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Items: 1 to 50 of 178

1.

Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils.

Trubl G, Roux S, Solonenko N, Li YF, Bolduc B, Rodríguez-Ramos J, Eloe-Fadrosh EA, Rich VI, Sullivan MB.

PeerJ. 2019 Jul 4;7:e7265. doi: 10.7717/peerj.7265. eCollection 2019.

2.

Prevalence of viral photosynthesis genes along a freshwater to saltwater transect in Southeast USA.

Ruiz-Perez CA, Tsementzi D, Hatt JK, Sullivan MB, Konstantinidis KT.

Environ Microbiol Rep. 2019 Jul 2. doi: 10.1111/1758-2229.12780. [Epub ahead of print]

PMID:
31265211
3.

Scientists' warning to humanity: microorganisms and climate change.

Cavicchioli R, Ripple WJ, Timmis KN, Azam F, Bakken LR, Baylis M, Behrenfeld MJ, Boetius A, Boyd PW, Classen AT, Crowther TW, Danovaro R, Foreman CM, Huisman J, Hutchins DA, Jansson JK, Karl DM, Koskella B, Mark Welch DB, Martiny JBH, Moran MA, Orphan VJ, Reay DS, Remais JV, Rich VI, Singh BK, Stein LY, Stewart FJ, Sullivan MB, van Oppen MJH, Weaver SC, Webb EA, Webster NS.

Nat Rev Microbiol. 2019 Sep;17(9):569-586. doi: 10.1038/s41579-019-0222-5. Epub 2019 Jun 18. Review.

PMID:
31213707
4.

Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages.

Barylski J, Enault F, Dutilh BE, Schuller MBP, Edwards RA, Gillis A, Klumpp J, Knezevic P, Krupovic M, Kuhn JH, Lavigne R, Oksanen HM, Sullivan MB, Jang HB, Simmonds P, Aiewsakun P, Wittmann J, Tolstoy I, Brister JR, Kropinski AM, Adriaenssens EM.

Syst Biol. 2019 May 25. pii: syz036. doi: 10.1093/sysbio/syz036. [Epub ahead of print]

PMID:
31127947
5.

Optimizing de novo genome assembly from PCR-amplified metagenomes.

Roux S, Trubl G, Goudeau D, Nath N, Couradeau E, Ahlgren NA, Zhan Y, Marsan D, Chen F, Fuhrman JA, Northen TR, Sullivan MB, Rich VI, Malmstrom RR, Eloe-Fadrosh EA.

PeerJ. 2019 May 9;7:e6902. doi: 10.7717/peerj.6902. eCollection 2019.

6.

Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands.

Warwick-Dugdale J, Solonenko N, Moore K, Chittick L, Gregory AC, Allen MJ, Sullivan MB, Temperton B.

PeerJ. 2019 Apr 25;7:e6800. doi: 10.7717/peerj.6800. eCollection 2019.

7.

Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales.

Wilpiszeski RL, Aufrecht JA, Retterer ST, Sullivan MB, Graham DE, Pierce EM, Zablocki OD, Palumbo AV, Elias DA.

Appl Environ Microbiol. 2019 Jul 1;85(14). pii: e00324-19. doi: 10.1128/AEM.00324-19. Print 2019 Jul 15. Review.

8.

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks.

Bin Jang H, Bolduc B, Zablocki O, Kuhn JH, Roux S, Adriaenssens EM, Brister JR, Kropinski AM, Krupovic M, Lavigne R, Turner D, Sullivan MB.

Nat Biotechnol. 2019 Jun;37(6):632-639. doi: 10.1038/s41587-019-0100-8. Epub 2019 May 6.

9.

Marine DNA Viral Macro- and Microdiversity from Pole to Pole.

Gregory AC, Zayed AA, Conceição-Neto N, Temperton B, Bolduc B, Alberti A, Ardyna M, Arkhipova K, Carmichael M, Cruaud C, Dimier C, Domínguez-Huerta G, Ferland J, Kandels S, Liu Y, Marec C, Pesant S, Picheral M, Pisarev S, Poulain J, Tremblay JÉ, Vik D; Tara Oceans Coordinators, Babin M, Bowler C, Culley AI, de Vargas C, Dutilh BE, Iudicone D, Karp-Boss L, Roux S, Sunagawa S, Wincker P, Sullivan MB.

