Publications

For a full list see below or go to Google Scholar

Highlights

Full publications list

2023

Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee
D Turner, AN Shkoporov, C Lood, AD Millard, BE Dutilh, P Alfenas-Zerbini, LJ van Zyl, RK Aziz, HM Oksanen, MM Poranen, AM Kropinski, J Barylski, JR Brister, N Chanisvili, RA Edwards, F Enault, A Gillis, P Knezevic, M Krupovic, I Kurtböke, A Kushkina, R Lavigne, S Lehman, M Lobocka, C Moraru, A Moreno Switt, V Morozova, J Nakavuma, A Reyes Muñoz, J Rūmnieks, B Sarkar, MB Sullivan, J Uchiyama, J Wittmann, T Yigang, EM Adriaenssens
Archives of Virology 168(2), 74 (2023)

Four principles to establish a universal virus taxonomy
P Simmonds, EM Adriaenssens, FM Zerbini, NGA Abrescia, P Aiewsakun, P Alfenas-Zerbini, Y Bao, J Barylski, C Drosten, S Duffy, WP Duprex, BE Dutilh, SF Elena, ML García, S Junglen, A Katzourakis, EV Koonin, M Krupovic, JH Kuhn, AJ Lambert, EJ Lefkowitz, M Łobocka, C Lood, J Mahony, JP Meier-Kolthoff, AR Mushegian, HM Oksanen, MM Poranen, A Reyes-Muñoz, DL Robertson, S Roux, L Rubino, S Sabanadzovic, S Siddell, T Skern, DB Smith, MB Sullivan, N Suzuki, D Turner, KV Doorslaer, A Vandamme, A Varsani, N Vasilakis
PLOS Biology 21(2), e3001922 (2023)

Rational Design of Profile HMMs for Sensitive and Specific Sequence Detection with Case Studies Applied to Viruses, Bacteriophages, and Casposons
LS Oliveira, A Reyes, BE Dutilh, A Gruber
Viruses 15(2), 519 (2023)

Bacteriophages playing nice: Lysogenic bacteriophage replication stable in the human gut microbiota
SG Sutcliffe, A Reyes, CF Maurice
iScience 26(2) (2023)

Genomic and Evolutionary Features of Nine AHPND Positive Vibrio parahaemolyticus Strains Isolated from South American Shrimp Farms
A Castellanos, L Restrepo, L Bajaña, I Betancourt, B Bayot, A Reyes
Microbiology Spectrum 11(4), e04851–22 (2023)

Comparative Genomics Identifies Conserved and Variable TAL Effectors in African Strains of the Cotton Pathogen Xanthomonas citri pv. malvacearum
AL Pérez-Quintero, LM Rodriguez-R, S Cuesta-Morrondo, E Hakalová, D Betancurt-Anzola, LCC Valera, LAC Cardenas, L Matiz-Céron, JM Jacobs, V Roman-Reyna, AR Muñoz, AJB Giraldo, R Koebnik
Phytopathology® 113(8), 1387–1393 (2023)

VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models
G Rangel-Pineros, A Almeida, M Beracochea, E Sakharova, M Marz, AR Muñoz, M Hölzer, RD Finn
PLOS Computational Biology 19(8), e1011422 (2023)

Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification
EM Adriaenssens, S Roux, JR Brister, I Karsch-Mizrachi, JH Kuhn, A Varsani, T Yigang, A Reyes, C Lood, EJ Lefkowitz, MB Sullivan, RA Edwards, P Simmonds, L Rubino, S Sabanadzovic, M Krupovic, BE Dutilh
Nature Biotechnology 41(7), 898–902 (2023)

Conserved, yet disruption-prone, gut microbiomes in neotropical bumblebees
N Villabona, N Moran, T Hammer, A Reyes
mSphere 8(6), e00139–23 (2023)

