• 27488 Citations
  • 30 Scopus h-Index
20042019
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Research Output 2004 2019

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Article
2019
1 Citation (Scopus)

Chromatin organization modulates the origin of heritable structural variations in human genome

Roychowdhury, T. & Abyzov, A., Apr 8 2019, In : Nucleic acids research. 47, 6, p. 2766-2777 12 p.

Research output: Contribution to journalArticle

Open Access
Human Genome
Chromatin
Homologous Recombination
Genomic Structural Variation
Alu Elements

Combining copy number, methylation markers, and mutations as a panel for endometrial cancer detection via intravaginal tampon collection

Sangtani, A., Wang, C., Weaver, A., Hoppman, N. L., Kerr, S. E., Abyzov, A., Shridhar, V., Staub, J., Kocher, J. P. A., Voss, J. S., Podratz, K. C., Wentzensen, N., Kisiel, J. B., Sherman, M. E. & Bakkum-Gamez, J. N., Jan 1 2019, (Accepted/In press) In : Gynecologic oncology.

Research output: Contribution to journalArticle

Endometrial Neoplasms
Methylation
Mutation
Hysterectomy
Sensitivity and Specificity
6 Citations (Scopus)

Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562

Zhou, B., Ho, S. S., Greer, S. U., Zhu, X., Bell, J. M., Arthur, J. G., Spies, N., Zhang, X., Byeon, S., Pattni, R., Ben-Efraim, N., Haney, M. S., Haraksingh, R. R., Song, G., Ji, H. P., Perrin, D., Wong, W. H., Abyzov, A. & Urban, A. E., Mar 1 2019, In : Genome Research. 29, 3, p. 472-484 13 p.

Research output: Contribution to journalArticle

Open Access
Genome
Cell Line
Aneuploidy
Clustered Regularly Interspaced Short Palindromic Repeats
Alleles
3 Citations (Scopus)

Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2

Zhou, B., Ho, S. S., Greer, S. U., Spies, N., Bell, J. M., Zhang, X., Zhu, X., Arthur, J. G., Byeon, S., Pattni, R., Saha, I., Huang, Y., Song, G., Perrin, D., Wong, W. H., Ji, H. P., Abyzov, A. & Urban, A. E., May 7 2019, In : Nucleic acids research. 47, 8, p. 3846-3861 16 p.

Research output: Contribution to journalArticle

Open Access
Haplotypes
Genome
Cell Line
Neoplasms
Aneuploidy
7 Citations (Scopus)

Molecular signatures of multiple myeloma progression through single cell RNA-Seq

Jang, J. S., Li, Y., Mitra, A. K., Bi, L., Abyzov, A., van Wijnen, A. J., Baughn, L., Van Ness, B., Rajkumar, S. V., Kumar, S. K. & Jen, J., Jan 1 2019, In : Blood Cancer Journal. 9, 1, 2.

Research output: Contribution to journalArticle

Multiple Myeloma
RNA
Genes
Oxidative Phosphorylation
Plasma Cells
2018

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

Kim, M., Druliner, B. R., Vasmatzis, N., Bae, T., Chia, N. D., Abyzov, A. & Boardman, L. A., Jan 1 2018, In : Oncotarget. 9, 6, p. 6780-6792 13 p.

Research output: Contribution to journalArticle

Polyps
Colorectal Neoplasms
Neoplasms
Nucleotides
Genetic Drift
54 Citations (Scopus)

Integrative functional genomic analysis of human brain development and neuropsychiatric risks

BrainSpan Consortium, PsychENCODE Consortium & PsychENCODE Developmental Subgroup, Dec 14 2018, In : Science. 362, 6420, 1264.

Research output: Contribution to journalArticle

Human Development
Epigenomics
Brain
Gene Regulatory Networks
Genes
5 Citations (Scopus)

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

Druliner, B. R., 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. C. & 6 others, Oberg, A. L., Wang, J., Chia, N. D., Abyzov, A., Ahlquist, D. & Boardman, L. A., Dec 1 2018, In : Scientific Reports. 8, 1, 3161.

Research output: Contribution to journalArticle

Polyps
Transcriptome
Adenoma
Genome
Neoplasms
22 Citations (Scopus)

Transcriptome and epigenome landscape of human cortical development modeled in organoids

Amiri, A., Coppola, G., Scuderi, S., Wu, F., Roychowdhury, T., Liu, F., Pochareddy, S., Shin, Y., Safi, A., Song, L., Zhu, Y., Sousa, A. M. M., Gerstein, M., Crawford, G. E., Sestan, N., Abyzov, A. & Vaccarino, F. M., Dec 14 2018, In : Science. 362, 6420, 1268.

Research output: Contribution to journalArticle

Organoids
Human Development
Transcriptome
Gene Regulatory Networks
Genes
2017
19 Citations (Scopus)

Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans

Haraksingh, R. R., Abyzov, A. & Urban, A. E., Apr 24 2017, In : BMC Genomics. 18, 1, 321.

Research output: Contribution to journalArticle

Genome
Single Nucleotide Polymorphism
Software
Human Genome
Genomics
51 Citations (Scopus)

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, B. J., Venturini, E., Riley-Gillis, B., Sestan, N., Urban, A. E., Abyzov, A. & Vaccarino, F. M., Dec 7 2017, (Accepted/In press) In : Science. p. 1-10 10 p.

Research output: Contribution to journalArticle

Neurogenesis
Nucleotides
Mutation Rate
Mutagenesis
Genome
82 Citations (Scopus)

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

Brain Somatic Mosaicism Network, Apr 28 2017, In : Science. 356, 6336, 395.

Research output: Contribution to journalArticle

Mosaicism
Brain Diseases
Genome
Brain
Neurons
6 Citations (Scopus)

Landscape and variation of novel retroduplications in 26 human populations

Zhang, Y., Li, S., Abyzov, A. & Gerstein, M. B., Jun 1 2017, In : PLoS Computational Biology. 13, 6, e1005567.

Research output: Contribution to journalArticle

human population
Insertion
Genome
genome
Superpopulation
26 Citations (Scopus)

One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin

Abyzov, A., Tomasini, L., Zhou, B., Vasmatzis, N., Coppola, G., Amenduni, M., Pattni, R., Wilson, M., Gerstein, M., Weissman, S., Urban, A. E. & Vaccarino, F. M., Apr 1 2017, In : Genome Research. 27, 4, p. 512-523 12 p.

Research output: Contribution to journalArticle

Fibroblasts
Skin
Mosaicism
Gene Frequency
Induced Pluripotent Stem Cells
15 Citations (Scopus)

Patient-reported (EORTC QLQ-CIPN20) versus physician-reported (CTCAE) quantification of oxaliplatin- and paclitaxel/carboplatin-induced peripheral neuropathy in NCCTG/Alliance clinical trials

Le-Rademacher, J., Kanwar, R., Seisler, D., Pachman, D. R., Qin, R., Abyzov, A., Ruddy, K. J., Banck, M. S., Lavoie Smith, E. M., Dorsey, S. G., Aaronson, N. K., Sloan, J. A., Loprinzi, C. L. & Beutler, A. S., Jun 20 2017, (Accepted/In press) In : Supportive Care in Cancer. p. 1-8 8 p.

Research output: Contribution to journalArticle

oxaliplatin
Carboplatin
Peripheral Nervous System Diseases
Paclitaxel
Terminology
2016
17 Citations (Scopus)

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals

Chen, J., Rozowsky, J., Galeev, T. R., Harmanci, A., Kitchen, R., Bedford, J., Abyzov, A., Kong, Y., Regan, L. & Gerstein, M., Apr 18 2016, In : Nature Communications. 7, 11101.

Research output: Contribution to journalArticle

genome
Allelic Imbalance
Genes
Alleles
nucleotides
6 Citations (Scopus)

Colorectal cancer with residual polyp of origin: A model of malignant transformation

Druliner, B. R., Rashtak, S., Ruan, X., Bae, T., Vasmatzis, N., O’Brien, D., Johnson, R., Felmlee-Devine, D., Washechek-Aletto, J., Basu, N., Liu, H. D., Smyrk, T. C., Abyzov, A. & Boardman, L. A., Aug 1 2016, In : Translational Oncology. 9, 4, p. 280-286 7 p.

Research output: Contribution to journalArticle

Polyps
Colorectal Neoplasms
Genome
Adenomatous Polyps
Atlases
2 Citations (Scopus)

Elevated variant density around SV breakpoints in germline lineage lends support to error-prone replication hypothesis

Dhokarh, D. & Abyzov, A., Jul 1 2016, In : Genome Research. 26, 7, p. 874-881 8 p.