Cell. 2019 May 16;177(5):1109-1123.e14. doi: 10.1016/j.cell.2019.03.040. Epub 2019 Apr 25.

PMID:
31031001
10.

Closely related viruses of the marine picoeukaryotic alga Ostreococcus lucimarinus exhibit different ecological strategies.

Zimmerman AE, Bachy C, Ma X, Roux S, Jang HB, Sullivan MB, Waldbauer JR, Worden AZ.

Environ Microbiol. 2019 Jun;21(6):2148-2170. doi: 10.1111/1462-2920.14608. Epub 2019 May 13.

11.

Multi Band Gap Electronic Structure in CH3NH3PbI3.

Ong KP, Wu S, Nguyen TH, Singh DJ, Fan Z, Sullivan MB, Dang C.

Sci Rep. 2019 Feb 14;9(1):2144. doi: 10.1038/s41598-018-38023-2.

12.

Numerous cultivated and uncultivated viruses encode ribosomal proteins.

Mizuno CM, Guyomar C, Roux S, Lavigne R, Rodriguez-Valera F, Sullivan MB, Gillet R, Forterre P, Krupovic M.

Nat Commun. 2019 Feb 14;10(1):752. doi: 10.1038/s41467-019-08672-6.

13.

Minimum Information about an Uncultivated Virus Genome (MIUViG).

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

Nat Biotechnol. 2019 Jan;37(1):29-37. doi: 10.1038/nbt.4306. Epub 2018 Dec 17.

PMID:
30556814
14.

Whole-Genome Sequences of Phages p000v and p000y, Which Infect the Bacterial Pathogen Shiga-Toxigenic Escherichia coli.

Howard-Varona C, Vik DR, Solonenko NE, Gazitua MC, Hobbs Z, Honaker RW, Kinkhabwala AA, Sullivan MB.

Microbiol Resour Announc. 2018 Nov 21;7(20). pii: e01400-18. doi: 10.1128/MRA.01400-18. eCollection 2018 Nov.

15.

Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing.

Daly RA, Roux S, Borton MA, Morgan DM, Johnston MD, Booker AE, Hoyt DW, Meulia T, Wolfe RA, Hanson AJ, Mouser PJ, Moore JD, Wunch K, Sullivan MB, Wrighton KC, Wilkins MJ.

Nat Microbiol. 2019 Feb;4(2):352-361. doi: 10.1038/s41564-018-0312-6. Epub 2018 Dec 3.

16.

Fighting Fire with Fire: Phage Potential for the Treatment of E. coli O157 Infection.

Howard-Varona C, Vik DR, Solonenko NE, Li YF, Gazitua MC, Chittick L, Samiec JK, Jensen AE, Anderson P, Howard-Varona A, Kinkhabwala AA, Abedon ST, Sullivan MB.

Antibiotics (Basel). 2018 Nov 16;7(4). pii: E101. doi: 10.3390/antibiotics7040101.

17.

Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem.

Solden LM, Naas AE, Roux S, Daly RA, Collins WB, Nicora CD, Purvine SO, Hoyt DW, Schückel J, Jørgensen B, Willats W, Spalinger DE, Firkins JL, Lipton MS, Sullivan MB, Pope PB, Wrighton KC.

Nat Microbiol. 2018 Nov;3(11):1274-1284. doi: 10.1038/s41564-018-0225-4. Epub 2018 Oct 24.

PMID:
30356154
18.

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing.

Trubl G, Jang HB, Roux S, Emerson JB, Solonenko N, Vik DR, Solden L, Ellenbogen J, Runyon AT, Bolduc B, Woodcroft BJ, Saleska SR, Tyson GW, Wrighton KC, Sullivan MB, Rich VI.

mSystems. 2018 Oct 2;3(5). pii: e00076-18. doi: 10.1128/mSystems.00076-18. eCollection 2018 Sep-Oct.

19.

Orbital-Engineering-Based Screening of π-Conjugated d8 Transition-Metal Coordination Polymers for High-Performance n-Type Thermoelectric Applications.

Shi W, Wu G, Yong X, Deng T, Wang JS, Zheng JC, Xu J, Sullivan MB, Yang SW.

