations of cortical development. Nature Genetics 2023, 55: 209-220. PMID: 36635388, PMCID: PMC9961399, DOI: 10.1038/s41588-022-01276-9.
Control-independent mosaic single nucleotide variant detection with DeepMosaicYang X, Xu X, Breuss M, Antaki D, Ball L, Chung C, Shen J, Li C, George R, Wang Y, Bae T, Cheng Y, Abyzov A, Wei L, Alexandrov L, Sebat J, Gleeson J. Control-independent mosaic single nucleotide variant detection with DeepMosaic. Nature Biotechnology 2023, 41: 870-877. PMID: 36593400, PMCID: PMC10314968, DOI: 10.1038/s41587-022-01559-w.
Somatic genomic mosaicism in the brain during aging: Scratching the surfaceBae T, Wang Y, Vaccarino F, Abyzov A. Somatic genomic mosaicism in the brain during aging: Scratching the surface. Clinical And Translational Medicine 2022, 12: e1138. PMID: 36495113, PMCID: PMC9736788, DOI: 10.1002/ctm2.1138.
A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formationYanchus C, Drucker K, Kollmeyer T, Tsai R, Winick-Ng W, Liang M, Malik A, Pawling J, De Lorenzo S, Ali A, Decker P, Kosel M, Panda A, Al-Zahrani K, Jiang L, Browning J, Lowden C, Geuenich M, Hernandez J, Gosio J, Ahmed M, Loganathan S, Berman J, Trcka D, Michealraj K, Fortin J, Carson B, Hollingsworth E, Jacinto S, Mazrooei P, Zhou L, Elia A, Lupien M, He H, Murphy D, Wang L, Abyzov A, Dennis J, Maass P, Campbell K, Wilson M, Lachance D, Wrensch M, Wiencke J, Mak T, Pennacchio L, Dickel D, Visel A, Wrana J, Taylor M, Zadeh G, Dirks P, Eckel-Passow J, Attisano L, Pombo A, Ida C, Kvon E, Jenkins R, Schramek D. A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation. Science 2022, 378: 68-78. PMID: 36201590, PMCID: PMC9926876, DOI: 10.1126/science.abj2890.
Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutabilityBae 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 A, Leckman J, Weinberger D, Vaccarino F, Abyzov A, Walsh C, Park P, Sestan N, Weinberger D, Moran J, Gage F, Vaccarino F, Gleeson J, Mathern G, Courchesne E, Roy S, Chess A, Akbarian S, Bizzotto S, Coulter M, Dias C, D’Gama A, Ganz J, Hill R, Huang A, Khoshkhoo S, Kim S, Lee A, Lodato M, Maury E, Miller M, Borges-Monroy R, Rodin R, Zhou Z, Bohrson C, Chu C, Cortes-Ciriano I, Dou Y, Galor A, Gulhan D, Kwon M, Luquette J, Sherman M, Viswanadham V, Jones A, Rosenbluh C, Cho S, Langmead B, Thorpe J, Erwin J, Jaffe A, McConnell M, Narurkar R, Paquola A, Shin J, Straub R, Abyzov A, Bae T, Jang Y, Wang Y, Molitor C, Peters M, Linker S, Reed P, Wang M, Urban A, Zhou B, Zhu X, Pattni R, Serres Amero A, Juan D, Lobon I, Marques-Bonet T, Solis Moruno M, Garcia Perez R, Povolotskaya I, Soriano E, Antaki D, Averbuj D, Ball L, Breuss M, Yang X, Chung C, Emery S, Flasch D, Kidd J, Kopera H, Kwan K, Mills R, Moldovan J, Sun C, Zhao X, Zhou W, Frisbie T, Cherskov A, Fasching L, Jourdon A, Pochareddy S, Scuderi S. Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability. Science 2022, 377: 511-517. PMID: 35901164, PMCID: PMC9420557, DOI: 10.1126/science.abm6222.
