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T. Abeel · SciRah

Researcher profile · Semantic Scholar

T. Abeel

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T. Abeel — researcher profile on SciRah

h-index: 35
Works: 123
Citations: 14K

Most-cited papers

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
Bruce J. Walker, T. Abeel, T. Shea, M. Priest +7 more
2014PLoS ONE8,356 citations Open access
Semantic Scholar
The Mycobacterium tuberculosis regulatory network and hypoxia
J. Galagan, K. Minch, Matthew Peterson, A. Lyubetskaya +41 more
2013Nature430 citations Open access
Semantic Scholar
Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal
K. Cohen, T. Abeel, Abigail Manson Mcguire, Christopher A. Desjardins +29 more
2015PLoS Medicine274 citations Open access
Semantic Scholar
ANGUSTIFOLIA3 Binds to SWI/SNF Chromatin Remodeling Complexes to Regulate Transcription during Arabidopsis Leaf Development[W]
L. Vercruyssen, Aurine Verkest, Nathalie Gonzalez, Ken S. Heyndrickx +20 more
2014The Plant Cell212 citations Open access
Semantic Scholar
ORCAE: online resource for community annotation of eukaryotes
L. Sterck, K. Billiau, T. Abeel, P. Rouzé +1 more
2012Nature Methods203 citations
Semantic Scholar
Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance
Christopher A. Desjardins, K. Cohen, Vanisha Munsamy, T. Abeel +14 more
2016Nature Genetics165 citations Open access
Semantic Scholar
GenomeView: a next-generation genome browser
T. Abeel, T. van Parys, Y. Saeys, J. Galagan +1 more
2011Nucleic Acids Research153 citations Open access
Semantic Scholar
Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges
K. Cohen, Abigail L. Manson, Christopher A. Desjardins, T. Abeel +1 more
2019Genome Medicine143 citations Open access
Semantic Scholar
Evolution of Invasion in a Diverse Set of Fusobacterium Species
Abigail Manson Mcguire, Kyla Cochrane, A. Griggs, B. Haas +8 more
2014mBio122 citations Open access
Semantic Scholar
Free-floating extracellular DNA: Systematic profiling of mobile genetic elements and antibiotic resistance from wastewater.
D. Calderón-Franco, M. van Loosdrecht, T. Abeel, D. Weissbrodt
2020Water Research113 citations Open access
Semantic Scholar
Nanopore sequencing enables near-complete de novo assembly of Saccharomyces cerevisiae reference strain CEN.PK113-7D
Alex N. Salazar, Arthur R. Gorter de Vries, M. A. van den Broek, M. Wijsman +5 more
2017bioRxiv105 citations Open access
Semantic Scholar
StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities
Lucas R. van Dijk, Bruce J. Walker, T. J. Straub, C. Worby +8 more
2021Genome Biology102 citations Open access
Semantic Scholar
Computational Methods for Strain-Level Microbial Detection in Colony and Metagenome Sequencing Data
Christine Anyansi, T. J. Straub, Abigail L. Manson, A. Earl +1 more
2020Frontiers in Microbiology102 citations Open access
Semantic Scholar
Comparative analysis of mycobacterium and related actinomycetes yields insight into the evolution of mycobacterium tuberculosis pathogenesis
A. McGuire, B. Weiner, S. T. Park, I. Wapinski +17 more
2012BMC Genomics96 citations Open access
Semantic Scholar
Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice
Gregory P. Donaldson, Wen-Chi Chou, Abigail L. Manson, P. Rogov +9 more
2020Nature Microbiology85 citations Open access
Semantic Scholar
Metagenomic profiling and transfer dynamics of antibiotic resistance determinants in a full-scale granular sludge wastewater treatment plant
D. Calderón-Franco, Roel Sarelse, Stella Christou, M. Pronk +3 more
2022bioRxiv72 citations Open access
Semantic Scholar
Mycobacterium tuberculosis Whole Genome Sequences From Southern India Suggest Novel Resistance Mechanisms and the Need for Region-Specific Diagnostics
Abigail L. Manson, T. Abeel, J. Galagan, J. C. Sundaramurthi +7 more
2017Clinical Infectious Diseases68 citations Open access