ACS Appl Mater Interfaces. 2018 Oct 17;10(41):35306-35315. doi: 10.1021/acsami.8b13877. Epub 2018 Oct 8.

PMID:
30251818
20.

Smoking is associated with quantifiable differences in the human lung DNA virome and metabolome.

Gregory AC, Sullivan MB, Segal LN, Keller BC.

Respir Res. 2018 Sep 12;19(1):174. doi: 10.1186/s12931-018-0878-9.

21.

Host-linked soil viral ecology along a permafrost thaw gradient.

Emerson JB, Roux S, Brum JR, Bolduc B, Woodcroft BJ, Jang HB, Singleton CM, Solden LM, Naas AE, Boyd JA, Hodgkins SB, Wilson RM, Trubl G, Li C, Frolking S, Pope PB, Wrighton KC, Crill PM, Chanton JP, Saleska SR, Tyson GW, Rich VI, Sullivan MB.

Nat Microbiol. 2018 Aug;3(8):870-880. doi: 10.1038/s41564-018-0190-y. Epub 2018 Jul 16.

PMID:
30013236
22.

Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms.

Zhong ZP, Solonenko NE, Gazitúa MC, Kenny DV, Mosley-Thompson E, Rich VI, Van Etten JL, Thompson LG, Sullivan MB.

Front Microbiol. 2018 May 25;9:1094. doi: 10.3389/fmicb.2018.01094. eCollection 2018.

23.

Multiple mechanisms drive phage infection efficiency in nearly identical hosts.

Howard-Varona C, Hargreaves KR, Solonenko NE, Markillie LM, White RA 3rd, Brewer HM, Ansong C, Orr G, Adkins JN, Sullivan MB.

ISME J. 2018 Jun;12(6):1605-1618. doi: 10.1038/s41396-018-0099-8. Epub 2018 Mar 22.

24.

Site specificity of halogen bonding involving aromatic acceptors.

Ang SJ, Mak AM, Sullivan MB, Wong MW.

Phys Chem Chem Phys. 2018 Mar 28;20(13):8685-8694. doi: 10.1039/c7cp08343b.

PMID:
29537006
25.

Yoga Therapy and Polyvagal Theory: The Convergence of Traditional Wisdom and Contemporary Neuroscience for Self-Regulation and Resilience.

Sullivan MB, Erb M, Schmalzl L, Moonaz S, Noggle Taylor J, Porges SW.

Front Hum Neurosci. 2018 Feb 27;12:67. doi: 10.3389/fnhum.2018.00067. eCollection 2018.

26.

A global ocean atlas of eukaryotic genes.

Carradec Q, Pelletier E, Da Silva C, Alberti A, Seeleuthner Y, Blanc-Mathieu R, Lima-Mendez G, Rocha F, Tirichine L, Labadie K, Kirilovsky A, Bertrand A, Engelen S, Madoui MA, Méheust R, Poulain J, Romac S, Richter DJ, Yoshikawa G, Dimier C, Kandels-Lewis S, Picheral M, Searson S; Tara Oceans Coordinators, Jaillon O, Aury JM, Karsenti E, Sullivan MB, Sunagawa S, Bork P, Not F, Hingamp P, Raes J, Guidi L, Ogata H, de Vargas C, Iudicone D, Bowler C, Wincker P.

Nat Commun. 2018 Jan 25;9(1):373. doi: 10.1038/s41467-017-02342-1.

27.

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans.

Seeleuthner Y, Mondy S, Lombard V, Carradec Q, Pelletier E, Wessner M, Leconte J, Mangot JF, Poulain J, Labadie K, Logares R, Sunagawa S, de Berardinis V, Salanoubat M, Dimier C, Kandels-Lewis S, Picheral M, Searson S; Tara Oceans Coordinators, Pesant S, Poulton N, Stepanauskas R, Bork P, Bowler C, Hingamp P, Sullivan MB, Iudicone D, Massana R, Aury JM, Henrissat B, Karsenti E, Jaillon O, Sieracki M, de Vargas C, Wincker P.

Nat Commun. 2018 Jan 22;9(1):310. doi: 10.1038/s41467-017-02235-3.

