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Benjamin J. Tully, Ph.D. - Publications

Affiliations: 
2013 Biology University of Southern California, Los Angeles, CA, United States 
Area:
Microbiology Biology
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28 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Zhong J, Osborn T, Del Rosario Hernández T, Kyrysyuk O, Tully BJ, Anderson RE. Increasing transposase abundance with ocean depth correlates with a particle-associated lifestyle. Msystems. e0006724. PMID 38380923 DOI: 10.1128/msystems.00067-24  0.476
2023 Alexander H, Hu SK, Krinos AI, Pachiadaki M, Tully BJ, Neely CJ, Reiter T. Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton. Mbio. e0167623. PMID 37947402 DOI: 10.1128/mbio.01676-23  0.55
2023 Reynolds R, Hyun S, Tully B, Bien J, Levine NM. Identification of microbial metabolic functional guilds from large genomic datasets. Frontiers in Microbiology. 14: 1197329. PMID 37455725 DOI: 10.3389/fmicb.2023.1197329  0.486
2020 Martí-Carreras J, Gener AR, Miller SD, Brito AF, Camacho CE, Connor R, Deboutte W, Glickman C, Kristensen DM, Meyer WK, Modha S, Norris AL, Saha S, Belford AK, Biederstedt E, ... ... Tully BJ, et al. NCBI's Virus Discovery Codeathon: Building "FIVE" -The Federated Index of Viral Experiments API Index. Viruses. 12. PMID 33322070 DOI: 10.3390/v12121424  0.335
2020 Seyler LM, Trembath-Reichert E, Tully BJ, Huber JA. Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community. The Isme Journal. PMID 33273721 DOI: 10.1038/s41396-020-00843-4  0.473
2020 Graham ED, Tully BJ. Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning. The Isme Journal. PMID 33230264 DOI: 10.1038/s41396-020-00834-5  0.523
2020 Nelson WC, Tully BJ, Mobberley JM. Biases in genome reconstruction from metagenomic data. Peerj. 8: e10119. PMID 33194386 DOI: 10.7717/peerj.10119  0.435
2020 Neely CJ, Graham ED, Tully BJ. MetaSanity: An integrated microbial genome evaluation and annotation pipeline. Bioinformatics (Oxford, England). PMID 32426808 DOI: 10.1093/Bioinformatics/Btaa512  0.5
2020 Meyer JL, Jaekel U, Tully BJ, Glazer BT, Wheat CG, Lin HT, Hsieh CC, Cowen JP, Hulme SM, Girguis PR, Huber JA. Author Correction: A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge. Scientific Reports. 10: 6691. PMID 32300242 DOI: 10.1038/S41598-020-63127-Z  0.338
2019 Lopez A, Albino D, Beraki S, Broomell S, Canela R, Dingmon T, Estrada S, Fernandez M, Savalia P, Nealson K, Emerson D, Barco R, Tully BJ, Amend JP. Genome Sequence of sp. Strain EBB-1, a Novel Marine Autotroph Isolated from an Iron-Sulfur Mineral. Microbiology Resource Announcements. 8. PMID 31558636 DOI: 10.1128/MRA.00995-19  0.325
2019 Connor R, Brister R, Buchmann JP, Deboutte W, Edwards R, Martí-Carreras J, Tisza M, Zalunin V, Andrade-Martínez J, Cantu A, D'Amour M, Efremov A, Fleischmann L, Forero-Junco L, Garmaeva S, ... ... Tully B, et al. NCBI's Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements. Genes. 10. PMID 31527408 DOI: 10.3390/Genes10090714  0.412
2019 Tully BJ. Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns. Nature Communications. 10: 271. PMID 30655514 DOI: 10.1038/S41467-018-07840-4  0.586
2018 Smith H, Abuyen K, Tremblay J, Savalia P, Pérez-Rodríguez I, Emerson D, Tully B, Amend J. Genome Sequence of sp. Strain HR-1, an Iron Reducer from the Lō'ihi Seamount, Hawai'i. Genome Announcements. 6. PMID 29798915 DOI: 10.1128/Genomea.00339-18  0.442