Postmortem Human Dura Mater Cells Exhibit Phenotypic, Transcriptomic and Genetic Abnormalities that Impact their Use for Disease ModelingArgouarch A, Schultz N, Yang A, Jang Y, Garcia K, Cosme C, Corrales C, Nana A, Karydas A, Spina S, Grinberg L, Miller B, Wyss-Coray T, Abyzov A, Goodarzi H, Seeley W, Kao A. Postmortem Human Dura Mater Cells Exhibit Phenotypic, Transcriptomic and Genetic Abnormalities that Impact their Use for Disease Modeling. Stem Cell Reviews And Reports 2022, 18: 3050-3065. PMID: 35809166, PMCID: PMC9622518, DOI: 10.1007/s12015-022-10416-x.
CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencingSuvakov 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, 10: giab074-. PMID: 34817058, PMCID: PMC8612020, DOI: 10.1093/gigascience/giab074.
Comprehensive identification of somatic nucleotide variants in human brain tissueWang 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, Marquès-Bonet T, Park PJ, Peters MA, Pevsner J, Walsh CA, Weinberger DR, Vaccarino F, Moran J, Urban A, Kidd J, Mills R, Abyzov A. Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biology 2021, 22: 92. PMID: 33781308, PMCID: PMC8006362, DOI: 10.1186/s13059-021-02285-3.
Landmarks of human embryonic development inscribed in somatic mutationsBizzotto S, Dou Y, Ganz J, Doan R, Kwon M, Bohrson C, Kim S, Bae T, Abyzov A, Network† N, Park P, Walsh C. Landmarks of human embryonic development inscribed in somatic mutations. Science 2021, 371: 1249-1253. PMID: 33737485, PMCID: PMC8170505, DOI: 10.1126/science.abe1544.
SCELLECTOR: ranking amplification bias in single cells using shallow sequencingSarangi V, Jourdon A, Bae T, Panda A, Vaccarino F, Abyzov A. SCELLECTOR: ranking amplification bias in single cells using shallow sequencing. BMC Bioinformatics 2020, 21: 521. PMID: 33183232, PMCID: PMC7663899, DOI: 10.1186/s12859-020-03858-y.
Complex mosaic structural variations in human fetal brainsSekar S, Tomasini L, Proukakis C, Bae T, Manlove L, Jang Y, Scuderi S, Zhou B, Kalyva M, Amiri A, Mariani J, Sedlazeck F, Urban AE, Vaccarino F, Abyzov A. Complex mosaic structural variations in human fetal brains. Genome Research 2020, 30: gr.262667.120. PMID: 33122304, PMCID: PMC7706730, DOI: 10.1101/gr.262667.120.
LongAGE: defining breakpoints of genomic structural variants through optimal and memory efficient alignments of long readsTran Q, Abyzov A. LongAGE: defining breakpoints of genomic structural variants through optimal and memory efficient alignments of long reads. Bioinformatics 2020, 37: btaa703. PMID: 32777815, PMCID: PMC8128450, DOI: 10.1093/bioinformatics/btaa703.
The role of somatic mosaicism in brain diseaseJourdon A, Fasching L, Scuderi S, Abyzov A, Vaccarino FM. The role of somatic mosaicism in brain disease. Current Opinion In Genetics & Development 2020, 65: 84-90. PMID: 32622340, PMCID: PMC7749073, DOI: 10.1016/j.gde.2020.05.002.
Cell Lineage Tracing and Cellular Diversity in HumansAbyzov A, Vaccarino FM. Cell Lineage Tracing and Cellular Diversity in Humans. Annual Review Of Genomics And Human Genetics 2020, 21: 101-116. PMID: 32413272, DOI: 10.1146/annurev-genom-083118-015241.
Adult diffuse glioma GWAS by molecular subtype identifies variants in D2HGDH and FAM20CEckel-Passow J, Drucker K, Kollmeyer T, Kosel M, Decker P, Molinaro A, Rice T, Praska C, Clark L, Caron A, Abyzov A, Batzler A, Song J, Pekmezci M, Hansen H, McCoy L, Bracci P, Wiemels J, Wiencke J, Francis S, Burns T, Giannini C, Lachance D, Wrensch M, Jenkins R. Adult diffuse glioma GWAS by molecular subtype identifies variants in D2HGDH and FAM20C. Neuro-Oncology 2020, 22: 1602-1613. PMID: 32386320, PMCID: PMC7690366, DOI: 10.1093/neuonc/noaa117.
