| Year |
Citation |
Score |
| 2023 |
McDaniel EA, Scarborough M, Mulat DG, Lin X, Sampara PS, Olson HM, Young RP, Eder EK, Attah IK, Markillie LM, Hoyt DW, Lipton MS, Hallam SJ, Ziels RM. Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium. The Isme Journal. PMID 37880541 DOI: 10.1038/s41396-023-01542-6 |
0.326 |
|
| 2023 |
Kieft B, Finke N, McLaughlin RJ, Nallan AN, Krzywinski M, Crowe SA, Hallam SJ. Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater. Nature Communications. 14: 5380. PMID 37666802 DOI: 10.1038/s41467-023-40907-5 |
0.324 |
|
| 2023 |
Anstett J, Plominsky AM, DeLong EF, Kiesser A, Jürgens K, Morgan-Lang C, Stepanauskas R, Stewart FJ, Ulloa O, Woyke T, Malmstrom R, Hallam SJ. A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters. Scientific Data. 10: 332. PMID 37244914 DOI: 10.1038/s41597-023-02222-y |
0.694 |
|
| 2023 |
Qiu Y, Noonan AJC, Dofher K, Koch M, Kieft B, Lin X, Ziels RM, Hallam SJ. Complete Genome Sequence of Phormidium yuhuli AB48, Isolated from an Industrial Photobioreactor Environment. Microbiology Resource Announcements. 12: e0075922. PMID 36625650 DOI: 10.1128/mra.00759-22 |
0.357 |
|
| 2022 |
Noonan AJC, Qiu Y, Kieft B, Formby S, Liu T, Dofher K, Koch M, Hallam SJ. Metagenome-Assembled Genomes for " Phormidium sp. Strain AB48" and Co-occurring Microorganisms from an Industrial Photobioreactor Environment. Microbiology Resource Announcements. e0044722. PMID 36409107 DOI: 10.1128/mra.00447-22 |
0.305 |
|
| 2022 |
Ou YF, Dong HP, McIlroy SJ, Crowe SA, Hallam SJ, Han P, Kallmeyer J, Simister RL, Vuillemin A, Leu AO, Liu Z, Zheng YL, Sun QL, Liu M, Tyson GW, et al. Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis. The Isme Journal. PMID 35810262 DOI: 10.1038/s41396-022-01281-0 |
0.753 |
|
| 2022 |
Chadwick GL, Skennerton CT, Laso-Pérez R, Leu AO, Speth DR, Yu H, Morgan-Lang C, Hatzenpichler R, Goudeau D, Malmstrom R, Brazelton WJ, Woyke T, Hallam SJ, Tyson GW, Wegener G, et al. Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. Plos Biology. 20: e3001508. PMID 34986141 DOI: 10.1371/journal.pbio.3001508 |
0.778 |
|
| 2021 |
Basher ARMA, Mclaughlin RJ, Hallam SJ. Metabolic Pathway Prediction Using Non-Negative Matrix Factorization with Improved Precision. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 34520674 DOI: 10.1089/cmb.2021.0258 |
0.339 |
|
| 2021 |
Roux S, Paul BG, Bagby SC, Nayfach S, Allen MA, Attwood G, Cavicchioli R, Chistoserdova L, Gruninger RJ, Hallam SJ, Hernandez ME, Hess M, Liu WT, McAllister TA, O'Malley MA, et al. Ecology and molecular targets of hypermutation in the global microbiome. Nature Communications. 12: 3076. PMID 34031405 DOI: 10.1038/s41467-021-23402-7 |
0.675 |
|
| 2020 |
M A Basher AR, McLaughlin RJ, Hallam SJ. Metabolic pathway inference using multi-label classification with rich pathway features. Plos Computational Biology. 16: e1008174. PMID 33001968 DOI: 10.1371/journal.pcbi.1008174 |
0.341 |
|
| 2020 |
Morgan-Lang C, McLaughlin R, Armstrong Z, Zhang G, Chan K, Hallam SJ. TreeSAPP: The Tree-based Sensitive and Accurate Phylogenetic Profiler. Bioinformatics (Oxford, England). PMID 32637989 DOI: 10.1093/Bioinformatics/Btaa588 |
0.359 |
|
| 2019 |
Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, ... Hallam SJ, et al. Consent insufficient for data release-Response. Science (New York, N.Y.). 364: 446. PMID 31048484 DOI: 10.1126/Science.Aax7509 |
0.608 |
|
| 2019 |
Borrel G, Adam PS, McKay LJ, Chen LX, Sierra-García IN, Sieber CMK, Letourneur Q, Ghozlane A, Andersen GL, Li WJ, Hallam SJ, Muyzer G, de Oliveira VM, Inskeep WP, Banfield JF, et al. Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nature Microbiology. PMID 30833729 DOI: 10.1038/S41564-019-0363-3 |
0.375 |
|
| 2019 |
Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, ... Hallam SJ, et al. Toward unrestricted use of public genomic data. Science (New York, N.Y.). 363: 350-352. PMID 30679363 DOI: 10.1126/Science.Aaw1280 |
