75- Community diversity is associated with intra-species genetic diversity and gene loss in the human gut microbiome
Journal Article
Madi N J , Chen D , Wolff R , Shapiro B J , Garud N R ,
2023 eLife (Date Added: 2023-04-21)

74- Efficient computation of contributional diversity metrics from microbiome data with FuncDiv
Journal Article
Douglas G M , Kim S , Langille M G I , Shapiro B J ,
2023 Bioinformatics (Oxford, England) (Date Added: 2023-04-21)

73- Genome-wide association studies reveal distinct genetic correlates and increased heritability of antimicrobial resistance in Vibrio cholerae under anaerobic conditions
Journal Article
Creasy-Marrazzo A , Saber M M , Kamat M , Bailey L S , Brinkley L , Cato E , Begum Y , Rashid M M , Khan A I , Qadri F , Basso K B , Shapiro B J , Nelson E J ,
2022 Microbial Genomics (Date Added: 2023-04-21)

72- Impact of Stagnation on the Diversity of Cyanobacteria in Drinking Water Treatment Plant Sludge
Journal Article
Jalili F , Trigui H , Maldonado J F G , Dorner S , Zamyadi A , Shapiro B J , Terrat Y , Fortin N , Sauvé S , Prévost M ,
2022 Toxins (Date Added: 2023-04-21)

71- Shotgun Metagenomic Sequencing to Assess Cyanobacterial Community Composition following Coagulation of Cyanobacterial Blooms
Journal Article
Le K T N , Maldonado J F G , Goitom E , Trigui H , Terrat Y , Nguyen T , Husk B , Shapiro B J , Sauvé S , Prévost M , Dorner S ,
2022 Toxins (Date Added: 2023-04-21)

70- Comprehensive Phylogenomics of Methylobacterium Reveals Four Evolutionary Distinct Groups and Underappreciated Phyllosphere Diversity
Journal Article
Leducq J , Sneddon D , Santos M , Condrain-Morel D , Bourret G , Martinez-Gomez N C , Lee J A , Foster J A , Stolyar S , Shapiro B J , Kembel S W , Sullivan J M , Marx C J ,
2022 Genome biology and evolution (Date Added: 2022-08-22)

69- Fine-Scale Adaptations to Environmental Variation and Growth Strategies Drive Phyllosphere Methylobacterium Diversity
Journal Article
,
2022 mBio (Date Added: 2022-05-31)

68- Population Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages
Journal Article
,
2022 Frontiers in Medicine (Date Added: 2022-05-31)

67- Oxidation to Control Cyanobacteria and Cyanotoxins in Drinking Water Treatment Plants: Challenges at the Laboratory and Full‐Scale Plants
Journal Article
Jalili F , Trigui H , Maldonado J F G , Dorner S , Zamyadi A , Shapiro B J , Terrat Y , Fortin N , Sauvé S , Prévost M ,
2022 Water (Switzerland) (Date Added: 2022-04-15)

66- Comparing microscopy and DNA metabarcoding techniques for identifying cyanobacteria assemblages across hundreds of lakes
Journal Article
MacKeigan P W , Garner R E , Monchamp M , Walsh D A , Onana V E , Kraemer S A , Pick F R , Beisner B E , Agbeti M D , da Costa N B , Shapiro B J , Gregory-Eaves I ,
2022 Harmful Algae (Date Added: 2022-02-08)

65- Genome Evolution in Bacteria Isolated from Million-Year-Old Subseafloor Sediment
Journal Article
,
2021 mBio (Date Added: 2022-04-27)

64- Metagenomic study to evaluate functional capacity of a cyanobacterial bloom during oxidation
Journal Article
Moradinejad S , Trigui H , Maldonado J F G , Shapiro B J , Terrat Y , Sauvé S , Fortin N , Zamyadi A , Dorner S , Prévost M ,
2021 Chemical Engineering Journal Advances (Date Added: 2022-04-15)

63- Genic Selection Within Prokaryotic Pangenomes
Journal Article
Douglas G M , Shapiro B J ,
2021 Genome biology and evolution (Date Added: 2022-04-15)