Neurological safety of oxaliplatin in patients with uncommon variants in Charcot-Marie-tooth disease genesLe-Rademacher J, Lopez C, Kanwar R, Major-Elechi B, Abyzov A, Banck M, Therneau T, Sloan J, Loprinzi C, Beutler A. Neurological safety of oxaliplatin in patients with uncommon variants in Charcot-Marie-tooth disease genes. Journal Of The Neurological Sciences 2020, 411: 116687. PMID: 32018185, PMCID: PMC7096263, DOI: 10.1016/j.jns.2020.116687.
Analysis of Cell and Nucleus Genome by Next-Generation SequencingOh J, Abyzov A. Analysis of Cell and Nucleus Genome by Next-Generation Sequencing. 2020, 35-65. DOI: 10.1007/978-3-030-62532-0_3.
Chapter 5 Induced pluripotent stem cells as models of human neurodevelopmental disordersJourdon A, Mariani J, Scuderi S, Amiri A, Wu F, Yuen E, Abyzov A, Vaccarino F. Chapter 5 Induced pluripotent stem cells as models of human neurodevelopmental disorders. 2020, 99-127. DOI: 10.1016/b978-0-12-814409-1.00005-7.
Combining copy number, methylation markers, and mutations as a panel for endometrial cancer detection via intravaginal tampon collectionSangtani A, Wang C, Weaver A, Hoppman N, Kerr S, Abyzov A, Shridhar V, Staub J, Kocher J, Voss J, Podratz K, Wentzensen N, Kisiel J, Sherman M, Bakkum-Gamez J. Combining copy number, methylation markers, and mutations as a panel for endometrial cancer detection via intravaginal tampon collection. Gynecologic Oncology 2019, 156: 387-392. PMID: 31787246, PMCID: PMC7018609, DOI: 10.1016/j.ygyno.2019.11.028.
Approaches and Methods for Variant Analysis in the Genome of a Single CellAbyzov A, Vaccarino F, Urban A, Sarangi V. Approaches and Methods for Variant Analysis in the Genome of a Single Cell. 2019, 10: 203-228. DOI: 10.1007/978-3-030-24970-0_14.
Combining methylation markers, genomic instability, and next generation sequencing as a panel for endometrial cancer detection via intravaginal tampon collectionSangtani A, Bakkum-Gamez J, Kipp B, Kerr S, Abyzov A, Voss J, Wang C. Combining methylation markers, genomic instability, and next generation sequencing as a panel for endometrial cancer detection via intravaginal tampon collection. Gynecologic Oncology 2019, 154: e10. DOI: 10.1016/j.ygyno.2019.03.180.
Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2Zhou B, Ho S, Greer S, Spies N, Bell J, Zhang X, Zhu X, Arthur J, Byeon S, Pattni R, Saha I, Huang Y, Song G, Perrin D, Wong W, Ji H, Abyzov A, Urban A. Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2. Nucleic Acids Research 2019, 47: gkz169-. PMID: 30864654, PMCID: PMC6486628, DOI: 10.1093/nar/gkz169.
Chromatin organization modulates the origin of heritable structural variations in human genomeRoychowdhury T, Abyzov A. Chromatin organization modulates the origin of heritable structural variations in human genome. Nucleic Acids Research 2019, 47: gkz103-. PMID: 30773596, PMCID: PMC6451188, DOI: 10.1093/nar/gkz103.
Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562Zhou B, Ho S, Greer S, Zhu X, Bell J, Arthur J, Spies N, Zhang X, Byeon S, Pattni R, Ben-Efraim N, Haney M, Haraksingh R, Song G, Ji H, Perrin D, Wong W, Abyzov A, Urban A. Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562. Genome Research 2019, 29: 472-484. PMID: 30737237, PMCID: PMC6396411, DOI: 10.1101/gr.234948.118.