2022

Comparing novel shotgun DNA sequencing and state-of-the-art proteomics approaches for authentication of fish species in mixed samples
MS Varunjikar, C Moreno-Ibarguen, JS Andrade-Martinez, H Tung, I Belghit, M Palmblad, PA Olsvik, A Reyes, JD Rasinger, KK Lie
Food Control 131, 108417 (2022)

The gut microbiota of chickens in a commercial farm treated with a Salmonella phage cocktail
V Clavijo, T Morales, MJ Vives-Flores, A Reyes Muñoz
Scientific Reports 12(1), 991 (2022)

Taxonomical Evaluation of Plant Chloroplastic Markers by Bayesian Classifier
L Matiz-Ceron, A Reyes, J Anzola
Frontiers in Plant Science 12 (2022)

Functional and Phylogenetic Characterization of Bacteria in Bovine Rumen Using Fractionation of Ruminal Fluid
R Hernández, M Chaib De Mares, H Jimenez, A Reyes, A Caro-Quintero
Frontiers in Microbiology 13 (2022)

Analysis and exploration of microbial traits in a wet coffee fermentation experiment using MGnify
A Peña González, A Reyes Muñoz
F1000Research 11(401), 401 (2022)

Computational Tools for the Analysis of Uncultivated Phage Genomes
JS Andrade-Martínez, LC Camelo Valera, LA Chica Cárdenas, L Forero-Junco, G López-Leal, JL Moreno-Gallego, G Rangel-Pineros, A Reyes
Microbiology and Molecular Biology Reviews 86(2), e00004–21 (2022)

Mining of Thousands of Prokaryotic Genomes Reveals High Abundance of Prophages with a Strictly Narrow Host Range
G López-Leal, LC Camelo-Valera, JM Hurtado-Ramírez, J Verleyen, S Castillo-Ramírez, A Reyes-Muñoz
mSystems 7(4), e00326–22 (2022)

2021

Bacterial meta-analysis of chicken cecal microbiota
LAC Cardenas, V Clavijo, M Vives, A Reyes
PeerJ 9, e10571 (2021)

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research
F Hufsky, K Lamkiewicz, A Almeida, A Aouacheria, C Arighi, A Bateman, J Baumbach, N Beerenwinkel, C Brandt, M Cacciabue, S Chuguransky, O Drechsel, RD Finn, A Fritz, S Fuchs, G Hattab, A Hauschild, D Heider, M Hoffmann, M Hölzer, S Hoops, L Kaderali, I Kalvari, M von Kleist, R Kmiecinski, D Kühnert, G Lasso, P Libin, M List, HF Löchel, MJ Martin, R Martin, J Matschinske, AC McHardy, P Mendes, J Mistry, V Navratil, EP Nawrocki, ÁN O’Toole, N Ontiveros-Palacios, AI Petrov, G Rangel-Pineros, N Redaschi, S Reimering, K Reinert, A Reyes, L Richardson, DL Robertson, S Sadegh, JB Singer, K Theys, C Upton, M Welzel, L Williams, M Marz
Briefings in Bioinformatics 22(2), 642–663 (2021)

Genome Sequence and Characterization of Lactobacillus casei Phage, vB_LcaM_Lbab1 Isolated from Raw Milk
V Gradaschi, F Payaslian, ME Dieterle, L Rondón Salazar, E Urdániz, M Di Paola, J Peña Cárcamo, F Zon, M Allievi, E Sosa, D Fernandez Do Porto, M Dunne, P Goeller, J Klumpp, RR Raya, A Reyes, M Piuri
PHAGE 2(1), 57–63 (2021)

Tightening Bonds in Latin America Through Phage Discovery
F Payaslian, V Gradaschi, L Rondón Salazar, ME Dieterle, E Urdániz, M Di Paola, F Zon, M Allievi, C Sanchez Rivas, RR Raya, A Reyes, M Piuri
PHAGE 2(1), 7–10 (2021)