62- A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Québec, Canada
Journal Article
Murall C L , Fournier E , Galvez J H , N’Guessan A , Reiling S J , Quirion P , Naderi S , Roy A , Chen S , Stretenowich P , Bourgey M , Bujold D , Gregoire R , Lepage P , St-Cyr J , Willet P , Dion R , Charest H , Lathrop M , Roger M , Bourque G , Ragoussis J , Shapiro B J , Moreira S ,
2021 Genome Medicine (Date Added: 2022-04-15)

61- Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria
Journal Article
Pérez-Carrascal O M , Tromas N , Terrat Y , Moreno E , Giani A , Corrêa Braga Marques L , Fortin N , Shapiro B J ,
2021 Microbiome (Date Added: 2021-10-27)

60- Mobile Gene Sequence Evolution within Individual Human Gut Microbiomes Is Better Explained by Gene-Specific Than Host-Specific Selective Pressures
Journal Article
N’Guessan A , Brito I L , Serohijos A W R , Shapiro B J ,
2021 Genome biology and evolution (Date Added: 2021-10-27)

59- A combination of metagenomic and cultivation approaches reveals hypermutator phenotypes within vibrio cholerae- infected patients
Journal Article
Levade I , Khan A I , Chowdhury F , Calderwood S B , Ryan E T , Harris J B , LaRocque R C , Bhuiyan T R , Qadri F , Weil A A , Shapiro B J ,
2021 mSystems (Date Added: 2021-10-27)

58- Erratum: Functional diversity: An epistemic roadmap (BioScience DOI: 10.1093/biosci/biz089)
Journal Erratum
Malaterre C , Dussault A C , Mermans E , Barker G , Beisner B E , Bouchard F , Desjardins E , Handa I T , Kembel S W , Lajoie G , Maris V , Munson A D , Odenbaugh J , Poisot T , Shapiro B J , Suttle C A ,
2021 BioScience (Date Added: 2021-10-17)

57- Widespread agrochemicals differentially affect zooplankton biomass and community structure
Journal Article
Hébert M , Fugère V , Beisner B E , Barbosa da Costa N , Barrett R D H , Bell G , Shapiro B J , Yargeau V , Gonzalez A , Fussmann G F ,
2021 Ecological Applications (Date Added: 2021-08-23)

56- Resistance, resilience, and functional redundancy of freshwater bacterioplankton communities facing a gradient of agricultural stressors in a mesocosm experiment
Journal Article
Barbosa da Costa N , Fugère V , Hébert M , Xu C C , Barrett R D , Beisner B E , Bell G , Yargeau V , Fussmann G F , Gonzalez A , Shapiro B J ,
2021 Molecular Ecology (Date Added: 2021-08-21)

55- Outbreak investigation of SARS-CoV-2 transmission in an emergency childcare centre
Journal Article
Soto J C , Barakat M , Hutter J A , Kiely M , Moreira S , Shapiro B J , Murall C L , Parenteau N , Désilets J , Lessard R ,
2021 Canadian Journal of Public Health (Date Added: 2021-07-21)

54- Elevated rates of horizontal gene transfer in the industrialized human microbiome
Journal Article
Groussin M , Poyet M , Sistiaga A , Kearney S M , Moniz K , Noel M , Hooker J , Gibbons S M , Segurel L , Froment A , Mohamed R S , Fezeu A , Juimo V A , Lafosse S , Tabe F E , Girard C , Iqaluk D , Nguyen L T T , Shapiro B J , Lehtimäki J , Ruokolainen L , Kettunen P P , Vatanen T , Sigwazi S , Mabulla A , Domínguez-Rodrigo M , Nartey Y A , Agyei-Nkansah A , Duah A , Awuku Y A , Valles K A , Asibey S O , Afihene M Y , Roberts L R , Plymoth A , Onyekwere C A , Summons R E , Xavier R J , Alm E J ,
2021 Cell (Date Added: 2021-04-23)

53- Translational activity is uncoupled from nucleic acid content in bacterial cells of the human gut microbiota
Journal Article
Taguer M , Shapiro B J , Maurice C F ,
2021 Gut Microbes (Date Added: 2021-04-11)