Molecular signatures of multiple myeloma progression through single cell RNA-SeqJang J, Li Y, Mitra A, Bi L, Abyzov A, van Wijnen A, Baughn L, Van Ness B, Rajkumar V, Kumar S, Jen J. Molecular signatures of multiple myeloma progression through single cell RNA-Seq. Blood Cancer Journal 2019, 9: 2. PMID: 30607001, PMCID: PMC6318319, DOI: 10.1038/s41408-018-0160-x.
Transcriptome and epigenome landscape of human cortical development modeled in organoidsAmiri 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 G, Sestan N, Abyzov A, Vaccarino F, Akbarian S, An J, Armoskus C, Ashley-Koch A, Beach T, Belmont J, Bendl J, Borrman T, Brown L, Brown M, Brown M, Brunetti T, Bryois J, Burke E, Camarena A, Carlyle B, Chae Y, Charney A, Chen C, Cheng L, Cherskov A, Choi J, Clarke D, Collado-Torres L, Dai R, De La Torre Ubieta L, DelValle D, Devillers O, Dracheva S, Emani P, Evgrafov O, Farnham P, Fitzgerald D, Flatow E, Francoeur N, Fullard J, Gandal M, Gao T, Garrett M, Geschwind D, Giase G, Girdhar K, Giusti-Rodriguez P, Goes F, Goodman T, Grennan K, Gu M, Gürsoy G, Hadjimichael E, Hahn C, Haroutunian V, Hauberg M, Hoffman G, Huey J, Hyde T, Ivanov N, Jacobov R, Jaffe A, Jiang Y, Jiang Y, Johnson G, Kassim B, Kefi A, Kim Y, Kitchen R, Kleiman J, Knowles J, Kozlenkov A, Li M, Li Z, Lipska B, Liu C, Liu S, Mangravite L, Mariani J, Mattei E, Miller D, Moore J, Nairn A, Navarro F, Park R, Peters M, Pinto D, Pochareddy S, Polioudakis D, Pratt H, Price A, Purcaro M, Ray M, Reddy T, Rhie S, Roussos P, Sanders S, Santpere G, Schreiner S, Sheppard B, Shi X, Shieh A, Shin J, Skarica M, Song L, Sousa A, Spitsyna V, State M, Sullivan P, Swarup V, Szatkiewicz J, Szekely A, Tao R, van Bakel H, Wang Y, Wang D, Warrell J, Webster M, Weissman S, Weng Z, Werling D, White K, Willsey J, Wiseman J, Witt H, Won H, Wray G, Xia Y, Xu M, Yang Y, Yang M, Zandi P, Zhang J, Zharovsky E. Transcriptome and epigenome landscape of human cortical development modeled in organoids. Science 2018, 362 PMID: 30545853, PMCID: PMC6426303, DOI: 10.1126/science.aat6720.
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 VariantsZhou 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. 2018, 1768: 173-190. PMID: 29717444, DOI: 10.1007/978-1-4939-7778-9_11.
Molecular characterization of colorectal adenomas with and without malignancy reveals distinguishing genome, transcriptome and methylome alterationsDruliner B, 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 L. Molecular characterization of colorectal adenomas with and without malignancy reveals distinguishing genome, transcriptome and methylome alterations. Scientific Reports 2018, 8: 3161. PMID: 29453410, PMCID: PMC5816667, DOI: 10.1038/s41598-018-21525-4.
Inferring modes of evolution from colorectal cancer with residual polyp of originKim M, Druliner B, Vasmatzis N, Bae T, Chia N, Abyzov A, Boardman L. Inferring modes of evolution from colorectal cancer with residual polyp of origin. Oncotarget 2017, 9: 6780-6792. PMID: 29467928, PMCID: PMC5805514, DOI: 10.18632/oncotarget.23687.
Principles and Approaches for Discovery and Validation of Somatic Mosaicism in the Human BrainAbyzov A, Urban A, Vaccarino F. Principles and Approaches for Discovery and Validation of Somatic Mosaicism in the Human Brain. 2017, 131: 3-24. DOI: 10.1007/978-1-4939-7280-7_1.
Landscape and variation of novel retroduplications in 26 human populationsZhang Y, Li S, Abyzov A, Gerstein MB. Landscape and variation of novel retroduplications in 26 human populations. PLOS Computational Biology 2017, 13: e1005567. PMID: 28662076, PMCID: PMC5510864, DOI: 10.1371/journal.pcbi.1005567.
