Terrance Shea

发表

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

Christina A. Cuomo, Q. Zeng, J. Wortman, 2014, PloS one.

Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes

James E. Allen, Mira V. Han, Matthew W. Hahn, 2014, Science.

Populations of latent Mycobacterium tuberculosis lack a cell wall: Isolation, visualization, and whole-genome characterization

B. Birren, Terrance P. Shea, A. Earl, 2016, International journal of mycobacteriology.

Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal

Thomas Abeel, Qiandong Zeng, Bruce W. Birren, 2015, PLoS medicine.

Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance

Christina A. Cuomo, R. Bhattacharyya, Terrance P. Shea, 2021, Genome Medicine.

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

A. Gnirke, C. Nusbaum, E. Lander, 2010, Proceedings of the National Academy of Sciences.

Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks

Q. Zeng, B. Birren, G. Cerqueira, 2017, Proceedings of the National Academy of Sciences.

Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance

Thomas Abeel, Abigail L Manson, Ashlee M Earl, 2016, Nature Genetics.

An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts

Eric S. Lander, Daniel Bessette, Andrew Zimmer, 2014, PloS one.

Diversity, multifaceted evolution, and facultative saprotrophism in the European Batrachochytrium salamandrivorans epidemic

Christina A. Cuomo, Terrance P. Shea, C. Cuomo, 2021, Nature Communications.

A New Lineage of Cryptococcus gattii (VGV) Discovered in the Central Zambezian Miombo Woodlands

Christina A. Cuomo, Michael J. Davis, Rhys A. Farrer, 2019, mBio.

Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase

J. Pritchard, J. Diedrich, J. Yates, 2019, Cell.

Comparative Genome Analysis of Trichophyton rubrum and Related Dermatophytes Reveals Candidate Genes Involved in Infection

Christina A. Cuomo, T. C. White, David I Heiman, 2012, mBio.

Comparative genomics and prediction of conditionally dispensable sequences in legume–infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors

James K. Hane, Terrance P. Shea, Sarwar Azam, 2016, BMC Genomics.

Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection

Huldrych F. Günthard, Michael C. Zody, Qiandong Zeng, 2012, PLoS pathogens.

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

A. Gnirke, C. Nusbaum, S. Ranade, 2009, Genome Biology.

Transmission of human-associated microbiota along family and social networks

Katherine H. Huang, D. Gevers, Terrance P. Shea, 2019, Nature Microbiology.

Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction

W. Bishai, Terrance P. Shea, A. Earl, 2016, PLoS neglected tropical diseases.

Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome

Vivek Krishnakumar, Michalis Hadjithomas, Cédric Feschotte, 2016, eLife.

RNAi is a critical determinant of centromere evolution in closely related fungi

Christina A. Cuomo, J. Heitman, Terrance P. Shea, 2018, Proceedings of the National Academy of Sciences.

Paired-end sequencing of Fosmid libraries by Illumina

A. Gnirke, C. Nusbaum, D. Tabbaa, 2012, Genome research.

The genome of opportunistic fungal pathogen Fusarium oxysporum carries a unique set of lineage-specific chromosomes

Dilay Hazal Ayhan, Q. Zeng, D. Schwartz, 2020, Communications Biology.

Genome Sequence of Lichtheimia ornata, an Emerging Opportunistic Mucorales Pathogen

A. Gnirke, J. Stajich, J. Livny, 2023, Microbiology resource announcements.

Comparative Genomics of Recent Shiga Toxin-Producing Escherichia coli O104:H4: Short-Term Evolution of an Emerging Pathogen

Allison D. Griggs, B. Haas, Q. Zeng, 2013, mBio.

Clade-specific chromosomal rearrangements and loss of subtelomeric adhesins in Candida auris

Christina A. Cuomo, Terrance P. Shea, C. Cuomo, 2021, Genetics.

Chromosomal rearrangements and loss of subtelomeric adhesins linked to clade-specific phenotypes in Candida auris

Christina A. Cuomo, Terrance P. Shea, C. Cuomo, 2019, bioRxiv.

Genome Sequence of Fusarium oxysporum f. sp. melonis Strain NRRL 26406, a Fungus Causing Wilt Disease on Melon

Q. Zeng, Terrance P. Shea, S. Young, 2014, Genome Announcements.

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning

Katherine H. Huang, Eric J Alm, Brian Cleary, 2015, Nature Biotechnology.

Complete Genome Sequences for Two Talaromyces marneffei Clinical Isolates from Northern and Southern Vietnam

P. Ashton, J. Perfect, Terrance P. Shea, 2020, Microbiology Resource Announcements.

Finished bacterial genomes from shotgun sequence data

C. Nusbaum, Shuangye Yin, Ted Sharpe, 2012, Genome research.

Chromosome-Level Genome Assembly of a Human Fungal Pathogen Reveals Synteny among Geographically Distinct Species

Terrance P. Shea, T. Michael, W. Goldman, 2021, bioRxiv.

Obligate sexual reproduction of a homothallic fungus closely related to the Cryptococcus pathogenic species complex

Christina A. Cuomo, J. Heitman, Terrance P. Shea, 2022, bioRxiv.

Whole-Genome Analysis Illustrates Global Clonal Population Structure of the Ubiquitous Dermatophyte Pathogen Trichophyton rubrum

Christina A. Cuomo, T. C. White, G. F. Persinoti, 2018, Genetics.

A new lineage of Cryptococcus gattii (VGV) discovered in the 1 Central Zambezi Miombo Woodlands 2

Christina A. Cuomo, Michael J. Davis, Rhys A. Farrer, 2019 .

Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance

R. Bhattacharyya, C. Worby, A. Earl, 2022, Genome Medicine.

Evolution of extensively drug-resistant tuberculosis over four decades revealed by whole genome sequencing of Mycobacterium tuberculosis from KwaZulu-Natal, South Africa

Q. Zeng, B. Birren, A. McGuire, 2015 .

Comparative genomics and prediction of conditionally dispensable sequences in legume–infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors

James K. Hane, Terrance P. Shea, Sarwar Azam, 2016, BMC Genomics.

Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance

B. Birren, J. Wortman, A. Earl, 2016, Nature Genetics.

Comparative genomics of the closely related fungal genera Cryptococcus and Kwoniella reveals karyotype dynamics and suggests evolutionary mechanisms of pathogenesis

Christina A. Cuomo, M. Nowrousian, Sheng Sun, 2024, PLoS biology.

Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase

Christina A. Cuomo, J. Pritchard, J. Diedrich, 2020, Cell.

Genome Sequence of Spizellomyces punctatus

Christina A. Cuomo, Q. Zeng, Zehua Chen, 2016, Genome Announcements.

Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany

Allison D. Griggs, B. Haas, B. Birren, 2012, Proceedings of the National Academy of Sciences.

Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase

Christina A. Cuomo, J. Pritchard, J. Diedrich, 2017, Cell.