52- Predicting Vibrio cholerae Infection and Disease Severity Using Metagenomics in a Prospective Cohort Study
Journal Article
Levade I , Saber M M , Midani F S , Chowdhury F , Khan A I , Begum Y A , Ryan E T , David L A , Calderwood S B , Harris J B , LaRocque R C , Qadri F , Shapiro B J , Weil A A ,
2021 The Journal of infectious diseases (Date Added: 2021-03-19)

51- Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France
Journal Article
Seguin-Orlando A , Donat R , Der Sarkissian C , Southon J , Thèves C , Manen C , Tchérémissinoff Y , Crubézy E , Shapiro B , Deleuze J , Dalén L , Guilaine J , Orlando L ,
2021 Current Biology (Date Added: 2021-02-07)

50- Can Cyanobacterial Diversity in the Source Predict the Diversity in Sludge and the Risk of Toxin Release in a Drinking Water Treatment Plant?
Journal Article
Jalili F , Trigui H , Guerra Maldonado J F , Dorner S , Zamyadi A , Shapiro B J , Terrat Y , Fortin N , Sauvé S , Prévost M ,
2021 Toxins (Date Added: 2021-01-27)

49- Diversity Assessment of Toxic Cyanobacterial Blooms during Oxidation
Journal Article
Moradinejad S , Trigui H , Guerra Maldonado J F , Shapiro J , Terrat Y , Zamyadi A , Dorner S , Prévost M ,
2020 Toxins (Date Added: 2021-05-22)

48- Relative Model Fit Does Not Predict Topological Accuracy in Single-Gene Protein Phylogenetics
Journal Article
Spielman S J ,
2020 Molecular Biology and Evolution (Date Added: 2020-12-24)

47- Does diversity beget diversity in microbiomes?
Journal Article
Madi N , Vos M , Murall C L , Legendre P , Shapiro B J ,
2020 eLife (Date Added: 2020-12-22)

46- A large-scale assessment of lakes reveals a pervasive signal of land use on bacterial communities
Journal Article
Kraemer S A , Barbosa da Costa N , Shapiro B J , Fradette M , Huot Y , Walsh D A ,
2020 ISME Journal (Date Added: 2020-08-17)

45- Two cases of type-a haemophilus influenzae meningitis within the same week in the same hospital are phylogenetically unrelated but recently exchanged capsule genes
Journal Article
Terrat Y , Farnaes L , Bradley J , Tromas N , Shapiro B J ,
2020 Microbial Genomics (Date Added: 2020-05-30)

44- Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes
Journal Article
Saber M M , Shapiro B J ,
2020 Microbial genomics (Date Added: 2020-04-10)

43- Community rescue in experimental phytoplankton communities facing severe herbicide pollution
Journal Article
Fugère, V, Hébert, M-P, da Costa, NB, Xu, CCY, Barrett, RDH, Beisner, BE, Bell, G, Fussmann, GF, Shapiro, BJ, Yargeau, V, Gonzalez, A
2020 Nature Ecology and Evolution (Date Added: 2020-03-24)

42- The evolution of realized niches within freshwater Synechococcus
Journal Article
Tromas N , Taranu Z E , Castelli M , Pimentel J S M , Pereira D A , Marcoz R , Shapiro B J , Giani A ,
2020 Environmental Microbiology (Date Added: 2020-02-24)

41- Functional Diversity: An Epistemic Roadmap
Journal Article
Malaterre, C, Dussault, AC, Rousseau-Mermans, S, Barker, G, Beisner, BE, Bouchard, F, Desjardins, E, Handa, IT, Kembel, SW, Lajoie, G, Maris, V, Munson, AD, Odenbaugh, J, Poisot, T, Shapiro, BJ, Suttle, CA
2019 BioScience (Date Added: 2019-10-25)

40- Coherence of Microcystis species revealed through population genomics
Journal Article
Pérez-Carrascal O M , Terrat Y , Giani A , Fortin N , Greer C W , Tromas N , Shapiro B J ,
2019 ISME Journal (Date Added: 2019-08-08)