Research output: Contribution to journalArticle

Single Nucleotide Polymorphism
Gene Frequency
Genome
Mutation
Mutation Rate
27 Citations (Scopus)

Single-cell analysis of targeted transcriptome predicts drug sensitivity of single cells within human myeloma tumors

Mitra, A. K., Mukherjee, U. K., Harding, T., Jang, J. S., Stessman, H., Li, Y., Abyzov, A., Jen, J., Kumar, S. K., Rajkumar, S. V. & Van Ness, B., May 1 2016, In : Leukemia. 30, 5, p. 1094-1102 9 p.

Research output: Contribution to journalArticle

Single-Cell Analysis
Transcriptome
Pharmaceutical Preparations
Neoplasms
Multiple Myeloma
19 Citations (Scopus)

Testing of candidate single nucleotide variants associated with paclitaxel neuropathy in the trial NCCTG N08C1 (Alliance)

Boora, G. K., Kanwar, R., Kulkarni, A. A., Abyzov, A., Sloan, J. A., Ruddy, K. J., Banck, M. S., Loprinzi, C. L. & Beutler, A. S., Apr 1 2016, In : Cancer Medicine. 5, 4, p. 631-639 9 p.

Research output: Contribution to journalArticle

Peripheral Nervous System Diseases
Paclitaxel
Nucleotides
Pharmacogenetics
Odds Ratio
2015
38 Citations (Scopus)

Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms

Abyzov, A., Li, S., Kim, D. R., Mohiyuddin, M., Stütz, A. M., Parrish, N. F., Mu, X. J., Clark, W., Chen, K., Hurles, M., Korbel, J. O., Lam, H. Y. K., Lee, C. & Gerstein, M. B., Jun 1 2015, In : Nature Communications. 6, 7256.

Research output: Contribution to journalArticle

deletion
Homologous Recombination
mutations
Genomic Structural Variation
Histone Code
608 Citations (Scopus)

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

Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Fritz, M. H. Y., Konkel, M. K., Malhotra, A., Stütz, A. M., Shi, X., Casale, F. P., Chen, J., Hormozdiari, F., Dayama, G., Chen, K., Malig, M. & 62 others, Chaisson, M. J. P., Walter, K., Meiers, S., Kashin, S., Garrison, E., Auton, A., Lam, H. Y. K., Mu, X. J., 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, J. M., Kong, Y., Lameijer, E. W., McCarthy, S., Flicek, P., Gibbs, R. A., Marth, G., Mason, C. E., Menelaou, A., Muzny, D. M., Nelson, B. J., Noor, A., Parrish, N. F., Pendleton, M., Quitadamo, A., Raeder, B., Schadt, E. E., Romanovitch, M., Schlattl, A., Sebra, R., Shabalin, A. A., Untergasser, A., Walker, J. A., Wang, M., Yu, F., Zhang, C., Zhang, J., Zheng-Bradley, X., Zhou, W., Zichner, T., Sebat, J., Batzer, M. A., McCarroll, S. A., Mills, R. E., Gerstein, M. B., Bashir, A., Stegle, O., Devine, S. E., Lee, C., Eichler, E. E. & Korbel, J. O., Sep 30 2015, In : Nature. 526, 7571, p. 75-81 7 p.

Research output: Contribution to journalArticle

Human Genome
Haplotypes
Gene Knockout Techniques
Quantitative Trait Loci
Genome-Wide Association Study
317 Citations (Scopus)

FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders

Mariani, J., Coppola, G., Zhang, P., Abyzov, A., Provini, L., Tomasini, L., Amenduni, M., Szekely, A., Palejev, D., Wilson, M., Gerstein, M., Grigorenko, E. L., Chawarska, K., Pelphrey, K. A., Howe, J. R. & Vaccarino, F. M., Jul 18 2015, In : Cell. 162, 2, p. 375-390 16 p., 8281.

Research output: Contribution to journalArticle

GABAergic Neurons
gamma-Aminobutyric Acid
Neurons
Glutamic Acid
Genes
44 Citations (Scopus)

MetaSV: An accurate and integrative structural-variant caller for next generation sequencing

Mohiyuddin, M., Mu, J. C., Li, J., Bani Asadi, N., Gerstein, M. B., Abyzov, A., Wong, W. H. & Lam, H. Y. K., Jan 19 2015, In : Bioinformatics. 31, 16, p. 2741-2744 4 p.

Research output: Contribution to journalArticle

Sequencing
Genomic Structural Variation
Boidae
Dynamic programming
Merging
2014
41 Citations (Scopus)

Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences

Colonna, V., Ayub, Q., Chen, Y., Pagani, L., Luisi, P., Pybus, M., Garrison, E., Xue, Y., Tyler-Smith, C., Abecasis, G. R., Auton, A., Brooks, L. D., Depristo, M. A., Durbin, R. M., Handsaker, R. E., Kang, H. M., Marth, G. T., McVean, G., Altshuler, D. M., Bentley, D. R. & 366 others, Chakravarti, A., Clark, A. G., Donnelly, P., Eichler, E. E., Flicek, P., Gabriel, S. B., Gibbs, R. A., Green, E. D., Hurles, M. E., Knoppers, B. M., Korbel, J. O., Lander, E. S., Lee, C., Lehrach, H., Mardis, E. R., McVean, G. A., Nickerson, D. A., Schmidt, J. P., Sherry, S. T., Wang, J., Wilson, R. K., Dinh, H., Kovar, C., Lee, S., Lewis, L., Muzny, D., Reid, J., Wang, M., Fang, X., Guo, X., Jian, M., Jiang, H., Jin, X., Li, G., Li, J., Li, Y., Li, Z., Liu, X., Lu, Y., Ma, X., Su, Z., Tai, S., Tang, M., Wang, B., Wang, G., Wu, H., Wu, R., Yin, Y., Zhang, W., Zhao, J., Zhao, M., Zheng, X., Zhou, Y., Gupta, N., Clarke, L., Leinonen, R., Smith, R. E., Zheng-Bradley, X., Grocock, R., Humphray, S., James, T., Kingsbury, Z., Sudbrak, R., Albrecht, M. W., Amstislavskiy, V. S., Borodina, T. A., Lienhard, M., Mertes, F., Sultan, M., Timmermann, B., Yaspo, M. L., Fulton, L., Fulton, R., Weinstock, G. M., Balasubramaniam, S., Burton, J., Danecek, P., Keane, T. M., Kolb-Kokocinski, A., McCarthy, S., Stalker, J., Quail, M., Davies, C. J., Gollub, J., Webster, T., Wong, B., Zhan, Y., Yu, F., Bainbridge, M., Challis, D., Evani, U. S., Lu, J., Nagaswamy, U., Sabo, A., Wang, Y., Yu, J., Coin, L. J., Fang, L., Li, Q., Lin, H., Liu, B., Luo, R., Qin, N., Shao, H., Xie, Y., Ye, C., Yu, C., Zhang, F., Zheng, H., Zhu, H., Garrison, E. P., Kural, D., Lee, W. P., Leong, W. F., Ward, A. N., Wu, J., Zhang, M., Griffin, L., Hsieh, C. H., Mills, R. E., Shi, X., von Grotthuss, M., Zhang, C., Daly, M. J., Banks, E., Bhatia, G., Carneiro, M. O., Del Angel, G., Genovese, G., Hartl, C., McCarroll, S. A., Nemesh, J. C., Poplin, R. E., Schaffner, S. F., Shakir, K., Yoon, S. C., Lihm, J., Makarov, V., Jin, H., Kim, W., Kim, K. C., Rausch, T., Beal, K., Cunningham, F., Herrero, J., McLaren, W. M., Ritchie, G. R., Gottipati, S., Keinan, A., Rodriguez-Flores, J. L., Sabeti, P. C., Grossman, S. R., Tabrizi, S., Tariyal, R., Cooper, D. N., Ball, E. V., Stenson, P. D., Barnes, B., Bauer, M., Cheetham, R., Cox, T., Eberle, M., Kahn, S., Murray, L., Peden, J., Shaw, R., Batzer, M. A., Konkel, M. K., Walker, J. A., Macarthur, D. G., Lek, M., Herwig, R., Shriver, M. D., Bustamante, C. D., Byrnes, J. K., De La Vega, F. M., Gravel, S., Kenny, E. E., Kidd, J. M., Lacroute, P., Maples, B. K., Moreno-Estrada, A., Zakharia, F., Halperin, E., Baran, Y., Craig, D. W., Christoforides, A., Homer, N., Izatt, T., Kurdoglu, A. A., Sinari, S. A., Squire, K., Xiao, C., Sebat, J., Bafna, V., Burchard, E. G., Hernandez, R. D., Gignoux, C. R., Haussler, D., Katzman, S. J., Kent, W. J., Howie, B., Ruiz-Linares, A., Dermitzakis, E. T., Lappalainen, T., Devine, S. E., Maroo, A., Tallon, L. J., Rosenfeld, J. A., Michelson, L. P., Anderson, P., Angius, A., Bigham, A., Blackwell, T., Busonero, F., Cucca, F., Fuchsberger, C., Jones, C., Lyons, R., Maschio, A., Porcu, E., Reinier, F., Sanna, S., Schlessinger, D., Sidore, C., Tan, A., Trost, M. K., Awadalla, P., Hodgkinson, A., Lunter, G., Marchini, J. L., Myers, S., Churchhouse, C., Delaneau, O., Gupta-Hinch, A., Iqbal, Z., Mathieson, I., Rimmer, A., Xifara, D. K., Oleksyk, T. K., Fu, Y., Xiong, M., Jorde, L., Witherspoon, D., Xing, J., Browning, B. L., Alkan, C., Hajirasouliha, I., Hormozdiari, F., Ko, A., Sudmant, P. H., Chen, K., Chinwalla, A., Ding, L., Dooling, D., Koboldt, D. C., McLellan, M. D., Wallis, J. W., Wendl, M. C., Zhang, Q., Albers, C. A., Coffey, A. J., Huang, N., Jostins, L., Li, H., Scally, A., Walter, K., Zhang, Y., Gerstein, M. B., Abyzov, A., Balasubramanian, S., Chen, J., Clarke, D., Habegger, L., Harmanci, A. O., Jin, M., Khurana, E., Mu, X. J., Sisu, C., Degenhardt, J., Stütz, A. M., Church, D., Michaelson, J. J., Blackburne, B., Lindsay, S. J., Ning, Z., Balasubramanian, S., Frankish, A., Harrow, J., Balasubramanian, S., Kalra, D., Hale, W., Fowler, G., Barker, J., Kelman, G., Kulesha, E., Radhakrishnan, R., Roa, A., Smirnov, D., Streeter, I., Toneva, I., Vaughan, B., Ananiev, V., Belaia, Z., Beloslyudtsev, D., Bouk, N., Chen, C., Cohen, R., Cook, C., Garner, J., Hefferon, T., Kimelman, M., Liu, C., Lopez, J., Meric, P., O'sullivan, C., Ostapchuk, Y., Ponomarov, S., Schneider, V., Shekhtman, E., Sirotkin, K., Slotta, D., Zhang, H., Barnes, K. C., Beiswanger, C., Cai, H., Cao, H., Gharani, N., Henn, B., Jones, D., Kaye, J. S., Kent, A., Kerasidou, A., Mathias, R., McVean, G., Ossorio, P. N., Parker, M., Reich, D., Rotimi, C. N., Royal, C. D., Sandoval, K., Su, Y., Tian, Z., Tishkoff, S., Toji, L. H., Via, M., Yang, H., Yang, L., Zhu, J., Bodmer, W., Bedoya, G., Ming, C. Z., Yang, G., You, C. J., Peltonen, L., Garcia-Montero, A., Orfao, A., Dutil, J., Martinez-Cruzado, J. C., Felsenfeld, A. L., McEwen, J. E., Clemm, N. C., Duncanson, A., Dunn, M., Guyer, M. S. & Peterson, J. L., Jun 30 2014, In : Genome biology. 15, 6, R88.