2018 Graham ED, Heidelberg JF, Tully BJ. Potential for primary productivity in a globally-distributed bacterial phototroph. The Isme Journal. PMID 29523891 DOI: 10.1038/S41396-018-0091-3  0.708
2018 Neely C, Bou Khalil C, Cervantes A, Diaz R, Escobar A, Ho K, Hoefler S, Smith HH, Abuyen K, Savalia P, Nealson KH, Emerson D, Tully B, Barco RA, Amend J. Genome Sequence ofsp. Strain SC-1, a Chemolithoautotrophic Sulfur and Iron Oxidizer. Genome Announcements. 6. PMID 29437113 DOI: 10.1128/Genomea.01581-17  0.421
2018 Tully BJ, Graham ED, Heidelberg JF. The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. Scientific Data. 5: 170203. PMID 29337314 DOI: 10.1038/Sdata.2017.203  0.719
2018 Reese BK, Zinke LA, Sobol MS, LaRowe DE, Orcutt BN, Zhang X, Jaekel U, Wang F, Dittmar T, Defforey D, Tully B, Paytan A, Sylvan JB, Amend JP, Edwards KJ, et al. Nitrogen Cycling of Active Bacteria within Oligotrophic Sediment of the Mid-Atlantic Ridge Flank Geomicrobiology Journal. 35: 468-483. DOI: 10.1080/01490451.2017.1392649  0.41
2017 Tully BJ, Wheat CG, Glazer BT, Huber JA. A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer. The Isme Journal. PMID 29099490 DOI: 10.1038/Ismej.2017.187  0.547
2017 Tully BJ, Sachdeva R, Graham ED, Heidelberg JF. 290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology. Peerj. 5: e3558. PMID 28713657 DOI: 10.7717/Peerj.3558  0.714
2017 Tully B, Savalia P, Abuyen K, Baughan C, Romero E, Ronkowski C, Torres B, Tremblay J, Trujillo A, Tyler M, Pérez-Rodríguez I, Amend J. Genome Sequence of Geothermobacter sp. Strain EPR-M, a Deep-Sea Hydrothermal Vent Iron Reducer. Genome Announcements. 5. PMID 28596393 DOI: 10.1128/Genomea.00424-17  0.425
2017 Graham ED, Heidelberg JF, Tully BJ. BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation. Peerj. 5: e3035. PMID 28289564 DOI: 10.7717/Peerj.3035  0.648
2016 Tully BJ, Heidelberg JF. Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep Sea Sediments. Applied and Environmental Microbiology. PMID 27208118 DOI: 10.1128/Aem.01023-16  0.709
2016 Meyer JL, Jaekel U, Tully BJ, Glazer BT, Wheat CG, Lin HT, Hsieh CC, Cowen JP, Hulme SM, Girguis PR, Huber JA. A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge. Scientific Reports. 6: 22541. PMID 26935537 DOI: 10.1038/Srep22541  0.446
2015 Tully BJ, Emerson JB, Andrade K, Brocks JJ, Allen EE, Banfield JF, Heidelberg KB. De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape. Archaea (Vancouver, B.C.). 2015: 875784. PMID 25709557 DOI: 10.1155/2015/875784  0.544
2014 Tully BJ, Sachdeva R, Heidelberg KB, Heidelberg JF. Comparative genomics of planktonic Flavobacteriaceae from the Gulf of Maine using metagenomic data. Microbiome. 2: 34. PMID 25258679 DOI: 10.1186/2049-2618-2-34  0.714
2013 Tully BJ, Heidelberg JF. Microbial communities associated with ferromanganese nodules and the surrounding sediments. Frontiers in Microbiology. 4: 161. PMID 23805131 DOI: 10.3389/Fmicb.2013.00161  0.667
2012 Tully BJ, Nelson WC, Heidelberg JF. Metagenomic analysis of a complex marine planktonic thaumarchaeal community from the Gulf of Maine. Environmental Microbiology. 14: 254-67. PMID 22050608 DOI: 10.1111/J.1462-2920.2011.02628.X  0.722
2011 Biddle JF, Sylvan JB, Brazelton WJ, Tully BJ, Edwards KJ, Moyer CL, Heidelberg JF, Nelson WC. Prospects for the study of evolution in the deep biosphere. Frontiers in Microbiology. 2: 285. PMID 22319515 DOI: 10.3389/Fmicb.2011.00285  0.644
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