Isolation and Characterization of vB_MsmS_Celfi: A New Mycobacterium tuberculosis Bacteriophage
F Payaslian, V Gradaschi, L Rondón Salazar, ME Dieterle, E Urdániz, M Di Paola, J Peña Cárcamo, F Zon, E Sosa, D Fernandez Do Porto, M Dunne, P Goeller, J Klumpp, RR Raya, A Reyes, M Piuri
PHAGE 2(1), 43–49 (2021)

Monitoring the variation in the gut microbiota of captive woolly monkeys related to changes in diet during a reintroduction process
C Quiroga-González, LAC Cardenas, M Ramírez, A Reyes, C González, PR Stevenson
Scientific Reports 11(1), 6522 (2021)

A novel vieuvirus from multidrug-resistant Acinetobacter baumannii
G López-Leal, A Reyes-Muñoz, RI Santamaria, MA Cevallos, C Pérez-Monter, S Castillo-Ramírez
Archives of Virology 166(5), 1401–1408 (2021)

Discovery of new potential CDK2/VEGFR2 type II inhibitors by fragmentation and virtual screening of natural products
AF Vásquez, A Reyes Muñoz, J Duitama, A González Barrios
Journal of Biomolecular Structure and Dynamics 39(9), 3285–3299 (2021)

Informative Regions In Viral Genomes
JL Moreno-Gallego, A Reyes
Viruses 13(6), 1164 (2021)

Disentangling the Complexity of the Rumen Microbial Diversity Through Fractionation Using a Sucrose Density Gradient
R Hernández, H Jimenez, C Vargas-Garcia, A Caro-Quintero, A Reyes
Frontiers in Microbiology 12 (2021)

Challenges and Considerations for Delivering Bioinformatics Training in LMICs: Perspectives From Pan-African and Latin American Bioinformatics Networks
V Ras, P Carvajal-López, P Gopalasingam, A Matimba, PA Chauke, N Mulder, F Guerfali, VD Del Angel, A Reyes, G Oliveira, J De Las Rivas, M Cristancho
Frontiers in Education 6 (2021)

Non-Extensive Fragmentation of Natural Products and Pharmacophore-Based Virtual Screening as a Practical Approach to Identify Novel Promising Chemical Scaffolds
AF Vásquez, A Reyes Muñoz, J Duitama, A González Barrios
Frontiers in Chemistry 9 (2021)

Practical metagenomics: The Study of human gut microbiome in health and disease: Applications in Acute Diarrheal Diseases (ADD)
A Peña González, A Reyes Muñoz, A Madrigal Leiva
F1000Research 10(861), 861 (2021)

Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: update of taxonomy changes in 2021
M Krupovic, D Turner, V Morozova, M Dyall-Smith, HM Oksanen, R Edwards, BE Dutilh, SM Lehman, A Reyes, DP Baquero, MB Sullivan, J Uchiyama, J Nakavuma, J Barylski, MJ Young, S Du, P Alfenas-Zerbini, A Kushkina, AM Kropinski, I Kurtböke, JR Brister, C Lood, BL Sarkar, T Yigang, Y Liu, L Huang, J Wittmann, N Chanishvili, LJ van Zyl, J Rumnieks, T Mochizuki, M Jalasvuori, RK Aziz, M Łobocka, KM Stedman, AN Shkoporov, A Gillis, X Peng, F Enault, P Knezevic, R Lavigne, S Rhee, V Cvirkaite-Krupovic, C Moraru, AI Moreno Switt, MM Poranen, A Millard, D Prangishvili, EM Adriaenssens
Archives of Virology 166(11), 3239–3244 (2021)

A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans
DA Ayala-Usma, M Cárdenas, R Guyot, MCD Mares, A Bernal, AR Muñoz, S Restrepo
BMC Genomics 22(1), 795 (2021)

Microbial community characterization of shrimp survivors to AHPND challenge test treated with an effective shrimp probiotic (Vibrio diabolicus)
L Restrepo, C Domínguez-Borbor, L Bajaña, I Betancourt, J Rodríguez, B Bayot, A Reyes
Microbiome 9(1), 88 (2021)

