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Works (50 of 58)

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Automatic detection of complex structural variation in human genomes across populations and in brains of individuals with psychiatric disorders

Cell
2024 | Journal article
Contributors: Zhou Bo; Arthur G. Joseph; Guo Hanmin
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Stanford University

Resolving the 22q11.2 deletion using CTLR-Seq reveals chromosomal rearrangement mechanisms and individual variance in breakpoints

Proceedings of the National Academy of Sciences
2024-07-30 | Journal article
Contributors: Bo Zhou; Carolin Purmann; Hanmin Guo; GiWon Shin; Yiling Huang; Reenal Pattni; Qingxi Meng; Stephanie U. Greer; Tanmoy Roychowdhury; Raegan N. Wood et al.
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Crossref
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Mapping recurrent mosaic copy number variation in human neurons

NATURE COMMUNICATIONS
2024-05-17 | Journal article
WOSUID:

WOS:001227428300016

Part of ISSN: 2041-1723
Contributors: Sun, Chen; Kathuria, Kunal; Emery, Sarah B.; Kim, ByungJun; Burbulis, Ian E.; Shin, Joo Heon; Weinberger, Daniel R.; Moran, John V.; Kidd, Jeffrey M.; Mills, Ryan E. et al.
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Stanford University

GVRP: Genome Variant Refinement Pipeline for variant analysis in non-human species using machine learning

2024-01-15 | Preprint
Contributors: Jeonghoon Choi; Bo Zhou; Giltae Song
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Crossref

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

Scientific data
2023-11-20 | Journal article
Part of ISSN: 2052-4463
Contributors: McKinzie A Garrison; Yeongjun Jang; Taejeong Bae; Adriana Cherskov; Sarah B Emery; Liana Fasching; Attila Jones; John B Moldovan; Cindy Molitor; Sirisha Pochareddy et al.
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Stanford University

Author Correction: Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia

Nature Neuroscience
2023-10 | Journal article
Contributors: Xiaowei Zhu; Bo Zhou; Reenal Pattni; Kelly Gleason; Chunfeng Tan; Agnieszka Kalinowski; Steven Sloan; Anna-Sophie Fiston-Lavier; Jessica Mariani; Dmitri Petrov et al.
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Crossref
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Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome.

Cell reports methods
2023-08-28 | Journal article
Part of ISSN: 2667-2375
Contributors: HoJoon Lee; Stephanie U Greer; Dmitri S Pavlichin; Bo Zhou; Alexander E Urban; Tsachy Weissman; Hanlee P Ji
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Stanford University

The Human Pangenome’s sequence conservation reveals a landscape of polymorphic structural variations

2022-10-07 | Preprint
Contributors: HoJoon Lee; Stephanie U. Greer; Dmitri S. Pavlichin; Christopher R. Hughes; Bo Zhou; Tsachy Weissman; Hanlee P. Ji
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Crossref

DETECTION OF COMPLEX STRUCTURAL GENOME VARIANTS USING ARC-SV AND THEIR ENRICHMENT INSIDE GENES OF NEURODEVELOPMENTAL PATHWAYS

2022-10-01 | Conference paper
WOSUID:

WOS:000898874200094

Part of ISSN: 1873-7862
Part of ISSN: 0924-977X
Contributors: Hughes, Christopher; Zhou, Bo; Arthur, Joseph G.; Kim, Taeyoung; Song, Giltae; Palejev, Dean; Wong, Wing H.; Urban, Alexander E.
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Stanford University

RESOLVING THE EXACT BREAKPOINTS AND SEQUENCE REARRANGEMENTS OF LARGE NEUROPSYCHIATRIC COPY NUMBER VARIATIONS (CNVS) AT SINGLE BASE-PAIR RESOLUTION USING CRISPR-TARGETED ULTRALONG READ SEQUENCING (CTLR-SEQ)

2022-10-01 | Conference paper
WOSUID:

WOS:000886075100051

Part of ISSN: 1873-7862
Part of ISSN: 0924-977X
Contributors: Zhou, Bo; Shin, GiWon; Vervoort, Lisanne; Greer, Stephanie; Huang, Yiling; Roychowdhury, Tanmoy; Pattni, Reenal; Abyzov, Alexej; Vermeesch, Joris; Ji, Hanlee et al.
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Stanford University

