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Items: 1 to 50 of 168

1.

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.

PMID:
30765739
2.

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.

PMID:
30765709
3.

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. 2018 Dec 17. doi: 10.1038/nbt.4306. [Epub ahead of print]

PMID:
30556814
4.

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.

5.

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.

6.

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.

7.

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
8.

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.

9.

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 8. doi: 10.1021/acsami.8b13877. [Epub ahead of print]

PMID:
30251818
10.

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.

11.

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
12.

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.

13.

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.

PMID:
29568113
14.

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
15.

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.

16.

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.

17.

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.

18.

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
19.

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
20.

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.

21.

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
22.

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
23.

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
24.

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
25.

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.

26.

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.

27.

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.

28.

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
29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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
37.

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.

38.

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
39.

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.

40.

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.

41.

Consensus statement: Virus taxonomy in the age of metagenomics.

Simmonds P, Adams MJ, Benkő M, Breitbart M, Brister JR, Carstens EB, Davison AJ, Delwart E, Gorbalenya AE, Harrach B, Hull R, King AM, Koonin EV, Krupovic M, Kuhn JH, Lefkowitz EJ, Nibert ML, Orton R, Roossinck MJ, Sabanadzovic S, Sullivan MB, Suttle CA, Tesh RB, van der Vlugt RA, Varsani A, Zerbini FM.

Nat Rev Microbiol. 2017 Mar;15(3):161-168. doi: 10.1038/nrmicro.2016.177. Epub 2017 Jan 3.

PMID:
28134265
42.

Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study.

Kang DW, Adams JB, Gregory AC, Borody T, Chittick L, Fasano A, Khoruts A, Geis E, Maldonado J, McDonough-Means S, Pollard EL, Roux S, Sadowsky MJ, Lipson KS, Sullivan MB, Caporaso JG, Krajmalnik-Brown R.

Microbiome. 2017 Jan 23;5(1):10. doi: 10.1186/s40168-016-0225-7.

43.

Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics.

Brum JR, Hurwitz BL, Schofield O, Ducklow HW, Sullivan MB.

ISME J. 2017 Feb;11(2):588. doi: 10.1038/ismej.2016.126. No abstract available.

44.

Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee.

Adriaenssens EM, Krupovic M, Knezevic P, Ackermann HW, Barylski J, Brister JR, Clokie MR, Duffy S, Dutilh BE, Edwards RA, Enault F, Jang HB, Klumpp J, Kropinski AM, Lavigne R, Poranen MM, Prangishvili D, Rumnieks J, Sullivan MB, Wittmann J, Oksanen HM, Gillis A, Kuhn JH.

Arch Virol. 2017 Apr;162(4):1153-1157. doi: 10.1007/s00705-016-3173-4. Epub 2016 Dec 31. No abstract available.

PMID:
28040838
45.

Towards quantitative viromics for both double-stranded and single-stranded DNA viruses.

Roux S, Solonenko NE, Dang VT, Poulos BT, Schwenck SM, Goldsmith DB, Coleman ML, Breitbart M, Sullivan MB.

PeerJ. 2016 Dec 8;4:e2777. doi: 10.7717/peerj.2777. eCollection 2016.

46.

Computational and Experimental Investigation of the Structure of Peptide Monolayers on Gold Nanoparticles.

Colangelo E, Chen Q, Davidson AM, Paramelle D, Sullivan MB, Volk M, Lévy R.

Langmuir. 2017 Jan 10;33(1):438-449. doi: 10.1021/acs.langmuir.6b04383. Epub 2016 Dec 30.

47.

Viral ecology comes of age.

Sullivan MB, Weitz JS, Wilhelm S.

Environ Microbiol Rep. 2017 Feb;9(1):33-35. doi: 10.1111/1758-2229.12504. No abstract available.

PMID:
27888577
48.

Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer.

Gregory AC, Solonenko SA, Ignacio-Espinoza JC, LaButti K, Copeland A, Sudek S, Maitland A, Chittick L, Dos Santos F, Weitz JS, Worden AZ, Woyke T, Sullivan MB.

BMC Genomics. 2016 Nov 16;17(1):930.

49.

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

Paez-Espino D, Chen IA, Palaniappan K, Ratner A, Chu K, Szeto E, Pillay M, Huang J, Markowitz VM, Nielsen T, Huntemann M, K Reddy TB, Pavlopoulos GA, Sullivan MB, Campbell BJ, Chen F, McMahon K, Hallam SJ, Denef V, Cavicchioli R, Caffrey SM, Streit WR, Webster J, Handley KM, Salekdeh GH, Tsesmetzis N, Setubal JC, Pope PB, Liu WT, Rivers AR, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2017 Jan 4;45(D1):D457-D465. doi: 10.1093/nar/gkw1030. Epub 2016 Oct 30.

50.

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.

Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, Pesant S, Kandels-Lewis S, Dimier C, Picheral M, Searson S, Cruaud C, Alberti A, Duarte CM, Gasol JM, Vaqué D; Tara Oceans Coordinators, Bork P, Acinas SG, Wincker P, Sullivan MB.

Nature. 2016 Sep 29;537(7622):689-693. doi: 10.1038/nature19366. Epub 2016 Sep 21.

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