39- Microbial evolutionary medicine: from theory to clinical practice
Journal Article
Andersen S B , Shapiro B J , Vandenbroucke-Grauls C , de Vos M G J ,
2019 The Lancet Infectious Diseases (Date Added: 2019-08-03)

38- Reuniting ecology and evolution
Journal Article
Shapiro B J ,
2018 Environmental Microbiology Reports (Date Added: 2018-12-26)

37- Niche separation increases with genetic distance among bloom-forming cyanobacteria
Journal Article
Tromas N , Taranu Z E , Martin B D , Willis A , Fortin N , Greer C W , Shapiro B J ,
2018 Frontiers in Microbiology (Date Added: 2018-04-04)

36- The Inuit gut microbiome is dynamic over time and shaped by traditional foods
Journal Article
Dubois G , Girard C , Lapointe F , Shapiro B J ,
2017 Microbiome (Date Added: 2018-08-08)

35- The population genetics of pangenomes
Journal Article
Shapiro B J ,
2017 Nature Microbiology (Date Added: 2017-12-06)

34- Cooking and co-ingested polyphenols reduce in vitro methylmercury bioaccessibility from fish and may alter exposure in humans
Journal Article
Girard, C, Charette, T, Leclerc M , Shapiro, J, Amyot, M
2017 Science of the Total Environment (Date Added: 2017-11-10)

33- Mitochondrial recombination and introgression during speciation by hybridization
Journal Article
Leducq J , Henault M , Charron G , Nielly-Thibault L , Terrat Y , Fiumera H L , Shapiro B J , Landry C R ,
2017 Molecular Biology and Evolution (Date Added: 2017-09-09)

32- Gut Microbiome of the Canadian Arctic Inuit
Journal Article
Girard, C, Tromas, N, Amyot, M, Shapiro, BJ
2017 MSphere (Date Added: 2017-08-16)

31- Characterising and predicting cyanobacterial blooms in an 8-year amplicon sequencing time course
Journal Article
Tromas N , Fortin N , Bedrani L , Terrat Y , Cardoso P , Bird D , Greer C W , Shapiro B J ,
2017 ISME Journal (Date Added: 2017-08-03)

30- AD-LIBS: Inferring ancestry across hybrid genomes using low-coverage sequence data
Journal Article
Schaefer N K , Shapiro B , Green R E ,
2017 BMC Bioinformatics (Date Added: 2017-04-20)

29- The evolutionary and phylogeographic history of woolly mammoths: A comprehensive mitogenomic analysis
Journal Article
Chang D , Knapp M , Enk J , Lippold S , Kircher M , Lister A , MacPhee R D E , Widga C , Czechowski P , Sommer R , Hodges E , Stümpel N , Barnes I , Dalén L , Derevianko A , Germonpré M , Hillebrand-Voiculescu A , Constantin S , Kuznetsova T , Mol D , Rathgeber T , Rosendahl W , Tikhonov A N , Willerslev E , Hannon G , Lalueza-Fox C , Joger U , Poinar H , Hofreiter M , Shapiro B ,
2017 Scientific Reports (Date Added: 2017-04-05)

28- Origins of pandemic Vibrio cholerae from environmental gene pools
Journal Article
Shapiro, BJ, Levade, I, Kovacikova, G, Taylor, RK, Almagro-Moreno, S
2016 Nature Microbiology (Date Added: 2017-02-14)

27- Phenotypic differentiation of Streptococcus pyogenes populations is induced by recombination-driven gene-specific sweeps
Journal Article
Bao, Y-J, Shapiro, BJ, Lee, SW, Ploplis, VA, Castellino, FJ
2016 Scientific Reports (Date Added: 2017-02-14)

26- How clonal are bacteria over time?
Journal Article
Shapiro, BJ
2016 Current Opinion in Microbiology (Date Added: 2017-02-14)

25- What Is Speciation?
Journal Article
Shapiro, BJ, Leducq, J-B, Mallet, J
2016 PLoS Genetics (Date Added: 2017-02-14)

24- Environment and host species shape the skin microbiome of captive neotropical bats
Journal Article
Lemieux-Labonte, V, Tromas, N, Shapiro, BJ, Lapointe, F-J
2016 PeerJ (Date Added: 2016-11-28)