Perspective on taxonomic classification of uncultivated viruses
BE Dutilh, A Varsani, Y Tong, P Simmonds, S Sabanadzovic, L Rubino, S Roux, AR Muñoz, C Lood, EJ Lefkowitz, JH Kuhn, M Krupovic, RA Edwards, JR Brister, EM Adriaenssens, MB Sullivan
Current Opinion in Virology 51, 207–215 (2021)

From Trees to Clouds: PhageClouds for Fast Comparison of ∼640,000 Phage Genomic Sequences and Host-Centric Visualization Using Genomic Network Graphs
G Rangel-Pineros, A Millard, S Michniewski, D Scanlan, K Sirén, A Reyes, B Petersen, MR Clokie, T Sicheritz-Pontén
PHAGE 2(4), 194–203 (2021)

Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries
B Moore, P Carvajal-López, PA Chauke, M Cristancho, VDD Angel, SL Fernandez-Valverde, A Ghouila, P Gopalasingam, FZ Guerfali, A Matimba, SL Morgan, G Oliveira, V Ras, A Reyes, JDL Rivas, N Mulder
PLOS Computational Biology 17(8), e1009218 (2021)

2020

International consensus definition of low anterior resection syndrome
C Keane, NS Fearnhead, L Bordeianou, P Christensen, E Espin Basany, S Laurberg, A Mellgren, C Messick, GR Orangio, A Verjee, K Wing, I Bissett, tLIC Group
Colorectal Disease 22(3), 331–341 (2020)

Fine Resolution Analysis of Microbial Communities Provides Insights Into the Variability of Cocoa Bean Fermentation
ME Pacheco-Montealegre, LL Dávila-Mora, LM Botero-Rute, A Reyes, A Caro-Quintero
Frontiers in Microbiology 11 (2020)

Genome-Scale Metabolic Model of Xanthomonas phaseoli pv. manihotis: An Approach to Elucidate Pathogenicity at the Metabolic Level
D Botero, J Monk, MJ Rodríguez Cubillos, A Rodríguez Cubillos, M Restrepo, V Bernal-Galeano, A Reyes, A González Barrios, BØ Palsson, S Restrepo, A Bernal
Frontiers in Genetics 11 (2020)

Paving the Way to Unveil the Diversity and Evolution of Phage Genomes
A Reyes, MJ Vives
Viruses 12(9), 905 (2020)

Diet Quality, Food Groups and Nutrients Associated with the Gut Microbiota in a Nonwestern Population
ÁS García-Vega, V Corrales-Agudelo, A Reyes, JS Escobar
Nutrients 12(10), 2938 (2020)

Essentials in metagenomics (Part I)
A Peña González, A Reyes Muñoz
F1000Research 9(1194), 1194 (2020)

Essentials in Metagenomics (Part II)
A Peña González, A Reyes Muñoz
F1000Research 9(1195), 1195 (2020)

2019

Minimum Information about an Uncultivated Virus Genome (MIUViG)
S Roux, EM Adriaenssens, BE Dutilh, EV Koonin, AM Kropinski, M Krupovic, JH Kuhn, R Lavigne, JR Brister, A Varsani, C Amid, RK Aziz, SR Bordenstein, P Bork, M Breitbart, GR Cochrane, RA Daly, C Desnues, MB Duhaime, JB Emerson, F Enault, JA Fuhrman, P Hingamp, P Hugenholtz, BL Hurwitz, NN Ivanova, JM Labonté, K Lee, RR Malmstrom, M Martinez-Garcia, IK Mizrachi, H Ogata, D Páez-Espino, M Petit, C Putonti, T Rattei, A Reyes, F Rodriguez-Valera, K Rosario, L Schriml, F Schulz, GF Steward, MB Sullivan, S Sunagawa, CA Suttle, B Temperton, SG Tringe, RV Thurber, NS Webster, KL Whiteson, SW Wilhelm, KE Wommack, T Woyke, KC Wrighton, P Yilmaz, T Yoshida, MJ Young, N Yutin, LZ Allen, NC Kyrpides, EA Eloe-Fadrosh
Nature Biotechnology 37(1), 29–37 (2019)