Research output: Contribution to journalArticle

Open Access
genomics
genome
Genome
loci
skin (animal)
136 Citations (Scopus)

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

Delaneau, O., Marchini, J., McVeanh, G. A., Donnelly, P., Lunter, G., Marchini, J. L., Myers, S., Gupta-Hinch, A., Iqbal, Z., Mathieson, I., Rimmer, A., Xifara, D. K., Kerasidou, A., Churchhouse, C., Altshuler, D. M., Gabriel, S. B., Lander, E. S., Gupta, N., Daly, M. J., DePristo, M. A. & 363 others, Banks, E., Bhatia, G., Carneiro, M. O., Del Angel, G., Genovese, G., Handsaker, R. E., Hartl, C., McCarroll, S. A., Nemesh, J. C., Poplin, R. E., Schaffner, S. F., Shakir, K., Sabeti, P. C., Grossman, S. R., Tabrizi, S., Tariyal, R., Li, H., Reich, D., Durbin, R. M., Hurles, M. E., Balasubramaniam, S., Burton, J., Danecek, P., Keane, T. M., Kolb-Kokocinski, A., McCarthy, S., Stalker, J., Quail, M., Ayub, Q., Chen, Y., Coffey, A. J., Colonna, V., Huang, N., Jostins, L., Scally, A., Walter, K., Xue, Y., Zhang, Y., Blackburne, B., Lindsay, S. J., Ning, Z., Frankish, A., Harrow, J., Chris, T. S., Abecasis, G. R., Kang, H. M., Anderson, P., Blackwell, T., Busonero, F., Fuchsberger, C., Jun, G., Maschio, A., Porcu, E., Sidore, C., Tan, A., Trost, M. K., Bentley, D. R., Grocock, R., Humphray, S., James, T., Kingsbury, Z., Bauer, M., Cheetham, R. K., Cox, T., Eberle, M., Murray, L., Shaw, R., Chakravarti, A., Clark, A. G., Keinan, A., Rodriguez-Flores, J. L., De LaVega, F. M., Degenhardt, J., Eichler, E. E., Flicek, P., Clarke, L., Leinonen, R., Smith, R. E., Zheng-Bradley, X., Beal, K., Cunningham, F., Herrero, J., McLaren, W. M., Ritchie, G. R. S., Barker, J., Kelman, G., Kulesha, E., Radhakrishnan, R., Roa, A., Smirnov, D., Streeter, I., Toneva, I., Gibbs, R. A., Dinh, H., Kovar, C., Lee, S., Lewis, L., Muzny, D., Reid, J., Wang, M., Yu, F., Bainbridge, M., Challis, D., Evani, U. S., Lu, J., Nagaswamy, U., Sabo, A., Wang, Y., Yu, J., Fowler, G., Hale, W., Kalra, D., Green, E. D., Knoppers, B. M., Korbel, J. O., Rausch, T., Sttz, A. M., Lee, C., Griffin, L., Hsieh, C. H., Mills, R. E., Von Grotthuss, M., Zhang, C., Shi, X., Lehrach, H., Sudbrak, R., Amstislavskiy, V. S., Lienhard, M., Mertes, F., Sultan, M., Timmermann, B., Yaspo, M. L., Herwig, S. R., Mardis, E. R., Wilson, R. K., Fulton, L., Fulton, R., Weinstock, G. M., Chinwalla, A., Ding, L., Dooling, D., Koboldt, D. C., McLellan, M. D., Wallis, J. W., Wendl, M. C., Zhang, Q., Marth, G. T., Garrison, E. P., Kural, D., Lee, W. P., Leong, W. F., Ward, A. N., Wu, J., Zhang, M., Nickerson, D. A., Alkan, C., Hormozdiari, F., Ko, A., Sudmant, P. H., Schmidt, J. P., Davies, C. J., Gollub, J., Webster, T., Wong, B., Zhan, Y., Sherry, S. T., Xiao, C., Church, D., Ananiev, V., Belaia, Z., Beloslyudtsev, D., Bouk, N., Chen, C., Cohen, R., Cook, C., Garner, J., Hefferon, T., Kimelman, M., Liu, C., Lopez, J., Meric, P., Ostapchuk, Y., Phan, L., Ponomarov, S., Schneider, V., Shekhtman, E., Sirotkin, K., Slotta, D., Zhang, H., Wang, J., Fang, X., Guo, X., Jian, M., Jiang, H., Jin, X., Li, G., Li, J., Li, Y., Liu, X., Lu, Y., Ma, X., Tai, S., Tang, M., Wang, B., Wang, G., Wu, H., Wu, R., Yin, Y., Zhang, W., Zhao, J., Zhao, M., Zheng, X., Lachlan, H., Fang, L., Li, Q., Li, Z., Lin, H., Liu, B., Luo, R., Shao, H., Wang, B., Xie, Y., Ye, C., Yu, C., Zheng, H., Zhu, H., Cai, H., Cao, H., Su, Y., Tian, Z., Yang, H., Yang, L., Zhu, J., Cai, Z., Wang, J., Albrecht, M. W., Borodina, T. A., Auton, A., Yoon, S. C., Lihm, J., Makarov, V., Jin, H., Kim, W., Kim, K. C., Gottipati, S., Jones, D., Cooper, D. N., Ball, E. V., Stenson, P. D., Barnes, B., Kahn, S., Ye, K., Batzer, M. A., Konkel, M. K., Walker, J. A., MacArthur, D. G., Lek, M., Shriver, M. D., Bustamante, C. D., Gravel, S., Kenny, E. E., Kidd, J. M., Lacroute, P., Maples, B. K., Moreno-Estrada, A., Zakharia, F., Henn, B., Sandoval, K., Byrnes, J. K., Halperin, E., Baran, Y., Craig, D. W., Christoforides, A., Izatt, T., Kurdoglu, A. A., Sinari, S. A., Homer, N., Squire, K., Sebat, J., Bafna, V., Ye, K., Burchard, E. G., Hernandez, R. D., Gignoux, C. R., Haussler, D., Katzman, S. J., Kent, W. J., Howie, B., Ruiz-Linares, A., Dermitzakis, E. T., Lappalainen, T., Devine, S. E., Liu, X., Maroo, A., Tallon, L. J., Rosenfeld, J. A., Michelson, L. P., Angius, A., Cucca, F., Sanna, S., Bigham, A., Jones, C., Reinier, F., Li, Y., Lyons, R., Schlessinger, D., Awadalla, P., Hodgkinson, A., Oleksyk, T. K., Martinez-Cruzado, J. C., Fu, Y., Liu, X., Xiong, M., Jorde, L., Witherspoon, D., Xing, J., Browning, B. L., Hajirasouliha, I., Chen, K., Albers, C. A., Gerstein, M. B., Abyzov, A., Chen, J., Fu, Y., Habegger, L., Harmanci, A. O., Mu, X. J., Sisu, C., Balasubramanian, S., Jin, M., Khurana, E., Clarke, D., Michaelson, J. J., OSullivan, C., Barnes, K. C., Gharani, N., Toji, L. H., Gerry, N., Kaye, J. S., Kent, A., Mathias, R., Ossorio, P. N., Parker, M., Rotimi, C. N., Royal, C. D., Tishkoff, S., Via, M., Bodmer, W., Bedoya, G., Yang, G., You, C. J., Garcia-Montero, A., Orfao, A., Dutil, J., Brooks, L. D., Felsenfeld, A. L., McEwen, J. E., Clemm, N. C., Guyer, M. S., Peterson, J. L., Duncanson, A., Dunn, M. & Peltonen, L., Jun 13 2014, In : Nature Communications. 5, 3934.