23- The advent of genome-wide association studies for bacteria
Journal Article
Chen, PE, Shapiro, BJ
2015 Current Opinion in Microbiology (Date Added: 2017-02-15)

22- Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus
Journal Article
Andersen, KG, Shapiro, BJ, Matranga, CB, Sealfon, R, Lin, AE, Moses, LM, Folarin, OA, Goba, A, Odia, I, Ehiane, PE, Momoh, M, England, EM, Winnicki, S, Branco, LM, Gire, SK, Phelan, E, Tariyal, R, Tewhey, R, Omoniwa, O, Fullah, M, Fonnie, R, Fonnie, M, Kanneh, L, Jalloh, S, Gbakie, M, Saffa, S, Karbo, K, Gladden, AD, Qu, J, Stremlau, M, Nekoui, M, Finucane, HK, Tabrizi, S, Vitti, JJ, Birren, B, Fitzgerald, M, McCowan, C, Ireland, A, Berlin, AM, Bochicchio, J, Tazon-Vega, B, Lennon, NJ, Ryan, EM, Bjornson, Z, Milner, DA, Lukens, AK, Broodie, N, Rowland, M, Heinrich, M, Akdag, M, Schieffelin, JS, Levy, D, Akpan, H, Bausch, DG, Rubins, K, McCormick, JB, Lander, ES, Günther, S, Hensley, L, Okogbenin, S, Schaffner, SF, Okokhere, PO, Khan, SH, Grant, DS, Akpede, GO, Asogun, DA, Gnirke, A, Levin, JZ, Happi, CT, Garry, RF, Sabeti, PC
2015 Cell (Date Added: 2017-02-15)

21- Microbial speciation
Journal Article
Shapiro, BJ, Polz, MF
2015 Cold Spring Harbor Perspectives in Biology (Date Added: 2017-02-15)

20- What is speciation? Studying closely related natural bacterial populations is leading to a more unified concept of speciation across the tree of life
Journal Article
Shapiro, BJ
2015 Microbe (Date Added: 2017-02-15)

19- A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens
Journal Article
Farhat, MR, Shapiro, BJ, Sheppard, SK, Colijn, C, Murray, M
2014 Genome Medicine (Date Added: 2017-02-15)

18- Signatures of natural selection and ecological differentiation in microbial genomes
Unsupported: Serial (Book, Monograph)
Shapiro, BJ
2014 Advances in Experimental Medicine and Biology (Date Added: 2017-02-15)

17- Signatures of natural selection and ecological differentiation inmicrobial genomes
Unsupported: Serial (Book, Monograph)
Shapiro, BJ
2014 Advances in Experimental Medicine and Biology (Date Added: 2017-02-15)

16- Ordering microbial diversity into ecologically and genetically cohesive units
Journal Article
Shapiro, BJ, Polz, MF
2014 Trends in Microbiology (Date Added: 2017-02-15)

15- Evolutionary consequences of intra-patient phage predation on microbial populations
Journal Article
Seed, KD, Yen, M, Shapiro, BJ, Hilaire, IJ, Charles, RC, Teng, JE, Ivers, LC, Boncy, J, Harris, JB, Camilli, A
2014 eLife (Date Added: 2017-02-15)

14- Reproducibility of Vibrionaceae population structure in coastal bacterioplankton
Journal Article
Szabo, G, Preheim, SP, Kauffman, KM, David, LA, Shapiro, J, Alm, EJ, Polz, MF
2013 The ISME Journal (Date Added: 2017-07-31)

13- Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis
Journal Article
Farhat, MR, Shapiro, BJ, Kieser, KJ, Sultana, R, Jacobson, KR, Victor, TC, Warren, RM, Streicher, EM, Calver, A, Sloutsky, A, Kaur, D, Posey, JE, Plikaytis, B, Oggioni, MR, Gardy, JL, Johnston, JC, Rodrigues, M, Tang, PKC, Kato-Maeda, M, Borowsky, ML, Muddukrishna, B, Kreiswirth, BN, Kurepina, N, Galagan, J, Gagneux, S, Birren, B, Rubin, EJ, Lander, ES, Sabeti, PC, Murray, M
2013 Nature Genetics (Date Added: 2017-02-15)