Semantic Scholar
Metagenomic-based surveillance systems for antibiotic resistance in non-clinical settings
Stephanie Pillay, D. Calderón-Franco, Aysun Urhan, T. Abeel
2022Frontiers in Microbiology64 citations Open access
Semantic Scholar
Whole-Genome Sequencing of Mycobacterium tuberculosis Provides Insight into the Evolution and Genetic Composition of Drug-Resistant Tuberculosis in Belarus
K. Wollenberg, Christopher A. Desjardins, A. Zalutskaya, Vervara Slodovnikova +12 more
2016Journal of Clinical Microbiology60 citations Open access
Semantic Scholar
Nucleus-specific expression in the multinuclear mushroom-forming fungus Agaricus bisporus reveals different nuclear regulatory programs
T. Gehrmann, J. Pelkmans, R. Ohm, A. M. Vos +5 more
2017Proceedings of the National Academy of Sciences of the United States of America59 citations Open access
Semantic Scholar
Simulated Design–Build–Test–Learn Cycles for Consistent Comparison of Machine Learning Methods in Metabolic Engineering
Paul van Lent, Joep Schmitz, T. Abeel
2023ACS Synthetic Biology51 citations Open access
Semantic Scholar
Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization
Alex N. Salazar, Arthur R. Gorter de Vries, M. A. van den Broek, N. Brouwers +4 more
2019BMC Genomics49 citations Open access
Semantic Scholar
Laboratory Evolution of a Saccharomyces cerevisiae × S. eubayanus Hybrid Under Simulated Lager-Brewing Conditions
Arthur R. Gorter de Vries, Maaike A. Voskamp, Aafke C. A. van Aalst, L. Kristensen +7 more
2019Frontiers in Genetics43 citations Open access
Semantic Scholar
Global diversity of enterococci and description of 18 previously unknown species
Julia A. Schwartzman, François Lebreton, Rauf Salamzade, Terrance Shea +17 more
2024Proceedings of the National Academy of Sciences of the United States of America40 citations Open access
Semantic Scholar
Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction
K. Winglee, Abigail Manson Mcguire, M. Maiga, T. Abeel +8 more
2016PLoS Neglected Tropical Diseases39 citations Open access
Semantic Scholar
Fatal Nosocomial MDR TB Identified through Routine Genetic Analysis and Whole-Genome Sequencing
O. M. Williams, T. Abeel, N. Casali, K. Cohen +7 more
2015Emerging Infectious Diseases38 citations Open access
Semantic Scholar
A Generic Tool for Transcription Factor Target Gene Discovery in Arabidopsis Cell Suspension Cultures Based on Tandem Chromatin Affinity Purification1[W][OPEN]
Aurine Verkest, T. Abeel, Ken S. Heyndrickx, J. Van Leene +9 more
2014Plant Physiology34 citations Open access
Semantic Scholar
QuantTB – a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data
Christine Anyansi, A. Keo, Bruce J. Walker, T. J. Straub +3 more
2019BMC Genomics33 citations Open access
Semantic Scholar
Explainable artificial intelligence in forensics: Realistic explanations for number of contributor predictions of DNA profiles.
Marthe S. Veldhuis, S. Ariëns, R. Ypma, T. Abeel +1 more
2021Forensic Science International: Genetics31 citations Open access
Semantic Scholar
Populations of latent Mycobacterium tuberculosis lack a cell wall: Isolation, visualization, and whole-genome characterization
A. Velayati, T. Abeel, T. Shea, G. Zhavnerko +5 more
2015International Journal of Mycobacteriology29 citations Open access
Semantic Scholar
Extensive global movement of multidrug-resistant M. tuberculosis strains revealed by whole-genome analysis
K. Cohen, Abigail L. Manson, T. Abeel, Christopher A. Desjardins +4 more
2019Thorax28 citations Open access
Semantic Scholar
Emergence of novel SARS-CoV-2 variants in the Netherlands
Aysun Urhan, T. Abeel
2020Scientific Reports26 citations Open access
Semantic Scholar
Soft Skills: An Important Asset Acquired from Organizing Regional Student Group Activities
J. de Ridder, P. Meysman, O. Oluwagbemi, T. Abeel
2014PLoS Comput. Biol.26 citations Open access