Research output: Contribution to journalArticle

genome
Haplotypes
polymorphism
nucleotides
Genes
25 Citations (Scopus)

VarSim: A high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications

Mu, J. C., Mohiyuddin, M., Li, J., Bani Asadi, N., Gerstein, M. B., Abyzov, A., Wong, W. H. & Lam, H. Y. K., Nov 5 2014, In : Bioinformatics. 31, 9, p. 1469-1471 3 p.

Research output: Contribution to journalArticle

Fidelity
Sequencing
High Throughput
Cancer
Mutation
2013
29 Citations (Scopus)

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division

Abyzov, A., Iskow, R., Gokcumen, O., Radke, D. W., Balasubramanian, S., Pei, B., Habegger, L., Lee, C. & Gerstein, M., Dec 2013, In : Genome Research. 23, 12, p. 2042-2052 11 p.

Research output: Contribution to journalArticle

Cell Division
Genome
Population
Genes
Untranslated RNA
11 Citations (Scopus)

Child Development and Structural Variation in the Human Genome

Zhang, Y., Haraksingh, R., Grubert, F., Abyzov, A., Gerstein, M., Weissman, S. & Urban, A. E., Jan 2013, In : Child Development. 84, 1, p. 34-48 15 p.

Research output: Contribution to journalArticle

Human Genome
Child Development
Genomic Structural Variation
Insertional Mutagenesis
Genomics
214 Citations (Scopus)

Integrative annotation of variants from 1092 humans: Application to cancer genomics

Khurana, E., Fu, Y., Colonna, V., Mu, X. J., Kang, H. M., 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. & 28 others, Evani, U. S., Flicek, P., Fragoza, R., Garrison, E., Gibbs, R., Gümüş, Z. H., Herrero, J., Kitabayashi, N., Kong, Y., Lage, K., Liluashvili, V., Lipkin, S. M., MacArthur, D. G., Marth, G., Muzny, D., Pers, T. H., Ritchie, G. R. S., Rosenfeld, J. A., Sisu, C., Wei, X., Wilson, M., Xue, Y., Yu, F., Dermitzakis, E. T., Yu, H., Rubin, M. A., Tyler-Smith, C. & Gerstein, M., 2013, In : Science. 342, 6154, 1235587.

Research output: Contribution to journalArticle

Genomics
Genome
Neoplasms
Transcription Factors
Nucleotides
2012
7499 Citations (Scopus)

An integrated encyclopedia of DNA elements in the human genome

The ENCODE Project Consortium, Data production leads (data production), Lead analysts (data analysis), Writing group, NHGRI project management (scientific management), Principal investigators (steering committee), Boise State University and University of North Carolina at Chapel Hill Proteomics groups (data production and analysis), Broad Institute Group (data production and analysis), Cold Spring Harbor University of Geneva Center for Genomic Regulation Barcelona RIKEN Sanger Institute University of Lausanne GenomeInstitute of Singapore group (data production and analysis), Data coordination center at UC Santa Cruz (production data coordination), Duke University EBI University of Texas Austin University of North Carolina-Chapel Hill group (data production and analysis), Genome Institute of Singapore group (data production and analysis), HudsonAlpha Institute Caltech UC Irvine Stanford group (data production and analysis), Lawrence Berkeley National Laboratory group (targeted experimental validation), NHGRI groups (data production and analysis), Sanger Institute Washington University Yale University Center for Genomic Regulation Barcelona UCSC MIT University of Lausanne CNIO group (data production and analysis), Stanford-Yale Harvard University of Massachusetts Medical School University of Southern California/UC Davis group (data production and analysis), University of Albany SUNY group (data production and analysis), University of Chicago Stanford group (data production and analysis), University of Heidelberg group (targeted experimental validation) & 3 others, University of Massachusetts Medical School Bioinformatics group (data production and analysis), University of Washington University of Massachusetts Medical Center group (data production and analysis) & Data Analysis Center (data analysis), Sep 6 2012, In : Nature. 489, 7414, p. 57-74 18 p.

Research output: Contribution to journalArticle

Encyclopedias
Human Genome
DNA
Histone Code
Genome
4600 Citations (Scopus)