Toward unrestricted use of public genomic data
RI Amann, S Baichoo, BJ Blencowe, P Bork, M Borodovsky, C Brooksbank, PSG Chain, RR Colwell, DG Daffonchio, A Danchin, V de Lorenzo, PC Dorrestein, RD Finn, CM Fraser, JA Gilbert, SJ Hallam, P Hugenholtz, JPA Ioannidis, JK Jansson, JF Kim, H Klenk, MG Klotz, R Knight, KT Konstantinidis, NC Kyrpides, CE Mason, AC McHardy, F Meyer, CA Ouzounis, AAN Patrinos, M Podar, KS Pollard, J Ravel, AR Muñoz, RJ Roberts, R Rosselló-Móra, S Sansone, PD Schloss, LM Schriml, JC Setubal, R Sorek, RL Stevens, JM Tiedje, A Turjanski, GW Tyson, DW Ussery, GM Weinstock, O White, WB Whitman, I Xenarios
Science 363(6425), 350–352 (2019)

Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins
JL Moreno-Gallego, S Chou, SCD Rienzi, JK Goodrich, TD Spector, JT Bell, ND Youngblut, I Hewson, A Reyes, RE Ley
Cell Host \& Microbe 25(2), 261–272.e5 (2019)

Defining a Core Genome for the Herpesvirales and Exploring their Evolutionary Relationship with the Caudovirales
JS Andrade-Martínez, JL Moreno-Gallego, A Reyes
Scientific Reports 9(1), 11342 (2019)

Bogotá River anthropogenic contamination alters microbial communities and promotes spread of antibiotic resistance genes
CE Posada-Perlaza, A Ramírez-Rojas, P Porras, B Adu-Oppong, A Botero-Coy, F Hernández, JM Anzola, L Díaz, G Dantas, A Reyes, MM Zambrano
Scientific Reports 9(1), 11764 (2019)

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
RA Edwards, AA Vega, HM Norman, M Ohaeri, K Levi, EA Dinsdale, O Cinek, RK Aziz, K McNair, JJ Barr, K Bibby, SJJ Brouns, A Cazares, PA de Jonge, C Desnues, SL Díaz Muñoz, PC Fineran, A Kurilshikov, R Lavigne, K Mazankova, DT McCarthy, FL Nobrega, A Reyes Muñoz, G Tapia, N Trefault, AV Tyakht, P Vinuesa, J Wagemans, A Zhernakova, FM Aarestrup, G Ahmadov, A Alassaf, J Anton, A Asangba, EK Billings, VA Cantu, JM Carlton, D Cazares, G Cho, T Condeff, P Cortés, M Cranfield, DA Cuevas, R De la Iglesia, P Decewicz, MP Doane, NJ Dominy, L Dziewit, BM Elwasila, AM Eren, C Franz, J Fu, C Garcia-Aljaro, E Ghedin, KM Gulino, JM Haggerty, SR Head, RS Hendriksen, C Hill, H Hyöty, EN Ilina, MT Irwin, TC Jeffries, J Jofre, RE Junge, ST Kelley, M Khan Mirzaei, M Kowalewski, D Kumaresan, SR Leigh, D Lipson, ES Lisitsyna, M Llagostera, JM Maritz, LC Marr, A McCann, S Molshanski-Mor, S Monteiro, B Moreira-Grez, M Morris, L Mugisha, M Muniesa, H Neve, N Nguyen, OD Nigro, AS Nilsson, T O’Connell, R Odeh, A Oliver, M Piuri, AJ Prussin II, U Qimron, Z Quan, P Rainetova, A Ramírez-Rojas, R Raya, K Reasor, GAO Rice, A Rossi, R Santos, J Shimashita, EN Stachler, LC Stene, R Strain, R Stumpf, PJ Torres, A Twaddle, M Ugochi Ibekwe, N Villagra, S Wandro, B White, A Whiteley, KL Whiteson, C Wijmenga, MM Zambrano, H Zschach, BE Dutilh
Nature Microbiology 4(10), 1727–1736 (2019)