Semantic Scholar
Schizophyllum commune has an extensive and functional alternative splicing repertoire
Thies Gehrmann, J. Pelkmans, L. Lugones, H. Wösten +2 more
2016Scientific Reports24 citations Open access
Semantic Scholar
An educational guide for nanopore sequencing in the classroom
Alex N. Salazar, Franklin L. Nobrega, Christine Anyansi, Cristian Aparicio-Maldonado +8 more
2020PLoS Comput. Biol.23 citations Open access
Semantic Scholar
Patterns of Conservation and Diversification in the Fungal Polarization Network
Eveline T. Diepeveen, Valérie Pourquié, Thies Gehrmann, T. Abeel +1 more
2017bioRxiv22 citations Open access
Semantic Scholar
Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction
Antonio L. C. Gomes, T. Abeel, Matthew Peterson, E. Azizi +3 more
2014Genome Research22 citations Open access
Semantic Scholar
Semantically linking molecular entities in literature through entity relationships
S. Van Landeghem, Jari Björne, T. Abeel, B. De Baets +2 more
2012BMC Bioinformatics20 citations Open access
Semantic Scholar
SynerClust: a highly scalable, synteny-aware orthologue clustering tool
Christophe Georgescu, Abigail L. Manson, Alexander D. Griggs, Christopher A. Desjardins +5 more
2018Microbial Genomics18 citations Open access
Semantic Scholar
The Regional Student Group Program of the ISCB Student Council: Stories from the Road
Geoff MacIntyre, M. Michaut, T. Abeel
2013PLoS Comput. Biol.16 citations Open access
Semantic Scholar
Identification of novel HLA-E-binding Mtb-derived epitopes through improved prediction models
Paula Ruibal, K. Franken, K. V. van Meijgaarden, Marjolein van Wolfswinkel +13 more
2022Journal of Immunology14 citations Open access
Semantic Scholar
A comparative study of pan-genome methods for microbial organisms: Acinetobacter baumannii pan-genome reveals structural variation in antimicrobial resistance-carrying plasmids
Aysun Urhan, T. Abeel
2021Microbial Genomics14 citations Open access
Semantic Scholar
The Upside of Failure: How Regional Student Groups Learn from Their Mistakes
Tarun Mishra, R. G. Parra, T. Abeel
2014PLoS Comput. Biol.14 citations Open access
Semantic Scholar
Highlights from the Eighth International Society for Computational Biology (ISCB) Student Council Symposium 2012
A. Goncearenco, P. Grynberg, O. Botvinnik, Geoff MacIntyre +1 more
2012BMC Bioinformatics14 citations Open access
Semantic Scholar
Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing
D. Calderón-Franco, M. van Loosdrecht, T. Abeel, D. Weissbrodt
2023Antonie van Leeuwenhoek13 citations Open access
Semantic Scholar
Evolution of extensively drug-resistant tuberculosis over four decades revealed by whole genome sequencing of Mycobacterium tuberculosis from KwaZulu-Natal, South Africa
K. Cohen, T. Abeel, A. McGuire, Christopher A. Desjardins +29 more
2015International Journal of Mycobacteriology13 citations Open access
Semantic Scholar
ISCB Computational Biology Wikipedia Competition
A. Bateman, J. Kelso, D. Mietchen, Geoff MacIntyre +5 more
2013PLoS Comput. Biol.12 citations Open access
Semantic Scholar
Genomes of four Streptomyces strains reveal insights into putative new species and pathogenicity of scab-causing organisms
L. Henao, Ramin Shirali Hossein Zade, S. Restrepo, J. Husserl +1 more
2023BMC Genomics10 citations Open access
Semantic Scholar
Global diversity of enterococci and description of 18 novel species
Julia A. Schwartzman, F. Lebreton, Rauf Salamzade, Melissa J. Martin +15 more
2023bioRxiv10 citations Open access
Semantic Scholar
A novel method to isolate free-floating extracellular DNA from wastewater for quantitation and metagenomic profiling of mobile genetic elements and antibiotic resistance genes
D. Calderón-Franco, M. van Loosdrecht, T. Abeel, D. Weissbrodt
2020bioRxiv10 citations Open access
Semantic Scholar

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