An integrated map of genetic variation from 1,092 human genomes

Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., Clark, A. G., Donnelly, P., Eichler, E. E., Flicek, P., Gabriel, S. B., Gibbs, R. A., Green, E. D., Hurles, M. E., Knoppers, B. M., Korbel, J. O., Lander, E. S., Lee, C., Lehrach, H., Mardis, E. R., Marth, G. T. & 371 others, McVean, G. A., Nickerson, D. A., Schmidt, J. P., Sherry, S. T., Wang, J., Wilson, R. K., Dinh, H., Kovar, C., Lee, S., Lewis, L., Muzny, D., Reid, J., Wang, M., Fang, X., Guo, X., Jian, M., Jiang, H., Jin, X., Li, G., Li, J., Li, Y., Li, Z., Liu, X., Lu, Y., Ma, X., Su, Z., Tai, S., Tang, M., Wang, B., Wang, G., Wu, H., Wu, R., Yin, Y., Zhang, W., Zhao, J., Zhao, M., Zheng, X., Zhou, Y., Gupta, N., Clarke, L., Leinonen, R., Smith, R. E., Zheng-Bradley, X., Grocock, R., Humphray, S., James, T., Kingsbury, Z., Sudbrak, R., Albrecht, M. W., Amstislavskiy, V. S., Borodina, T. A., Lienhard, M., Mertes, F., Sultan, M., Timmermann, B., Yaspo, M. L., Fulton, L., Fulton, R., Weinstock, G. M., Balasubramaniam, S., Burton, J., Danecek, P., Keane, T. M., Kolb-Kokocinski, A., McCarthy, S., Stalker, J., Quail, M., Davies, C. J., Gollub, J., Webster, T., Wong, B., Zhan, Y., Auton, A., Yu, F., Bainbridge, M., Challis, D., Evani, U. S., Lu, J., Nagaswamy, U., Sabo, A., Wang, Y., Yu, J., Coin, L. J. M., Fang, L., Li, Q., Li, Z., Lin, H., Liu, B., Luo, R., Qin, N., Shao, H., Wang, B., Xie, Y., Ye, C., Yu, C., Zhang, F., Zheng, H., Zhu, H., Garrison, E. P., Kural, D., Lee, W. P., Fung Leong, W., Ward, A. N., Wu, J., Zhang, M., Griffin, L., Hsieh, C. H., Mills, R. E., Shi, X., Von Grotthuss, M., Zhang, C., Daly, M. J., Depristo, M. A., Banks, E., Bhatia, G., Carneiro, M. O., Del Angel, G., Genovese, G., Handsaker, R. E., Hartl, C., McCarroll, S. A., Nemesh, J. C., Poplin, R. E., Schaffner, S. F., Shakir, K., Yoon, S. C., Lihm, J., Makarov, V., Jin, H., Kim, W., Cheol Kim, K., Rausch, T., Beal, K., Cunningham, F., Herrero, J., McLaren, W. M., Ritchie, G. R. S., Gottipati, S., Keinan, A., Rodriguez-Flores, J. L., Sabeti, P. C., Grossman, S. R., Tabrizi, S., Tariyal, R., Cooper, D. N., Ball, E. V., Stenson, P. D., Barnes, B., Bauer, M., Keira Cheetham, R., Cox, T., Eberle, M., Kahn, S., Murray, L., Peden, J., Shaw, R., Ye, K., Batzer, M. A., Konkel, M. K., Walker, J. A., MacArthur, D. G., Lek, M., Herwig, R., Shriver, M. D., Bustamante, C. D., Byrnes, J. K., De La Vega, F. M., Gravel, S., Kenny, E. E., Kidd, J. M., Maples, B. K., Moreno-Estrada, A., Zakharia, F., Halperin, E., Baran, Y., Craig, D. W., Christoforides, A., Homer, N., Izatt, T., Kurdoglu, A. A., Sinari, S. A., Squire, K., Xiao, C., Sebat, J., Bafna, V., Ye, K., Burchard, E. G., Hernandez, R. D., Gignoux, C. R., Haussler, D., Katzman, S. J., James Kent, W., Howie, B., Ruiz-Linares, A., Dermitzakis, E. T., Lappalainen, T., Devine, S. E., Liu, X., Maroo, A., Tallon, L. J., Rosenfeld, J. A., Michelson, L. P., Min Kang, H., Anderson, P., Angius, A., Bigham, A., Blackwell, T., Busonero, F., Cucca, F., Fuchsberger, C., Jones, C., Jun, G., Li, Y., Lyons, R., Maschio, A., Porcu, E., Reinier, F., Sanna, S., Schlessinger, D., Sidore, C., Tan, A., Kate Trost, M., Awadalla, P., Hodgkinson, A., Lunter, G., Marchini, J. L., Myers, S., Churchhouse, C., Delaneau, O., Gupta-Hinch, A., Iqbal, Z., Mathieson, I., Rimmer, A., Xifara, D. K., Oleksyk, T. K., Fu, Y., Liu, X., Xiong, M., Jorde, L., Witherspoon, D., Xing, J., Browning, B. L., Alkan, C., Hajirasouliha, I., Hormozdiari, F., Ko, A., Sudmant, P. H., Chen, K., Chinwalla, A., Ding, L., Dooling, D., Koboldt, D. C., McLellan, M. D., Wallis, J. W., Wendl, M. C., Zhang, Q., Tyler-Smith, C., Albers, C. A., Ayub, Q., Chen, Y., Coffey, A. J., Colonna, V., Huang, N., Jostins, L., Li, H., Scally, A., Walter, K., Xue, Y., Zhang, Y., Gerstein, M. B., Abyzov, A., Balasubramanian, S., Chen, J., Clarke, D., Fu, Y., Habegger, L., Harmanci, A. O., Jin, M., Khurana, E., Jasmine Mu, X., Sisu, C., Degenhardt, J., Stütz, A. M., Keira Cheetham, R., Church, D., Michaelson, J. J., Blackburne, B., Lindsay, S. J., Ning, Z., Frankish, A., Harrow, J., Mu, X. J., Fowler, G., Hale, W., Kalra, D., Barker, J., Kelman, G., Kulesha, E., Radhakrishnan, R., Roa, A., Smirnov, D., Streeter, I., Toneva, I., Vaughan, B., Ananiev, V., Belaia, Z., Beloslyudtsev, D., Bouk, N., Chen, C., Cohen, R., Cook, C., Garner, J., Hefferon, T., Kimelman, M., Liu, C., Lopez, J., Meric, P., O'Sullivan, C., Ostapchuk, Y., Phan, L., Ponomarov, S., Schneider, V., Shekhtman, E., Sirotkin, K., Slotta, D., Zhang, H., Barnes, K. C., Beiswanger, C., Cai, H., Cao, H., Gharani, N., Henn, B., Jones, D., Kaye, J. S., Kent, A., Kerasidou, A., Mathias, R., Ossorio, P. N., Parker, M., Reich, D., Rotimi, C. N., Royal, C. D., Sandoval, K., Su, Y., Tian, Z., Tishkoff, S., Toji, L. H., Via, M., Wang, Y., Yang, H., Yang, L., Zhu, J., Bodmer, W., Bedoya, G., Ming, C. Z., Yang, G., Jia You, C., Peltonen, L., Garcia-Montero, A., Orfao, A., Dutil, J., Martinez-Cruzado, J. C., Brooks, L. D., Felsenfeld, A. L., McEwen, J. E., Clemm, N. C., Duncanson, A., Dunn, M., Guyer, M. S., Peterson, J. L. & Lacroute, P., Nov 1 2012, In : Nature. 491, 7422, p. 56-65 10 p.

Research output: Contribution to journalArticle

Human Genome
Genome
Population
Single Nucleotide Polymorphism
Exome
857 Citations (Scopus)

Architecture of the human regulatory network derived from ENCODE data

Gerstein, M. B., Kundaje, A., Hariharan, M., Landt, S. G., Yan, K. K., Cheng, C., Mu, X. J., Khurana, E., Rozowsky, J., Alexander, R., Min, R., Alves, P., Abyzov, A., Addleman, N., Bhardwaj, N., Boyle, A. P., Cayting, P., Charos, A., Chen, D. Z., Cheng, Y. & 36 others, 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., Oĝgeen, H., Ouyang, Z., Partridge, E. C., Patacsil, D., Pauli, F., Raha, D., Ramirez, L., Reddy, T. E., Reed, B., Shi, M., Slifer, T., Wang, J., Wu, L., Yang, X., Yip, K. Y., Zilberman-Schapira, G., Batzoglou, S., Sidow, A., Farnham, P. J., Myers, R. M., Weissman, S. M. & Snyder, M., Sep 6 2012, In : Nature. 489, 7414, p. 91-100 10 p.

Research output: Contribution to journalArticle

Transcription Factors
Alleles
Gene Regulatory Networks
MicroRNAs
Genes
17 Citations (Scopus)

Regulatory element copy number differences shape primate expression profiles

Iskow, R. C., Gokcumen, O., Abyzov, A., Malukiewicz, J., Zhu, Q., Sukumar, A. T., Pai, A. A., Mills, R. E., Habegger, L., Cusanovich, D. A., Rubel, M. A., Perry, G. H., Gerstein, M., Stone, A. C., Gilad, Y. & Lee, C., Jul 31 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 31, p. 12656-12661 6 p.

Research output: Contribution to journalArticle

Conserved Sequence
Primates
Long Noncoding RNA
Pseudogenes
Gene Dosage
246 Citations (Scopus)

Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells

Abyzov, A., Mariani, J., Palejev, D., Zhang, Y., Haney, M. S., Tomasini, L., Ferrandino, A. F., Rosenberg Belmaker, L. A., Szekely, A., Wilson, M., Kocabas, A., Calixto, N. E., Grigorenko, E. L., Huttner, A., Chawarska, K., Weissman, S., Urban, A. E., Gerstein, M. & Vaccarino, F. M., Dec 20 2012, In : Nature. 492, 7429, p. 438-442 5 p.

Research output: Contribution to journalArticle

Induced Pluripotent Stem Cells
Mosaicism
Skin
Fibroblasts
Cell Line
2011
60 Citations (Scopus)

AGE: Defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision

Abyzov, A. & Gerstein, M., Mar 2011, In : Bioinformatics. 27, 5, p. 595-603 9 p., btq713.

Research output: Contribution to journalArticle

Genomic Structural Variation
Sequence Alignment
Nucleotides
Genomics
Alignment
161 Citations (Scopus)

AlleleSeq: Analysis of allele-specific expression and binding in a network framework

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., 2011, In : Molecular Systems Biology. 7, 522.