Computational search for UV radiation resistance strategies in Deinococcus swuensis isolated from Paramo ecosystems
J Díaz-Riaño, L Posada, IC Acosta, C Ruíz-Pérez, C García-Castillo, A Reyes, MM Zambrano
PLOS ONE 14(12), e0221540 (2019)

2018

Holobiont Diversity in a Reef-Building Coral over Its Entire Depth Range in the Mesophotic Zone
FL Gonzalez-Zapata, P Bongaerts, C Ramírez-Portilla, B Adu-Oppong, G Walljasper, A Reyes, JA Sanchez
Frontiers in Marine Science 5 (2018)

Draft Genome Sequence of a White Spot Syndrome Virus Isolate Obtained in Ecuador
L Restrepo, A Reyes, L Bajaña, I Betancourt, B Bayot
Genome Announcements 6(26), 10.1128/genomea.00605–18 (2018)

PirVP genes causing AHPND identified in a new Vibrio species (Vibrio punensis) within the commensal Orientalis clade
L Restrepo, B Bayot, S Arciniegas, L Bajaña, I Betancourt, F Panchana, A Reyes Muñoz
Scientific Reports 8(1), 13080 (2018)

Local confinement of disease-related microbiome facilitates recovery of gorgonian sea fans from necrotic-patch disease
E Quintanilla, C Ramírez-Portilla, B Adu-Oppong, G Walljasper, SP Glaeser, T Wilke, AR Muñoz, JA Sánchez
Scientific Reports 8(1), 14636 (2018)

2017

Advances in Gut Microbiome Research, Opening New Strategies to Cope with a Western Lifestyle
GP Rodriguez-Castaño, A Caro-Quintero, A Reyes, F Lizcano
Frontiers in Genetics 7 (2017)

Captivity Shapes the Gut Microbiota of Andean Bears: Insights into Health Surveillance
A Borbón-García, A Reyes, M Vives-Flórez, S Caballero
Frontiers in Microbiology 8 (2017)

Use of profile hidden Markov models in viral discovery: current insights
A Reyes, J Marcelo P Alves, AM Durham, A Gruber
Advances in Genomics and Genetics 7, 29–45 (2017)

Changing a Generation’s Way of Thinking: Teaching Computational Thinking Through Programming
F Buitrago Flórez, R Casallas, M Hernández, A Reyes, S Restrepo, G Danies
Review of Educational Research 87(4), 834–860 (2017)

Editorial: Virus Discovery by Metagenomics: The (Im)possibilities
BE Dutilh, A Reyes, RJ Hall, KL Whiteson
Frontiers in Microbiology 8 (2017)

2016

GenSeed-HMM: A Tool for Progressive Assembly Using Profile HMMs as Seeds and its Application in Alpavirinae Viral Discovery from Metagenomic Data
JMP Alves, AL de Oliveira, TOM Sandberg, JL Moreno-Gallego, MAF de Toledo, EMM de Moura, LS Oliveira, AM Durham, DU Mehnert, PMdA Zanotto, A Reyes, A Gruber
Frontiers in Microbiology 7 (2016)

2015

Gut DNA viromes of Malawian twins discordant for severe acute malnutrition
A Reyes, LV Blanton, S Cao, G Zhao, M Manary, I Trehan, MI Smith, D Wang, HW Virgin, F Rohwer, JI Gordon
Proceedings of the National Academy of Sciences 112(38), 11941–11946 (2015)