Patient-reported (EORTC QLQ-CIPN20) versus physician-reported (CTCAE) quantification of oxaliplatin- and paclitaxel/carboplatin-induced peripheral neuropathy in NCCTG/Alliance clinical trialsLe-Rademacher J, Kanwar R, Seisler D, Pachman D, Qin R, Abyzov A, Ruddy K, Banck M, Lavoie Smith E, Dorsey S, Aaronson N, Sloan J, Loprinzi C, Beutler A. Patient-reported (EORTC QLQ-CIPN20) versus physician-reported (CTCAE) quantification of oxaliplatin- and paclitaxel/carboplatin-induced peripheral neuropathy in NCCTG/Alliance clinical trials. Supportive Care In Cancer 2017, 25: 3537-3544. PMID: 28634656, PMCID: PMC5693734, DOI: 10.1007/s00520-017-3780-y.
Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism NetworkMcConnell 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, Barton A, Bekiranov S, Bohrson C, Burbulis I, Chronister W, Coppola G, Daily K, D’Gama A, Emery S, Frisbie T, Gao T, Gulyás-Kovács A, Haakenson M, Keil J, Kopera H, Lam M, Lee E, Marques-Bonet T, Mathern G, Moldovan J, Oetjens M, Omberg L, Peters M, Pochareddy S, Pramparo T, Ratan A, Sanavia T, Shi L, Skarica M, Wang J, Wang M, Wang Y, Wierman M, Wolpert M, Woodworth M, Zhao X, Zhou W. Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network. Science 2017, 356 PMID: 28450582, PMCID: PMC5558435, DOI: 10.1126/science.aal1641.
Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humansHaraksingh 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, 18: 321. PMID: 28438122, PMCID: PMC5402652, DOI: 10.1186/s12864-017-3658-x.
Human induced pluripotent stem cells for modelling neurodevelopmental disordersArdhanareeswaran K, Mariani J, Coppola G, Abyzov A, Vaccarino FM. Human induced pluripotent stem cells for modelling neurodevelopmental disorders. Nature Reviews Neurology 2017, 13: 265-278. PMID: 28418023, PMCID: PMC5782822, DOI: 10.1038/nrneurol.2017.45.
One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative originAbyzov 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 Research 2017, 27: 512-523. PMID: 28235832, PMCID: PMC5378170, DOI: 10.1101/gr.215517.116.
Colorectal Cancer with Residual Polyp of Origin: A Model of Malignant TransformationDruliner B, 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 L. Colorectal Cancer with Residual Polyp of Origin: A Model of Malignant Transformation. Translational Oncology 2016, 9: 280-286. PMID: 27567950, PMCID: PMC4941582, DOI: 10.1016/j.tranon.2016.06.002.
Elevated variant density around SV breakpoints in germline lineage lends support to error-prone replication hypothesisDhokarh D, Abyzov A. Elevated variant density around SV breakpoints in germline lineage lends support to error-prone replication hypothesis. Genome Research 2016, 26: 874-881. PMID: 27216746, PMCID: PMC4937565, DOI: 10.1101/gr.205484.116.
A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individualsChen 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. Nature Communications 2016, 7: 11101. PMID: 27089393, PMCID: PMC4837449, DOI: 10.1038/ncomms11101.
Testing of candidate single nucleotide variants associated with paclitaxel neuropathy in the trial NCCTG N08C1 (Alliance)Boora G, Kanwar R, Kulkarni A, Abyzov A, Sloan J, Ruddy K, Banck M, Loprinzi C, Beutler A. Testing of candidate single nucleotide variants associated with paclitaxel neuropathy in the trial NCCTG N08C1 (Alliance). Cancer Medicine 2016, 5: 631-639. PMID: 26763541, PMCID: PMC4831281, DOI: 10.1002/cam4.625.
Single-cell analysis of targeted transcriptome predicts drug sensitivity of single cells within human myeloma tumorsMitra A, Mukherjee U, Harding T, Jang J, 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 2015, 30: 1094-1102. PMID: 26710886, DOI: 10.1038/leu.2015.361.