Research output: Contribution to journalArticle

Genes
Alleles
alleles
Genome
Pipelines
933 Citations (Scopus)

A user's guide to the Encyclopedia of DNA elements (ENCODE)

Myers, R. M., Stamatoyannopoulos, J., Snyder, M., Dunham, I., Hardison, R. C., Bernstein, B. E., Gingeras, T. R., Kent, W. J., Birney, E., Wold, B., Crawford, G. E., Bernstein, B. E., Epstein, C. B., Shoresh, N., Ernst, J., Mikkelsen, T. S., Kheradpour, P., Zhang, X., Wang, L., Issner, R. & 340 others, Coyne, M. J., Durham, T., Ku, M., Truong, T., Ward, L. D., Altshuler, R. C., Lin, M. F., Kellis, M., Gingeras, T. R., Davis, C. A., Kapranov, P., Dobin, A., Zaleski, C., Schlesinger, F., Batut, P., Chakrabortty, S., Jha, S., Lin, W., Drenkow, J., Wang, H., Bell, K., Gao, H., Bell, I., Dumais, E., Dumais, J., Antonarakis, S. E., Ucla, C., Borel, C., Guigo, R., Djebali, S., Lagarde, J., Kingswood, C., Ribeca, P., Sammeth, M., Alioto, T., Merkel, A., Tilgner, H., Carninci, P., Hayashizaki, Y., Lassmann, T., Takahashi, H., Abdelhamid, R. F., Hannon, G., Fejes, K. T., Preall, J., Gordon, A., Sotirova, V., Reymond, A., Howald, C., Graison, E. A. Y., Chrast, J., Ruan, Y., Ruan, X., Shahab, A., Poh, W. T., Wei, C. L., Crawford, G. E., Furey, T. S., Boyle, A. P., Sheffield, N. C., Song, L., Shibata, Y., Vales, T., Winter, D., Zhang, Z., London, D., Wang, T., Birney, E., Keefe, D., Iyer, V. R., Lee, B. K., McDaniell, R. M., Liu, Z., Battenhouse, A., Bhinge, A. A., Lieb, J. D., Grasfeder, L. L., Showers, K. A., Giresi, P. G., Kim, S. K. C., Shestak, C., Myers, R. M., Pauli, F., Reddy, T. E., Gertz, J., Partridge, E. C., Jain, P., Sprouse, R. O., Bansal, A., Pusey, B., Muratet, M. A., Varley, K. E., Bowling, K. M., Newberry, K. M., Nesmith, A. S., Dilocker, J. A., Parker, S. L., Waite, L. L., Thibeault, K., Roberts, K., Absher, D. M., Wold, B., Mortazavi, A., Williams, B., Marinov, G., Trout, D., Pepke, S., King, B., McCue, K., Kirilusha, A., DeSalvo, G., Fisher, K. A., Amrhein, H., Vielmetter, J., Sherlock, G., Sidow, A., Batzoglou, S., Rauch, R., Kundaje, A., Libbrecht, M., Margulies, E. H., Parker, S. C. J., Elnitski, L., Green, E. D., Hubbard, T., Harrow, J., Searle, S., Kokocinski, F., Aken, B., Frankish, A., Hunt, T., Despacio-Reyes, G., Kay, M., Mukherjee, G., Bignell, A., Saunders, G., Boychenko, V., Brent, M., van Baren, M. J., Brown, R. H., Gerstein, M., Khurana, E., Balasubramanian, S., Zhang, Z., Lam, H., Cayting, P., Robilotto, R., Lu, Z., Guigo, R., Derrien, T., Tanzer, A., Knowles, D. G., Mariotti, M., Kent, W. J., Haussler, D., Harte, R., Diekhans, M., Kellis, M., Lin, M., Kheradpour, P., Ernst, J., Reymond, A., Howald, C., Graison, E. A. Y., Chrast, J., Valencia, A., Tress, M., Rodriguez, J. M., Snyder, M., Landt, S. G., Raha, D., Abyzov, A., Euskirchen, G., Grubert, F., Kasowski, M., Lian, J., Cayting, P., Lacroute, P., Xu, Y., Monahan, H., Patacsil, D., Slifer, T., Yang, X., Charos, A., Reed, B., Wu, L., Auerbach, R. K., Habegger, L., Hariharan, M., Rozowsky, J., Abyzov, A., Weissman, S. M., Gerstein, M., Struhl, K., Lamarre, N. V., Lindahl, M. A., Miotto, B., Moqtaderi, Z., Fleming, J. D., Newburger, P., Farnham, P. J., Frietze, S., O'Geen, H., Xu, X., Blahnik, K. R., Cao, A. R., Iyengar, S., Stamatoyannopoulos, J. A., Kaul, R., Thurman, R. E., Wang, H., Navas, P. A., Sandstrom, R., Sabo, P. J., Weaver, M., Canfield, T., Lee, K., Neph, S., Roach, V., Reynolds, A., Johnson, A., Rynes, E., Giste, E., Vong, S., Neri, J., Frum, T., Johnson, E. M., Nguyen, E. D., Ebersol, A. K., Sanchez, M. E., Sheffer, H. H., Lotakis, D., Haugen, E., Humbert, R., Kutyavin, T., Shafer, T., Dekker, J., Lajoie, B. R., Sanyal, A., Kent, W. J., Rosenbloom, K. R., Dreszer, T. R., Raney, B. J., Barber, G. P., Meyer, L. R., Sloan, C. A., Malladi, V. S., Cline, M. S., Learned, K., Swing, V. K., Zweig, A. S., Rhead, B., Fujita, P. A., Roskin, K., Karolchik, D., Kuhn, R. M., Haussler, D., Birney, E., Dunham, I., Wilder, S. P., Keefe, D., Sobral, D., Herrero, J., Beal, K., Lukk, M., Brazma, A., Vaquerizas, J. M., Luscombe, N. M., Bickel, P. J., Boley, N., Brown, J. B., Li, Q., Huang, H., Gerstein, M., Habegger, L., Sboner, A., Rozowsky, J., Auerbach, R. K., Yip, K. Y., Cheng, C., Yan, K. K., Bhardwaj, N., Wang, J., Lochovsky, L., Jee, J., Gibson, T., Leng, J., Du, J., Hardison, R. C., Harris, R. S., Song, G., Miller, W., Haussler, D., Roskin, K., Suh, B., Wang, T., Paten, B., Noble, W. S., Hoffman, M. M., Buske, O. J., Weng, Z., Dong, X., Wang, J., Xi, H., Tenenbaum, S. A., Doyle, F., Penalva, L. O., Chittur, S., Tullius, T. D., Parker, S. C. J., White, K. P., Karmakar, S., Victorsen, A., Jameel, N., Bild, N., Grossman, R. L., Snyder, M., Landt, S. G., Yang, X., Patacsil, D., Slifer, T., Dekker, J., Lajoie, B. R., Sanyal, A., Whitfield, T. W., Wang, J., Collins, P. J., Trinklein, N. D., Partridge, E. C., Giddings, M. C., Chen, X., Khatun, J., Maier, C., Yu, Y., Gunawardena, H., Feingold, E. A., Risk, B., Lowdon, R. F., Dillon, L. A. L. & Good, P. J., Apr 1 2011, In : PLoS Biology. 9, 4, e1001046.

Research output: Contribution to journalArticle

Encyclopedias
Human Genome
Genes
DNA
genome
580 Citations (Scopus)

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

Abyzov, A., Urban, A. E., Snyder, M. & Gerstein, M., Jun 2011, In : Genome Research. 21, 6, p. 974-984 11 p.

Research output: Contribution to journalArticle

Genotype
Genome
Population
Alleles
47 Citations (Scopus)

Genome-wide mapping of copy number variation in humans: Comparative analysis of high resolution array platforms

Haraksingh, R. R., Abyzov, A., Gerstein, M., Urban, A. E. & Snyder, M., Nov 30 2011, In : PLoS One. 6, 11, e27859.

Research output: Contribution to journalArticle

Chromosome Mapping
Genes
Genome
genome
single nucleotide polymorphism
46 Citations (Scopus)

Identification of genomic indels and structural variations using split reads

Zhang, Z. D., Du, J., Lam, H., Abyzov, A., Urban, A. E., Snyder, M. & Gerstein, M., Jul 25 2011, In : BMC Genomics. 12, 375.

Research output: Contribution to journalArticle

Genomic Structural Variation
Genome
Technology
Insertional Mutagenesis
Chromosomes, Human, Pair 1
23 Citations (Scopus)

Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions

Bhardwaj, N., Abyzov, A., Clarke, D., Shou, C. & Gerstein, M. B., Oct 2011, In : Protein Science. 20, 10, p. 1745-1754 10 p.

Research output: Contribution to journalArticle

Protein Interaction Maps
Protein Conformation
Proteins
Sexual Partners
Molecular Dynamics Simulation
696 Citations (Scopus)

Mapping copy number variation by population-scale genome sequencing

Mills, R. E., Walter, K., Stewart, C., Handsaker, R. E., Chen, K., Alkan, C., Abyzov, A., Yoon, S. C., Ye, K., Cheetham, R. K., Chinwalla, A., Conrad, D. F., Fu, Y., Grubert, F., Hajirasouliha, I., Hormozdiari, F., Iakoucheva, L. M., Iqbal, Z., Kang, S., Kidd, J. M. & 37 others, Konkel, M. K., Korn, J., Khurana, E., Kural, D., Lam, H. Y. K., Leng, J., Li, R., Li, Y., Lin, C. Y., Luo, R., Mu, X. J., Nemesh, J., Peckham, H. E., Rausch, T., Scally, A., Shi, X., Stromberg, M. P., Sütz, A. M., Urban, A. E., Walker, J. A., Wu, J., Zhang, Y., Zhang, Z. D., Batzer, M. A., Ding, L., Marth, G. T., McVean, G., Sebat, J., Snyder, M., Wang, J., Ye, K., Eichler, E. E., Gerstein, M. B., Hurles, M. E., Lee, C., McCarroll, S. A. & Korbel, J. O., Feb 3 2011, In : Nature. 470, 7332, p. 59-65 7 p.