2014

Bacteria from Diverse Habitats Colonize and Compete in the Mouse Gut
H Seedorf, NW Griffin, VK Ridaura, A Reyes, J Cheng, FE Rey, MI Smith, GM Simon, RH Scheffrahn, D Woebken, AM Spormann, W Van Treuren, LK Ursell, M Pirrung, A Robbins-Pianka, BL Cantarel, V Lombard, B Henrissat, R Knight, JI Gordon
Cell 159(2), 253–266 (2014)

HCoDES Reveals Chromosomal DNA End Structures with Single-Nucleotide Resolution
Y Dorsett, Y Zhou, AT Tubbs, B Chen, C Purman, B Lee, R George, AL Bredemeyer, J Zhao, E Sodergen, GM Weinstock, ND Han, A Reyes, EM Oltz, D Dorsett, Z Misulovin, JE Payton, BP Sleckman
Molecular Cell 56(6), 808–818 (2014)

2013

Discovery of STL polyomavirus, a polyomavirus of ancestral recombinant origin that encodes a unique T antigen by alternative splicing
ES Lim, A Reyes, M Antonio, D Saha, UN Ikumapayi, M Adeyemi, OC Stine, R Skelton, DC Brennan, RS Mkakosya, MJ Manary, JI Gordon, D Wang
Virology 436(2), 295–303 (2013)

Gnotobiotic mouse model of phage–bacterial host dynamics in the human gut
A Reyes, M Wu, NP McNulty, FL Rohwer, JI Gordon
Proceedings of the National Academy of Sciences 110(50), 20236–20241 (2013)

2012

A Noncomplementation Screen for Quantitative Trait Alleles in Saccharomyces cerevisiae
HS Kim, J Huh, L Riles, A Reyes, JC Fay
G3 Genes{\textbar}Genomes{\textbar}Genetics 2(7), 753–760 (2012)

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens
KJ Forsberg, A Reyes, B Wang, EM Selleck, MOA Sommer, G Dantas
Science 337(6098), 1107–1111 (2012)

Going viral: next-generation sequencing applied to phage populations in the human gut
A Reyes, NP Semenkovich, K Whiteson, F Rohwer, JI Gordon
Nature Reviews Microbiology 10(9), 607–617 (2012)

Identification of MW Polyomavirus, a Novel Polyomavirus in Human Stool
EA Siebrasse, A Reyes, ES Lim, G Zhao, RS Mkakosya, MJ Manary, JI Gordon, D Wang
Journal of Virology 86(19), 10321–10326 (2012)

IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes
A Reyes, A Sandoval, A Cubillos-Ruiz, KE Varley, I Hernández-Neuta, S Samper, C Martín, MJ García, V Ritacco, L López, J Robledo, MM Zambrano, RD Mitra, P Del Portillo
BMC Genomics 13(1), 249 (2012)

2011

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice
AL Goodman, G Kallstrom, JJ Faith, A Reyes, A Moore, G Dantas, JI Gordon
Proceedings of the National Academy of Sciences 108(15), 6252–6257 (2011)

2010

Viruses in the faecal microbiota of monozygotic twins and their mothers
A Reyes, M Haynes, N Hanson, FE Angly, AC Heath, F Rohwer, JI Gordon
Nature 466(7304), 334–338 (2010)

2009

Differential gene expression in White Spot Syndrome Virus (WSSV)-infected naïve and previously challenged Pacific white shrimp Penaeus (Litopenaeus) vannamei
JC García, A Reyes, M Salazar, CB Granja
Aquaculture 289(3), 253–258 (2009)

2007

Temperature modifies gene expression in subcuticular epithelial cells of white spot syndrome virus-infected Litopenaeus vannamei
A Reyes, M Salazar, C Granja
Developmental \& Comparative Immunology 31(1), 23–29 (2007)

Mutations in DNA repair genes are associated with the Haarlem lineage of Mycobacterium tuberculosis independently of their antibiotic resistance
J Olano, B López, A Reyes, M del Pilar Lemos, N Correa, P Del Portillo, L Barrera, J Robledo, V Ritacco, M Mercedes Zambrano
Tuberculosis 87(6), 502–508 (2007)