28.

Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee.

Adriaenssens EM, Wittmann J, Kuhn JH, Turner D, Sullivan MB, Dutilh BE, Jang HB, van Zyl LJ, Klumpp J, Lobocka M, Moreno Switt AI, Rumnieks J, Edwards RA, Uchiyama J, Alfenas-Zerbini P, Petty NK, Kropinski AM, Barylski J, Gillis A, Clokie MRC, Prangishvili D, Lavigne R, Aziz RK, Duffy S, Krupovic M, Poranen MM, Knezevic P, Enault F, Tong Y, Oksanen HM, Rodney Brister J.

Arch Virol. 2018 Apr;163(4):1125-1129. doi: 10.1007/s00705-018-3723-z. Epub 2018 Jan 22. No abstract available.

PMID:
29356990
29.

Photophysical properties of acetylene-linked syn bimane oligomers: a molecular photonic wire.

Chwee TS, Wong ZC, Sullivan MB, Fan WY.

Phys Chem Chem Phys. 2018 Jan 3;20(2):1150-1163. doi: 10.1039/c7cp06673b.

PMID:
29239433
30.

Dietary energy drives the dynamic response of bovine rumen viral communities.

Anderson CL, Sullivan MB, Fernando SC.

Microbiome. 2017 Nov 28;5(1):155. doi: 10.1186/s40168-017-0374-3.

31.

Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods.

Pasulka AL, Thamatrakoln K, Kopf SH, Guan Y, Poulos B, Moradian A, Sweredoski MJ, Hess S, Sullivan MB, Bidle KD, Orphan VJ.

Environ Microbiol. 2018 Feb;20(2):671-692. doi: 10.1111/1462-2920.13996. Epub 2017 Dec 14.

PMID:
29159966
32.

Toward an Explanatory Framework for Yoga Therapy Informed by Philosophical and Ethical Perspectives.

Sullivan MB, Moonaz S, Weber K, Taylor JN, Schmalzl L.

Altern Ther Health Med. 2018 Jan;24(1):38-47.

PMID:
29135457
33.

Iron Chloride Flocculation of Bacteriophages from Seawater.

Poulos BT, John SG, Sullivan MB.

Methods Mol Biol. 2018;1681:49-57. doi: 10.1007/978-1-4939-7343-9_4.

PMID:
29134586
34.

Thioamide-Directed Cobalt(III)-Catalyzed Selective Amidation of C(sp3 )-H Bonds.

Tan PW, Mak AM, Sullivan MB, Dixon DJ, Seayad J.

Angew Chem Int Ed Engl. 2017 Dec 22;56(52):16550-16554. doi: 10.1002/anie.201709273. Epub 2017 Nov 30.

PMID:
29080308
35.

Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics.

Roux S, Chan LK, Egan R, Malmstrom RR, McMahon KD, Sullivan MB.

Nat Commun. 2017 Oct 11;8(1):858. doi: 10.1038/s41467-017-01086-2.

36.

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity.

Roux S, Emerson JB, Eloe-Fadrosh EA, Sullivan MB.

PeerJ. 2017 Sep 21;5:e3817. doi: 10.7717/peerj.3817. eCollection 2017.

37.

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.

Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M; Genoscope Technical Team, Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernández-Gómez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL; Tara Oceans Consortium Coordinators, Pesant S, Karsenti E, Wincker P.

Sci Data. 2017 Aug 1;4:170093. doi: 10.1038/sdata.2017.93.

38.

Using non-empirically tuned range-separated functionals with simulated emission bands to model fluorescence lifetimes.

Wong ZC, Fan WY, Chwee TS, Sullivan MB.

Phys Chem Chem Phys. 2017 Aug 9;19(31):21046-21057. doi: 10.1039/c7cp03418k.

PMID:
28748247
39.

Osteosarcoma enters a post genomic era with in silico opportunities: Generation of the High Dimensional Database for facilitating sarcoma biology research: A report from the Children's Oncology Group and the QuadW Foundation.

Glover J, Man TK, Barkauskas DA, Hall D, Tello T, Sullivan MB, Gorlick R, Janeway K, Grier H, Lau C, Toretsky JA, Borinstein SC, Khanna C, Fan TM; COG Osteosarcoma Biology Group.