Research output: Contribution to journalArticle

Genomic Structural Variation
Nucleotides
Genome
Gene Deletion
Human Genome
2010
5026 Citations (Scopus)

A map of human genome variation from population-scale sequencing

Altshuler, D. L., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., Clark, A. G., Collins, F. S., De La Vega, F. M., Donnelly, P., Egholm, M., Flicek, P., Gabriel, S. B., Gibbs, R. A., Knoppers, B. M., Lander, E. S., Lehrach, H., Mardis, E. R., McVean, G. A., Nickerson, D. A., Peltonen, L. & 348 others, Schafer, A. J., Sherry, S. T., Wang, J., Wilson, R. K., Deiros, D., Metzker, M., Muzny, D., Reid, J., Wheeler, D., Wang, S. J., Li, J., Jian, M., Li, G., Li, R., Liang, H., Tian, G., Wang, B., Wang, J., Wang, W., Yang, H., Zhang, X., Zheng, H., Ambrogio, L., Bloom, T., Cibulskis, K., Fennell, T. J., Jaffe, D. B., Shefler, E., Sougnez, C. L., Bentley, I. D. R., Gormley, N., Humphray, S., Kingsbury, Z., Koko-Gonzales, P., Stone, J., Mc Kernan, K. J., Costa, G. L., Ichikawa, J. K., Lee, C. C., Sudbrak, R., Borodina, T. A., Dahl, A., Davydov, A. N., Marquardt, P., Mertes, F., Nietfeld, W., Rosenstiel, P., Schreiber, S., Soldatov, A. V., Timmermann, B., Tolzmann, M., Affourtit, J., Ashworth, D., Attiya, S., Bachorski, M., Buglione, E., Burke, A., Caprio, A., Celone, C., Clark, S., Conners, D., Desany, B., Gu, L., Guccione, L., Kao, K., Kebbel, A., Knowlton, J., Labrecque, M., McDade, L., Mealmaker, C., Minderman, M., Nawrocki, A., Niazi, F., Pareja, K., Ramenani, R., Riches, D., Song, W., Turcotte, C., Wang, S., Dooling, D., Fulton, L., Fulton, R., Weinstock, G., Burton, J., Carter, D. M., Churcher, C., Coffey, A., Cox, A., Palotie, A., Quail, M., Skelly, T., Stalker, J., Swerdlow, H. P., Turner, D., De Witte, A., Giles, S., Bainbridge, M., Challis, D., Sabo, A., Yu, F., Yu, J., Fang, X., Guo, X., Li, Y., Luo, R., Tai, S., Wu, H., Zheng, H., Zheng, X., Zhou, Y., Marth, G. T., Garrison, E. P., Huang, W., Indap, A., Kural, D., Lee, W. P., Leong, W. F., Quinlan, A. R., Stewart, C., Stromberg, M. P., Ward, A. N., Wu, J., Lee, C., Mills, R. E., Shi, X., Daly, M. J., DePristo, M. A., Ball, A. D., Banks, E., Browning, B. L., Garimella, K. V., Grossman, S. R., Handsaker, R. E., Hanna, M., Hartl, C., Kernytsky, A. M., Korn, J. M., Li, H., Maguire, J. R., McKenna, A., Nemesh, J. C., Philippakis, A. A., Poplin, R. E., Price, A., Rivas, M. A., Sabeti, P. C., Schaffner, S. F., Shlyakhter, I. A., Cooper, D. N., Ball, E. V., Mort, M., Phillips, A. D., Stenson, P. D., Sebat, J., Makarov, V., Ye, K., Yoon, S. C., Bustamante, C. D., Boyko, A., Degenhardt, J., Gravel, S., Gutenkunst, R. N., Kaganovich, M., Keinan, A., Lacroute, P., Ma, X., Reynolds, A., Clarke, L., Cunningham, F., Herrero, J., Keenen, S., Kulesha, E., Leinonen, R., McLaren, W. M., Radhakrishnan, R., Smith, R. E., Zalunin, V., Korbel, J. O., Stütz, A. M., Humphray, I. S., Bauer, M., Cheetham, R. K., Cox, T., Eberle, M., James, T., Kahn, S., Murray, L., Ye, K., Fu, Y., Hyland, F. C. L., Manning, J. M., Stephen, F. M., Peckham, H. E., Sakarya, O., Sun, Y. A., Tsung, E. F., Mark, A. B., Konkel, M. K., Walker, J. A., Albrecht, M. W., Amstislavskiy, V. S., Herwig, R., Parkhomchuk, D. V., Agarwala, R., Khouri, H. M., Morgulis, A. O., Paschall, J. E., Phan, L. D., Rotmistrovsky, K. E., Sanders, R. D., Shumway, M. F., Xiao, C., Gil, A. M., Auton, A., Iqbal, Z., Lunter, G., Marchini, J. L., Moutsianas, L., Myers, S., Tumian, A., Knight, J., Winer, R., Craig, D. W., Beckstrom-Sternberg, S. M., Christoforides, A., Kurdoglu, A. A., Pearson, J. V., Sinari, S. A., Tembe, W. D., Haussler, D., Hinrichs, A. S., Katzman, S. J., Kern, A., Kuhn, R. M., Przeworski, M., Hernandez, R. D., Howie, B., Kelley, J. L., Melton, S. C., Li, Y., Anderson, P., Blackwell, T., Chen, W., Cookson, W. O., Ding, J., Kang, H. M., Lathrop, M., Liang, L., Moffatt, M. F., Scheet, P., Sidore, C., Snyder, M., Zhan, X., Zöllner, S., Awadalla, P., Casals, F., Idaghdour, Y., Keebler, J., Stone, E. A., Zilversmit, M., Jorde, L., Xing, J., Eichler, E. E., Aksay, G., Alkan, C., Hajirasouliha, I., Hormozdiari, F., Kidd, J. M., CenkSahinalp, S., Sudmant, P. H., Chen, K., Chinwalla, A., Ding, L., Koboldt, D. C., McLellan, M. D., Wallis, J. W., Wendl, M. C., Zhang, Q., Albers, C. A., Ayub, Q., Balasubramaniam, S., Barrett, J. C., Chen, Y., Conrad, D. F., Danecek, P., Dermitzakis, E. T., Hu, M., Huang, N., Matt, E. H., Jin, H., Jostins, L., Keane, T. M., Quang Le, S., Lindsay, S., Long, Q., MacArthur, D. G., Montgomery, S. B., Parts, L., Chris Tyler-Smith, T-S., Walter, K., Zhang, Y., Gerstein, M. B., Snyder, M., Abyzov, A., Balasubramanian, S., Bjornson, R., Grubert, F., Habegger, L., Haraksingh, R., Khurana, E., Lam, H. Y. K., Leng, J., Mu, X. J., Urban, A. E., Zhang, Z., McCarroll, S. A., Zheng-Bradley, X., Batzer, M. A., Hurles, M. E., Du, J., Jee, J., Coafra, C., Dinh, H., Kovar, C., Lee, S., Nazareth, L., Wilkinson, J., Coffey, A., Scott, C., Tyler-Smith, C., Gharani, N., Kaye, J. S., Kent, A., Li, T., McGuire, A. L., Ossorio, P. N., Rotimi, C. N., Su, Y., Toji, L. H., Felsenfeld, A. L., McEwen, J. E., Abdallah, A., Juenger, C. R., Clemm, N. C., Duncanson, A., Green, E. D., Guyer, M. S. & Peterson, J. L., Oct 28 2010, In : Nature. 467, 7319, p. 1061-1073 13 p.

Research output: Contribution to journalArticle

Human Genome
Genome
Population
Genetic Research
Genetic Selection
19 Citations (Scopus)

Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets.