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

Science (New York, N.Y.)
2022-07-29 | Journal article
Part of ISSN: 1095-9203
Contributors: Taejeong Bae; Liana Fasching; Yifan Wang; Joo Heon Shin; Milovan Suvakov; Yeongjun Jang; Scott Norton; Caroline Dias; Jessica Mariani; Alexandre Jourdon et al.
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Stanford University

Somatic mosaicism reveals clonal distributions of neocortical development

NATURE
2022-04-20 | Journal article
WOSUID:

WOS:000784115900004

Part of ISSN: 1476-4687
Part of ISSN: 0028-0836
Contributors: Breuss, Martin W.; Yang, Xiaoxu; Schlachetzki, Johannes C. M.; Antaki, Danny; Lana, Addison J.; Xu, Xin; Chung, Changuk; Chai, Guoliang; Stanley, Valentina; Song, Qiong et al.
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Stanford University

Comprehensive identification of somatic nucleotide variants in human brain tissue.

Genome biology
2021-03-29 | Journal article
WOSUID:

MEDLINE:33781308

Part of ISSN: 1474-760X
Part of ISSN: 1474-7596
Contributors: Wang, Yifan; Bae, Taejeong; Thorpe, Jeremy; Sherman, Maxwell A.; Jones, Attila G.; Cho, Sean; Daily, Kenneth; Dou, Yanmei; Ganz, Javier; Galor, Alon et al.
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Stanford University

Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia

Nature Neuroscience
2021-02 | Journal article
Contributors: Xiaowei Zhu; Bo Zhou; Reenal Pattni; Kelly Gleason; Chunfeng Tan; Agnieszka Kalinowski; Steven Sloan; Anna-Sophie Fiston-Lavier; Jessica Mariani; Dmitri Petrov et al.
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Crossref
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Complex mosaic structural variations in human fetal brains

Genome Research
2020-12-29 | Journal article
Contributors: Shobana Sekar; Livia Tomasini; Christos Proukakis; Taejeong Bae; Logan Manlove; Yeongjun Jang; Soraya Scuderi; Bo Zhou; Maria Kalyva; Anahita Amiri et al.
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Crossref
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Complete and haplotype-specific sequence assembly of segmental duplication-mediated genome rearrangements using CRISPR-targeted ultra-long read sequencing (CTLR-Seq)

2020-10-23 | Preprint
Contributors: Bo Zhou; GiWon Shin; Stephanie U. Greer; Lisanne Vervoort; Yiling Huang; Reenal Pattni; Marcus Ho; Wing H. Wong; Joris R. Vermeesch; Hanlee P. Ji et al.
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Crossref

Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing.

2020-09-01 | Conference paper
WOSUID:

WOS:000572825800109

Part of ISSN: 1557-3265
Part of ISSN: 1078-0432
Contributors: Li, Chenyu; Debruyne, David N.; Spencer, Julia; Kapoor, Vidushi; Liu, Lily Y.; Zhou, Bo; Pandey, Utsav; Bootwalla, Moiz; Ostrow, Dejerianne; Maglinte, Dennis T. et al.
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Stanford University

Genome-wide molecular effects of the neuropsychiatric 16p11 CNVs in an iPSC-to-iN neuronal model

2020-02-10 | Preprint
Contributors: Thomas R. Ward; Xianglong Zhang; Louis C. Leung; Bo Zhou; Kristin Muench; Julien G. Roth; Arineh Khechaduri; Melanie J. Plastini; Carol Charlton; Reenal Pattni et al.
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Crossref

Full-length LINE-1s with functional ORFs are favoured by host-level selection in human genomes

2020-01-09 | Preprint
Contributors: Heinrich zu Dohna; Bo Zhou; Xiaowei Zhu; Alexander E. Urban
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Crossref

COMPARATIVE FUNCTIONAL GENOMICS ANALYSES OF THE 16P11.2 DELETION AND DUPLICATION CNVS IN A HUMAN IPSC-TO-INDUCED NEURON MODEL

2019-10-01 | Conference paper
WOSUID:

WOS:000488216600128

Part of ISSN: 1873-7862
Part of ISSN: 0924-977X
Contributors: Zhang, Xianglong; Thomas, Ward; Leung, Louis; Zhou, Bo; Muench, Kristin; Plastini, Melanie; Pattni, Reenal; Ho, Steve; Ho, Marcus; Huang, Yiling et al.
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Stanford University