12- Sympatric Speciation: When Is It Possible in Bacteria?
Journal Article
Friedman, J, Alm, EJ, Shapiro, BJ
2013 PLoS ONE (Date Added: 2017-02-15)

11- Population genomics of early events in the ecological differentiation of bacteria
Journal Article
Shapiro, BJ, Friedman, J, Cordero, OX, Preheim, SP, Timberlake, SC, Szabó, G, Polz, MF, Alm, EJ
2012 Science (Date Added: 2017-02-15)

10- The slow:fast substitution ratio reveals changing patterns of natural selection in γ-proteobacterial genomes
Journal Article
Shapiro, BJ, Alm, E
2009 ISME Journal (Date Added: 2017-02-15)

9- Looking for Darwin's footprints in the microbial world
Journal Article
Shapiro, BJ, David, LA, Friedman, J, Alm, EJ
2009 Trends in Microbiology (Date Added: 2017-02-15)

8- Comparing patterns of natural selection across species using selective signatures
Journal Article
Shapiro, BJ, Alm, EJ
2008 PLoS Genetics (Date Added: 2017-02-15)

7- Multiple independent origins of a protease inhibitor resistance mutation in salvage therapy patients
Journal Article
Kapoor, A, Shapiro, B, Shafer, RW, Shulman, N, Rhee, S-Y, Delwart, EL
2008 Retrovirology (Date Added: 2017-02-15)

6- Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: Subtype G is a circulating recombinant form
Journal Article
Abecasis, AB, Lemey, P, Vidal, N, De Oliveira, T, Peeters, M, Camacho, R, Shapiro, B, Rambaut, A, Vandamme, A-M
2007 Journal of Virology (Date Added: 2017-02-15)

5- An experimental test of the causes of small-scale phenotypic differentiation in a population of great tits
Journal Article
Shapiro, BJ, Garant, D, Wilkin, TA, Sheldon, BC
2006 Journal of Evolutionary Biology (Date Added: 2017-02-16)

4- An interactional network of genes involved in chitin synthesis in Saccharomyces cerevisiae
Journal Article
Lesage, G, Shapiro, J, Specht, CA, Sdicu, A-M, Menard, P, Hussein, S, Tong, AHY, Boone, C, Bussey, H
2005 BMC Genetics (Date Added: 2017-02-16)

3- VSG switching in Trypanosoma brucei: antigenic variation analysed using RNAi in the absence of immune selection
Journal Article
Aitcheson, N, Talbot, S, Shapiro, J, Hughes, K, Adkin, C, Butt, T, Sheader, K, Rudenko, G
2005 Molecular Microbiology (Date Added: 2017-02-16)

2- Global mapping of the yeast genetic interaction network
Journal Article
Tong, AHY, Lesage, G, Bader, GD, Ding, H, Xu, H, Xin, X, Young, J, Berriz, GF, Brost, RL, Chang, M, Chen, YQ, Cheng, X, Chua, G, Friesen, H, Goldberg, DS, Haynes, J, Humphries, C, He, G, Hussein, S, Ke, L, Krogan, N, Li, Z, Levinson, JN, Lu, H, Menard, P, Munyana, C, Parsons, AB, Ryan, O, Tonikian, R, Roberts, T, Sdicu, A-M, Shapiro, J, Sheikh, B, Suter, B, Wong, SL, Zhang, LV, Zhu, H, Burd, CG, Munro, S, Sander, C, Rine, J, Greenblatt, J, Peter, M, Bretscher, A, Bell, G, Roth, FP, Brown, GW, Andrews, B, Bussey, H, Boone, C
2004 Science (New York, N.Y.) (Date Added: 2017-02-16)

1- Analysis of  -1,3-Glucan Assembly in Saccharomyces cerevisiae Using a Synthetic Interaction Network and Altered Sensitivity to Caspofungin
Journal Article
Lesage, G
2004 Genetics (Date Added: 2017-02-16)