Understanding genome structural variationsAbyzov A, Li S, Gerstein MB. Understanding genome structural variations. Oncotarget 2015, 7: 7370-7371. PMID: 26657727, PMCID: PMC4884923, DOI: 10.18632/oncotarget.6485.
The PsychENCODE projectAkbarian 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. The PsychENCODE project. Nature Neuroscience 2015, 18: 1707-1712. PMID: 26605881, PMCID: PMC4675669, DOI: 10.1038/nn.4156.
An integrated map of structural variation in 2,504 human genomesSudmant 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, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Jasmine Mu X, 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 R, Gerstein M, Bashir A, Stegle O, Devine S, Lee C, Eichler E, Korbel J. An integrated map of structural variation in 2,504 human genomes. Nature 2015, 526: 75-81. PMID: 26432246, PMCID: PMC4617611, DOI: 10.1038/nature15394.
FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum DisordersMariani 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: 375-390. PMID: 26186191, PMCID: PMC4519016, DOI: 10.1016/j.cell.2015.06.034.
Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanismsAbyzov A, Li S, Kim DR, Mohiyuddin M, Stütz 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. Nature Communications 2015, 6: 7256. PMID: 26028266, PMCID: PMC4451611, DOI: 10.1038/ncomms8256.
MetaSV: an accurate and integrative structural-variant caller for next generation sequencingMohiyuddin 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, 31: 2741-2744. PMID: 25861968, PMCID: PMC4528635, DOI: 10.1093/bioinformatics/btv204.
VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applicationsMu 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 2014, 31: 1469-1471. PMID: 25524895, PMCID: PMC4410653, DOI: 10.1093/bioinformatics/btu828.
Integrative Annotation of Variants from 1092 Humans: Application to Cancer GenomicsKhurana 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, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Consortium 1, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics. Science 2013, 342: 1235587. PMID: 24092746, PMCID: PMC3947637, DOI: 10.1126/science.1235587.
Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell divisionAbyzov A, Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, Habegger L, Consortium T, Lee C, Gerstein M. Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division. Genome Research 2013, 23: 2042-2052. PMID: 24026178, PMCID: PMC3847774, DOI: 10.1101/gr.154625.113.
Child Development and Structural Variation in the Human GenomeZhang Y, Haraksingh R, Grubert F, Abyzov A, Gerstein M, Weissman S, Urban AE. Child Development and Structural Variation in the Human Genome. Child Development 2013, 84: 34-48. PMID: 23311762, DOI: 10.1111/cdev.12051.
Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cellsAbyzov 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, 492: 438-442. PMID: 23160490, PMCID: PMC3532053, DOI: 10.1038/nature11629.
Architecture of the human regulatory network derived from ENCODE dataGerstein 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, 489: 91-100. PMID: 22955619, PMCID: PMC4154057, DOI: 10.1038/nature11245.
Regulatory element copy number differences shape primate expression profilesIskow 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. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 12656-12661. PMID: 22797897, PMCID: PMC3411951, DOI: 10.1073/pnas.1205199109.
Genome-Wide Mapping of Copy Number Variation in Humans: Comparative Analysis of High Resolution Array PlatformsHaraksingh 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: e27859. PMID: 22140474, PMCID: PMC3227574, DOI: 10.1371/journal.pone.0027859.
Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactionsBhardwaj 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 Science 2011, 20: 1745-1754. PMID: 21826754, PMCID: PMC3218368, DOI: 10.1002/pro.710.
CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencingAbyzov 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 Research 2011, 21: 974-984. PMID: 21324876, PMCID: PMC3106330, DOI: 10.1101/gr.114876.110.
Mapping copy number variation by population-scale genome sequencingMills 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, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, 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. Mapping copy number variation by population-scale genome sequencing. Nature 2011, 470: 59-65. PMID: 21293372, PMCID: PMC3077050, DOI: 10.1038/nature09708.
AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excisionAbyzov A, Gerstein M. AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision. Bioinformatics 2011, 27: 595-603. PMID: 21233167, PMCID: PMC3042181, DOI: 10.1093/bioinformatics/btq713.