MACHINE LEARNING REVEALS BILATERAL DISTRIBUTION OF SOMATIC L1 INSERTIONS IN HUMAN NEURONS AND GLIA

2019-10-01 | Conference paper
WOSUID:

WOS:000488216600131

Part of ISSN: 1873-7862
Part of ISSN: 0924-977X
Contributors: Zhu, Xiaowei; Zhou, Bo; Pattni, Reenal; Gleason, Kelly; Tan, Chunfeng; Kalinowski, Agnieszka; Sloan, Steven; Fiston-Lavier, Anna-Sophie; Mariani, Jessica; Vogel, Hannes et al.
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Stanford University

SMALL-SCALE SOMATIC STRUCTURAL VARIANTS IN FETAL AND ADULT HUMAN BRAINS

2019-10-01 | Conference paper
WOSUID:

WOS:000488216600300

Part of ISSN: 1873-7862
Part of ISSN: 0924-977X
Contributors: Zhou, Bo; Arthur, Joseph; Pattni, Reenal; Zhu, Xiaowei; Wong, Wing; Urban, Alexander
Source: check_circle
Stanford University

Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia

2019-06-06 | Other
Contributors: Xiaowei Zhu; Bo Zhou; Reenal Pattni; Kelly Gleason; Chunfeng Tan; Agnieszka Kalinowski; Steven Sloan; Anna-Sophie Fiston-Lavier; Jessica Mariani; Alexej Abyzov et al.
Source: check_circle
Crossref

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

Nucleic Acids Research
2019-05-07 | Journal article
Contributors: Bo Zhou; Steve S Ho; Stephanie U Greer; Noah Spies; John M Bell; Xianglong Zhang; Xiaowei Zhu; Joseph G Arthur; Seunggyu Byeon; Reenal Pattni et al.
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Crossref
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Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA

Nature Communications
2019-03-22 | Journal article
Contributors: Ei-Wen Yang; Jae Hoon Bahn; Esther Yun-Hua Hsiao; Boon Xin Tan; Yiwei Sun; Ting Fu; Bo Zhou; Eric L. Van Nostrand; Gabriel A. Pratt; Peter Freese et al.
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Crossref
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Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA.

Nature communications
2019-03-22 | Journal article
Part of ISSN: 2041-1723
Contributors: Yang, Ei-Wen; Bahn, Jae Hoon; Hsiao, Esther Yun-Hua; Tan, Boon Xin; Sun, Yiwei; Fu, Ting; Zhou, Bo; Van Nostrand, Eric L.; Pratt, Gabriel A.; Freese, Peter et al.
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Stanford University

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

Nucleic acids research
2019-03-13 | Journal article
Part of ISSN: 1362-4962
Part of ISSN: 0305-1048
Contributors: Zhou, Bo; Ho, Steve S.; Greer, Stephanie U.; Spies, Noah; Bell, John M.; Zhang, Xianglong; Zhu, Xiaowei; Arthur, Joseph G.; Byeon, Seunggyu; Pattni, Reenal et al.
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Stanford University

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

Genome Research
2019-03-08 | Journal article
Contributors: Bo Zhou; Steve S. Ho; Stephanie U. Greer; Xiaowei Zhu; John M. Bell; Joseph G. Arthur; Noah Spies; Xianglong Zhang; Seunggyu Byeon; Reenal Pattni et al.
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Crossref
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Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562.

Genome research
2019-02-08 | Journal article
Part of ISSN: 1549-5469
Part of ISSN: 1088-9051
Contributors: Zhou, Bo; Ho, Steve S.; Greer, Stephanie U.; Zhu, Xiaowei; Bell, John M.; Arthur, Joseph G.; Spies, Noah; Zhang, Xianglong; Byeon, Seunggyu; Pattni, Reenal et al.
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Stanford University

MACHINE LEARNING ANALYSIS OF ULTRA-DEEP WHOLE-GENOME SEQUENCING IN HUMAN BRAIN REVEALS SOMATIC GENOMIC RETROTRANSPOSITION IN GLIA AS WELL AS IN NEURONS

2019-01-01 | Conference paper
WOSUID:

WOS:000477708400398

Part of ISSN: 1873-7862
Part of ISSN: 0924-977X
Contributors: Urban, Alexander; Zhu, Xiaowei; Zhou, Bo; Sloan, Steven; Pattni, Reenal; Fiston-Lavier, Anne-Sophie; Snyder, Michael; Petrov, Dmitri; Abyzov, Alexej; Vaccarino, Flora et al.
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Stanford University

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

Digital PCR
2018 | Other
Part of ISBN: 9781493977765
Part of ISSN: 1064-3745
Contributors: Bo Zhou; Michael S. Haney; Xiaowei Zhu; Reenal Pattni; Alexej Abyzov; Alexander E. Urban
Source: Self-asserted source
Bo Zhou via Crossref Metadata Search
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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 in molecular biology (Clifton, N.J.)
2018 | Journal article
Part of ISSN: 1940-6029
Contributors: Bo Zhou; Michael S Haney; Xiaowei Zhu; Reenal Pattni; Alexej Abyzov; Alexander E Urban
Source: check_circle
Stanford University

Extensive and deep sequencing of the Venter/HuRef genome for developing and benchmarking genome analysis tools

Scientific Data
2018-12-18 | Journal article
Contributors: Bo Zhou; Joseph G. Arthur; Steve S. Ho; Reenal Pattni; Yiling Huang; Wing H. Wong; Alexander E. Urban
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Crossref
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Extensive and deep sequencing of the Venter/HuRef genome for developing and benchmarking genome analysis tools.

Scientific data
2018-12-18 | Journal article
Part of ISSN: 2052-4463
Contributors: Zhou, Bo; Arthur, Joseph G.; Ho, Steve S.; Pattni, Reenal; Huang, Yiling; Wong, Wing H.; Urban, Alexander E.
Source: check_circle
Stanford University

Whole-genome sequencing analysis of CNV using low-coverage and paired-end strategies is efficient and outperforms array-based CNV analysis

Journal of Medical Genetics
2018-11-30 | Journal article
Contributors: Bo Zhou; Steve S Ho; Xianglong Zhang; Reenal Pattni; Rajini R Haraksingh; Alexander E Urban
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Crossref
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1q21.1 microduplication: large verbal-nonverbal performance discrepancy and ddPCR assays of HYDIN/HYDIN2 copy number

NPJ GENOMIC MEDICINE
2018-08-22 | Journal article
Part of ISSN: 2056-7944
Contributors: Xavier, Jean; Zhou, Bo; Bilan, Frederic; Zhang, Xianglong; Gilbert-Dussardier, Brigitte; Viaux-Savelon, Sylvie; Pattni, Reenal; Ho, Steve S.; Cohen, David; Levinson, Douglas F. et al.
Source: check_circle
Stanford University

1q21.1 microduplication: large verbal–nonverbal performance discrepancy and ddPCR assays of HYDIN/HYDIN2 copy number

npj Genomic Medicine
2018-08-22 | Journal article
Contributors: Jean Xavier; Bo Zhou; Frédéric Bilan; Xianglong Zhang; Brigitte Gilbert-Dussardier; Sylvie Viaux-Savelon; Reenal Pattni; Steve S. Ho; David Cohen; Douglas F. Levinson et al.
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Crossref

Haplotype-phased common marmoset embryonic stem cells for genome editing using CRISPR/Cas9

2018-07-30 | Other
Contributors: Bo Zhou; Steve S. Ho; Louis C. Leung; Thomas R. Ward; Marcus Ho; Melanie J. Plastini; Scott C. Vermilyea; Marina E. Emborg; Thaddeus G. Golos; Megan A. Albertelli et al.
Source: check_circle
Crossref

Whole-genome sequencing analysis of CNV using low-coverage and paired-end strategies is efficient and outperforms array-based CNV analysis.

Journal of medical genetics
2018-07-30 | Journal article
Part of ISSN: 1468-6244
Part of ISSN: 0022-2593
Contributors: Zhou, Bo; Ho, Steve S.; Zhang, Xianglong; Pattni, Reenal; Haraksingh, Rajini R.; Urban, Alexander E.
Source: check_circle
Stanford University

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

2018-07-27 | Other
Contributors: Bo Zhou; Steve S. Ho; Stephanie U. Greer; Noah Spies; John M. Bell; Xianglong Zhang; Xiaowei Zhu; Joseph G. Arthur; Seunggyu Byeon; Reenal Pattni et al.
Source: check_circle
Crossref

Extensive and deep sequencing of the Venter/HuRef genome for developing and benchmarking genome analysis tools