PLoS One. 2017 Jul 21;12(7):e0181204. doi: 10.1371/journal.pone.0181204. eCollection 2017.

40.

Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept.

Duhaime MB, Solonenko N, Roux S, Verberkmoes NC, Wichels A, Sullivan MB.

Front Microbiol. 2017 Jul 6;8:1241. doi: 10.3389/fmicb.2017.01241. eCollection 2017.

41.

Regulation of infection efficiency in a globally abundant marine Bacteriodetes virus.

Howard-Varona C, Roux S, Dore H, Solonenko NE, Holmfeldt K, Markillie LM, Orr G, Sullivan MB.

ISME J. 2017 Aug;11(8):1942. doi: 10.1038/ismej.2017.92.

42.

On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires.

Silas S, Makarova KS, Shmakov S, Páez-Espino D, Mohr G, Liu Y, Davison M, Roux S, Krishnamurthy SR, Fu BXH, Hansen LL, Wang D, Sullivan MB, Millard A, Clokie MR, Bhaya D, Lambowitz AM, Kyrpides NC, Koonin EV, Fire AZ.

MBio. 2017 Jul 11;8(4). pii: e00897-17. doi: 10.1128/mBio.00897-17.

43.

Single-virus genomics reveals hidden cosmopolitan and abundant viruses.

Martinez-Hernandez F, Fornas O, Lluesma Gomez M, Bolduc B, de la Cruz Peña MJ, Martínez JM, Anton J, Gasol JM, Rosselli R, Rodriguez-Valera F, Sullivan MB, Acinas SG, Martinez-Garcia M.

Nat Commun. 2017 Jun 23;8:15892. doi: 10.1038/ncomms15892.

44.

Putative archaeal viruses from the mesopelagic ocean.

Vik DR, Roux S, Brum JR, Bolduc B, Emerson JB, Padilla CC, Stewart FJ, Sullivan MB.

PeerJ. 2017 Jun 15;5:e3428. doi: 10.7717/peerj.3428. eCollection 2017.

45.

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria.

Bolduc B, Jang HB, Doulcier G, You ZQ, Roux S, Sullivan MB.

PeerJ. 2017 May 3;5:e3243. doi: 10.7717/peerj.3243. eCollection 2017.

46.

High-Throughput Survey of Ordering Configurations in MXene Alloys Across Compositions and Temperatures.

Tan TL, Jin HM, Sullivan MB, Anasori B, Gogotsi Y.

ACS Nano. 2017 May 23;11(5):4407-4418. doi: 10.1021/acsnano.6b08227. Epub 2017 Mar 23.

PMID:
28297600
47.

Lysogeny in nature: mechanisms, impact and ecology of temperate phages.

Howard-Varona C, Hargreaves KR, Abedon ST, Sullivan MB.

ISME J. 2017 Jul;11(7):1511-1520. doi: 10.1038/ismej.2017.16. Epub 2017 Mar 14.

48.

Modelling plankton ecosystems in the meta-omics era. Are we ready?

Stec KF, Caputi L, Buttigieg PL, D'Alelio D, Ibarbalz FM, Sullivan MB, Chaffron S, Bowler C, Ribera d'Alcalà M, Iudicone D.

Mar Genomics. 2017 Apr;32:1-17. doi: 10.1016/j.margen.2017.02.006. Epub 2017 Mar 7. Review.

PMID:
28283424
49.

Visualizing Adsorption of Cyanophage P-SSP7 onto Marine Prochlorococcus.

Murata K, Zhang Q, Gerardo Galaz-Montoya J, Fu C, Coleman ML, Osburne MS, Schmid MF, Sullivan MB, Chisholm SW, Chiu W.

Sci Rep. 2017 Mar 10;7:44176. doi: 10.1038/srep44176.

50.

Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean.

Nishimura Y, Watai H, Honda T, Mihara T, Omae K, Roux S, Blanc-Mathieu R, Yamamoto K, Hingamp P, Sako Y, Sullivan MB, Goto S, Ogata H, Yoshida T.

mSphere. 2017 Mar 1;2(2). pii: e00359-16. doi: 10.1128/mSphere.00359-16. eCollection 2017 Mar-Apr.

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