AlleleSeq: analysis of allele‐specific expression and binding in a network frameworkRozowsky 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. Molecular Systems Biology 2011, 7: 522-522. PMID: 21811232, PMCID: PMC3208341, DOI: 10.1038/msb.2011.54.
Analysis of Combinatorial Regulation: Scaling of Partnerships between Regulators with the Number of Governed TargetsBhardwaj 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 Computational Biology 2010, 6: e1000755. PMID: 20523742, PMCID: PMC2877725, DOI: 10.1371/journal.pcbi.1000755.
RigidFinder: A fast and sensitive method to detect rigid blocks in large macromolecular complexesAbyzov A, Bjornson R, Felipe M, Gerstein M. RigidFinder: A fast and sensitive method to detect rigid blocks in large macromolecular complexes. Proteins Structure Function And Bioinformatics 2009, 78: 309-324. PMID: 19705487, DOI: 10.1002/prot.22544.
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing dataKorbel 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 Biology 2009, 10: r23. PMID: 19236709, PMCID: PMC2688268, DOI: 10.1186/gb-2009-10-2-r23.
MSB: A mean-shift-based approach for the analysis of structural variation in the genomeWang 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 Research 2008, 19: 106-117. PMID: 19037015, PMCID: PMC2612956, DOI: 10.1101/gr.080069.108.
An AP Endonuclease 1–DNA Polymerase β Complex: Theoretical Prediction of Interacting SurfacesAbyzov A, Uzun A, Strauss P, Ilyin V. An AP Endonuclease 1–DNA Polymerase β Complex: Theoretical Prediction of Interacting Surfaces. PLOS Computational Biology 2008, 4: e1000066. PMID: 18437203, PMCID: PMC2289873, DOI: 10.1371/journal.pcbi.1000066.
UmuD and RecA Directly Modulate the Mutagenic Potential of the Y Family DNA Polymerase DinBGodoy V, Jarosz D, Simon S, Abyzov A, Ilyin V, Walker G. UmuD and RecA Directly Modulate the Mutagenic Potential of the Y Family DNA Polymerase DinB. Molecular Cell 2007, 28: 1058-1070. PMID: 18158902, PMCID: PMC2265384, DOI: 10.1016/j.molcel.2007.10.025.
A comprehensive analysis of non-sequential alignments between all protein structuresAbyzov A, Ilyin V. A comprehensive analysis of non-sequential alignments between all protein structures. BMC Molecular And Cell Biology 2007, 7: 78. PMID: 18005453, PMCID: PMC2213659, DOI: 10.1186/1472-6807-7-78.
Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathwaysUzun A, Leslin C, 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 Research 2007, 35: w384-w392. PMID: 17537826, PMCID: PMC1933130, DOI: 10.1093/nar/gkm232.
TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT methodLeslin C, Abyzov A, Ilyin V. TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. Nucleic Acids Research 2006, 35: d317-d321. PMID: 17065464, PMCID: PMC1635338, DOI: 10.1093/nar/gkl809.
Friend, an integrated analytical front-end application for bioinformaticsAbyzov A, Errami M, Leslin C, Ilyin V. Friend, an integrated analytical front-end application for bioinformatics. Bioinformatics 2005, 21: 3677-3678. PMID: 16076889, DOI: 10.1093/bioinformatics/bti602.
ACTIVE SITE PREDICTION FOR COMPARATIVE MODEL STRUCTURES WITH THEMATICSSHEHADI I, ABYZOV A, UZUN A, WEI Y, MURGA L, ILYIN V, ONDRECHEN M. ACTIVE SITE PREDICTION FOR COMPARATIVE MODEL STRUCTURES WITH THEMATICS. Journal Of Bioinformatics And Computational Biology 2005, 3: 127-143. PMID: 15751116, DOI: 10.1142/s0219720005000916.
Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax pointIlyin V, Abyzov A, Leslin C. Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point. Protein Science 2004, 13: 1865-1874. PMID: 15215530, PMCID: PMC2279929, DOI: 10.1110/ps.04672604.

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