2018-05-09 | Other
Contributors: Bo Zhou; Joseph G. Arthur; Steve S. Ho; Reenal Pattni; Yiling Huang; Wing H. Wong; Alexander E. Urban
Source: check_circle
Crossref

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

Science
2018-02-02 | Journal article
Contributors: Taejeong Bae; Livia Tomasini; Jessica Mariani; Bo Zhou; Tanmoy Roychowdhury; Daniel Franjic; Mihovil Pletikos; Reenal Pattni; Bo-Juen Chen; Elisa Venturini et al.
Source: check_circle
Crossref

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

SCIENCE
2018-02-02 | Journal article
WOSUID:

WOS:000423795800036

Part of ISSN: 1095-9203
Part of ISSN: 0036-8075
Contributors: Bae, Taejeong; Tomasini, Livia; Mariani, Jessica; Zhou, Bo; Roychowdhury, Tanmoy; Franjic, Daniel; Pletikos, Mihovil; Pattni, Reenal; Chen, Bo-Juen; Venturini, Elisa et al.
Source: check_circle
Stanford University

Comprehensive, Integrated, and Phased Whole-Genome Analysis of the Primary ENCODE Cell Line K562

2017 | Other
Contributors: Bo Zhou; Steve S Ho; Xiaowei Zhu; Xianglong Zhang; Noah Spies; Seunggyu Byeon; Joseph G Arthur; Reenal Pattni; Noa Ben-Efraim; Michael S Haney et al.
Source: Self-asserted source
Bo Zhou via Crossref Metadata Search
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Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network

Science
2017 | Journal article
EID:

2-s2.0-85018280420

Contributors: McConnell, M.J.; Moran, J.V.; Abyzov, A.; Akbarian, S.; Bae, T.; Cortes-Ciriano, I.; Erwin, J.A.; Fasching, L.; Flasch, D.A.; Freed, D. et al.
Source: Self-asserted source
Bo Zhou via Scopus - Elsevier
grade
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One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin

Genome Research
2017 | Journal article
EID:

2-s2.0-85017546676

Contributors: Abyzov, A.; Tomasini, L.; Zhou, B.; Vasmatzis, N.; Coppola, G.; Amenduni, M.; Pattni, R.; Wilson, M.; Gerstein, M.; Weissman, S. et al.
Source: Self-asserted source
Bo Zhou via Scopus - Elsevier
grade
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Whole-genome sequencing analysis of genomic copy number variation (CNV) using low-coverage and paired-end strategies is highly efficient and outperforms array based CNV analysis

2017-11-04 | Other
Contributors: Bo Zhou; Steve S Ho; Xianglong Zhang; Reenal Pattni; Rajini R Haraksingh; Alexander E Urban
Source: Self-asserted source
Bo Zhou via Crossref Metadata Search
grade
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Detection of complex structural variation from paired-end sequencing data

2017-10-08 | Other
Contributors: Joseph G. Arthur; Xi Chen; Bo Zhou; Alexander E. Urban; Wing Hung Wong
Source: Self-asserted source
Bo Zhou via Crossref Metadata Search
grade
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The Global Regulatory Architecture of Transcription during the Caulobacter Cell Cycle

PLoS Genetics
2015 | Journal article
EID:

2-s2.0-84924366615

Contributors: Zhou, B.; Schrader, J.M.; Kalogeraki, V.S.; Abeliuk, E.; Dinh, C.B.; Pham, J.Q.; Cui, Z.Z.; Dill, D.L.; McAdams, H.H.; Shapiro, L.
Source: Self-asserted source
Bo Zhou via Scopus - Elsevier
grade
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The Coding and Noncoding Architecture of the Caulobacter crescentus Genome

PLoS Genetics
2014 | Journal article
EID:

2-s2.0-84905454831

Contributors: Schrader, J.M.; Zhou, B.; Li, G.-W.; Lasker, K.; Childers, W.S.; Williams, B.; Long, T.; Crosson, S.; McAdams, H.H.; Weissman, J.S. et al.
Source: Self-asserted source
Bo Zhou via Scopus - Elsevier
grade
Preferred source (of 2)‎
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Peer review (2 reviews for 2 publications/grants)

Review activity for Computational and Structural Biotechnology Journal (1)
Review activity for Human Genetics and Genomics advances. (1)