Bhardwaj, N., Carson, M. B., Abyzov, A., Yan, K. K., Lu, H. & Gerstein, M. B., 2010, In : PLoS Computational Biology. 6, 5

Research output: Contribution to journalArticle

Regulator
Genes
Scaling
saturation
Escherichia coli
403 Citations (Scopus)

Diversity of human copy number variation and multicopy genes

Sudmant, P. H., Kitzman, J. O., Antonacci, F., Alkan, C., Malig, M., Tsalenko, A., Sampas, N., Bruhn, L., Shendure, J., Eichler, E. E., Altshuler, D. L., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., Clark, A. G., Collins, F. S., De La Vega, F. M., Donnelly, P., Egholm, M. & 343 others, Flicek, P., Gabriel, S. B., Gibbs, R. A., Knoppers, B. M., Lander, E. S., Lehrach, H., Mardis, E. R., McVean, G. A., Nickerson, D. A., Peltonen, L., Schafer, A. J., Sherry, S. T., Wang, J., Wilson, R. K., Deiros, D., Metzker, M., Muzny, D., Reid, J., Wheeler, D., Li, J., Jian, M., Li, G., Li, R., Liang, H., Tian, G., Wang, B., Wang, W., Yang, H., Zhang, X., Zheng, H., Ambrogio, L., Bloom, T., Cibulskis, K., Fennell, T. J., Jaffe, D. B., Shefler, E., Sougnez, C. L., Gormley, N., Humphray, S., Kingsbury, Z., Koko-Gonzales, P., Stone, J., McKernan, K. J., Costa, G. L., Ichikawa, J. K., Lee, C. C., Sudbrak, R., Borodina, T. A., Dahl, A., Davydov, A. N., Marquardt, P., Mertes, F., Nietfeld, W., Rosenstiel, P., Schreiber, S., Soldatov, A. V., Timmermann, B., Tolzmann, M., Affourtit, J., Ashworth, D., Attiya, S., Bachorski, M., Buglione, E., Burke, A., Caprio, A., Celone, C., Clark, S., Conners, D., Desany, B., Gu, L., Guccione, L., Kao, K., Kebbel, A., Knowlton, J., Labrecque, M., McDade, L., Mealmaker, C., Minderman, M., Nawrocki, A., Niazi, F., Pareja, K., Ramenani, R., Riches, D., Song, W., Turcotte, C., Wang, S., Dooling, D., Fulton, L., Fulton, R., Weinstock, G., Burton, J., Carter, D. M., Churcher, C., Coffey, A., Cox, A., Palotie, A., Quail, M., Skelly, T., Stalker, J., Swerdlow, H. P., Turner, D., De Witte, A., Giles, S., Bainbridge, M., Challis, D., Sabo, A., Yu, F., Yu, J., Fang, X., Guo, X., Li, Y., Luo, R., Tai, S., Wu, H., Zheng, X., Zhou, Y., Marth, G. T., Garrison, E. P., Huang, W., Indap, A., Kural, D., Lee, W. P., Leong, W. F., Quinlan, A. R., Stewart, C., Stromberg, M. P., Ward, A. N., Wu, J., Lee, C., Mills, R. E., Shi, X., Daly, M. J., DePristo, M. A., Ball, A. D., Banks, E., Browning, B. L., Garimella, K. V., Grossman, S. R., Handsaker, R. E., Hanna, M., Hartl, C., Kernytsky, A. M., Korn, J. M., Li, H., Maguire, J. R., McCarroll, S. A., McKenna, A., Nemesh, J. C., Philippakis, A. A., Poplin, R. E., Price, A., Rivas, M. A., Sabeti, P. C., Schaffner, S. F., Shlyakhter, I. A., Cooper, D. N., Ball, E. V., Mort, M., Phillips, A. D., Stenson, P. D., Sebat, J., Makarov, V., Ye, K., Yoon, S. C., Bustamante, C. D., Boyko, A., Degenhardt, J., Gravel, S., Gutenkunst, R. N., Kaganovich, M., Keinan, A., Lacroute, P., Ma, X., Reynolds, A., Clarke, L., Cunningham, F., Herrero, J., Keenen, S., Kulesha, E., Leinonen, R., McLaren, W. M., Radhakrishnan, R., Smith, R. E., Zalunin, V., Zheng-Bradley, X., Korbel, J. O., Stütz, A. M., Bauer, M., Cheetham, R. K., Cox, T., Eberle, M., James, T., Kahn, S., Murray, L., Fu, Y., Hyland, F. C., Manning, J. M., McLaughlin, S. F., Peckham, H. E., Sakarya, O., Sun, Y. A., Tsung, E. F., Batzer, M. A., Konkel, M. K., Walker, J. A., Albrecht, M. W., Amstislavskiy, V. S., Herwig, R., Parkhomchuk, D. V., Agarwala, R., Khouri, H. M., Morgulis, A. O., Paschall, J. E., Phan, L. D., Rotmistrovsky, K. E., Sanders, R. D., Shumway, M. F., Xiao, C., Auton, A., Iqbal, Z., Lunter, G., Marchini, J. L., Moutsianas, L., Myers, S., Tumian, A., Knight, J., Winer, R., Craig, D. W., Beckstrom-Sternberg, S. M., Christoforides, A., Kurdoglu, A. A., Pearson, J. V., Sinari, S. A., Tembe, W. D., Haussler, D., Hinrichs, A. S., Katzman, S. J., Kern, A., Kuhn, R. M., Przeworski, M., Hernandez, R. D., Howie, B., Kelley, J. L., Melton, S. C., Anderson, P., Blackwell, T., Chen, W., Cookson, W. O., Ding, J., Kang, H. M., Lathrop, M., Liang, L., Moffatt, M. F., Scheet, P., Sidore, C., Snyder, M., Zhan, X., Zöllner, S., Awadalla, P., Casals, F., Idaghdour, Y., Keebler, J., Stone, E. A., Zilversmit, M., Jorde, L., Xing, J., Aksay, G., Hajirasouliha, I., Hormozdiari, F., Kidd, J. M., Sahinalp, S. C., Chen, K., Chinwalla, A., Ding, L., Koboldt, D. C., McLellan, M. D., Wallis, J. W., Wendl, M. C., Zhang, Q., Albers, C. A., Ayub, Q., Balasubramaniam, S., Barrett, J. C., Chen, Y., Conrad, D. F., Danecek, P., Dermitzakis, E. T., Hu, M., Huang, N., Hurles, M. E., Jin, H., Jostins, L., Keane, T. M., Le, S. Q., Lindsay, S., Long, Q., MacArthur, D. G., Montgomery, S. B., Parts, L., Tyler-Smith, C., Walter, K., Zhang, Y., Gerstein, M. B., Abyzov, A., Balasubramanian, S., Bjornson, R., Du, J., Grubert, F., Habegger, L., Haraksingh, R., Jee, J., Khurana, E., Lam, H. Y., Leng, J., Mu, X. J., Urban, A. E., Zhang, Z., Coafra, C., Dinh, H., Kovar, C., Lee, S., Nazareth, L., Wilkinson, J., Scott, C., Gharani, N., Kaye, J. S., Kent, A., Li, T., McGuire, A. L., Ossorio, P. N., Rotimi, C. N., Su, Y., Toji, L. H., Brooks, L. D., Felsenfeld, A. L., McEwen, J. E., Abdallah, A., Juenger, C. R., Clemm, N. C., Duncanson, A., Green, E. D., Guyer, M. S. & Peterson, J. L., Oct 29 2010, In : Science. 330, 6004, p. 641-646 6 p.

Research output: Contribution to journalArticle

Genes
Gene Conversion
Inborn Genetic Diseases
Population Genetics
Human Genome
23 Citations (Scopus)

RigidFinder: A fast and sensitive method to detect rigid blocks in large macromolecular compleses

Abyzov, A., Bjornson, R., Felipe, M. & Gerstein, M., 2010, In : Proteins: Structure, Function and Bioinformatics. 78, 2, p. 309-324 16 p.

Research output: Contribution to journalArticle

Conformations
Orthophosphate Dikinase Pyruvate
Servers
Macromolecular Substances
RNA Polymerase II
2009
25 Citations (Scopus)

MSB: A mean-shift-based approach for the analysis of structural variation in the genome

Wang, L. Y., Abyzov, A., Korbel, J. O., Snyder, M. & Gerstein, M., Jan 2009, In : Genome Research. 19, 1, p. 106-117 12 p.

Research output: Contribution to journalArticle

Genomic Structural Variation
Comparative Genomic Hybridization
Chromosomes
Genomic Segmental Duplications
Likelihood Functions
178 Citations (Scopus)

PEMer: A computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

Korbel, J. O., Abyzov, A., Mu, X. J., Carriero, N., Cayting, P., Zhang, Z., Snyder, M. & Gerstein, M. B., Feb 23 2009, In : Genome Biology. 10, 2, R23.

Research output: Contribution to journalArticle

Genomic Structural Variation
genomics
genome
Genome
Genomics
2008
14 Citations (Scopus)

An AP endonuclease 1-DNA polymerase β complex: Theoretical prediction of interacting surfaces

Abyzov, A., Uzun, A., Strauss, P. R. & Ilyin, V. A., Apr 2008, In : PLoS Computational Biology. 4, 4, e1000066.

Research output: Contribution to journalArticle

DNA-(Apurinic or Apyrimidinic Site) Lyase
Transcription Factor AP-1
DNA-directed DNA polymerase
DNA-Directed DNA Polymerase
DNA