0.612 |
|
| 2018 |
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, ... ... Hallam SJ, et al. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology. 36: 660. PMID 29979671 DOI: 10.1038/Nbt0718-660A |
0.657 |
|
| 2018 |
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, ... ... Hallam SJ, et al. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology. 36: 196. PMID 29406516 DOI: 10.1038/Nbt0218-196A |
0.691 |
|
| 2018 |
Holert J, Cardenas E, Bergstrand LH, Zaikova E, Hahn AS, Hallam SJ, Mohn WW. Metagenomes Reveal Global Distribution of Bacterial Steroid Catabolism in Natural, Engineered, and Host Environments. Mbio. 9. PMID 29382738 DOI: 10.1128/Mbio.02345-17 |
0.303 |
|
| 2017 |
Pachiadaki MG, Sintes E, Bergauer K, Brown JM, Record NR, Swan BK, Mathyer ME, Hallam SJ, Lopez-Garcia P, Takaki Y, Nunoura T, Woyke T, Herndl GJ, Stepanauskas R. Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation. Science (New York, N.Y.). 358: 1046-1051. PMID 29170234 DOI: 10.1126/science.aan8260 |
0.328 |
|
| 2017 |
Hawley AK, Nobu MK, Wright JJ, Durno WE, Morgan-Lang C, Sage B, Schwientek P, Swan BK, Rinke C, Torres-Beltrán M, Mewis K, Liu WT, Stepanauskas R, Woyke T, Hallam SJ. Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients. Nature Communications. 8: 1507. PMID 29142241 DOI: 10.1038/S41467-017-01376-9 |
0.303 |
|
| 2017 |
Strassert JFH, Karnkowska A, Hehenberger E, Del Campo J, Kolisko M, Okamoto N, Burki F, Janouškovec J, Poirier C, Leonard G, Hallam SJ, Richards TA, Worden AZ, Santoro AE, Keeling PJ. Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates. The Isme Journal. PMID 28994824 DOI: 10.1038/Ismej.2017.167 |
0.392 |
|
| 2017 |
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, ... ... Hallam SJ, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology. 35: 725-731. PMID 28787424 DOI: 10.1038/Nbt.3893 |
0.707 |
|
| 2017 |
Collingro A, Köstlbacher S, Mussmann M, Stepanauskas R, Hallam SJ, Horn M. Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae. The Isme Journal. PMID 28644443 DOI: 10.1038/ismej.2017.95 |
0.371 |
|
| 2017 |
Hahn AS, Altman T, Konwar KM, Hanson NW, Kim D, Relman DA, Dill DL, Hallam SJ. A geographically-diverse collection of 418 human gut microbiome pathway genome databases. Scientific Data. 4: 170035. PMID 28398290 DOI: 10.1038/Sdata.2017.35 |
0.307 |
|
| 2017 |
Crowe SA, Hahn AS, Morgan-Lang C, Thompson KJ, Simister RL, Llirós M, Hirst M, Hallam SJ. Draft Genome Sequence of the Pelagic Photoferrotroph Chlorobium phaeoferrooxidans. Genome Announcements. 5. PMID 28360175 DOI: 10.1128/genomeA.01584-16 |
0.371 |
|
| 2016 |
Louca S, Hawley AK, Katsev S, Torres-Beltran M, Bhatia MP, Kheirandish S, Michiels CC, Capelle D, Lavik G, Doebeli M, Crowe SA, Hallam SJ. Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone. Proceedings of the National Academy of Sciences of the United States of America. PMID 27655888 DOI: 10.1073/Pnas.1602897113 |
0.323 |
|
| 2016 |
Hanson NW, Konwar KM, Hallam SJ. LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes. Bioinformatics (Oxford, England). PMID 27515739 DOI: 10.1093/bioinformatics/btw400 |
0.329 |
|
| 2016 |
Singer E, Bushnell B, Coleman-Derr D, Bowman B, Bowers RM, Levy A, Gies EA, Cheng JF, Copeland A, Klenk HP, Hallam SJ, Hugenholtz P, Tringe SG, Woyke T. High-resolution phylogenetic microbial community profiling. The Isme Journal. PMID 26859772 DOI: 10.1038/Ismej.2015.249 |
0.319 |
|
| 2015 |
Lawson CE, Strachan CR, Williams DD, Koziel S, Hallam SJ, Budwill K. Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities. Applied and Environmental Microbiology. 81: 7924-37. PMID 26341214 DOI: 10.1128/AEM.01737-15 |
0.377 |
|
| 2015 |
Roux S, Hallam SJ, Woyke T, Sullivan MB. Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. Elife. 4. PMID 26200428 DOI: 10.7554/eLife.08490 |
0.343 |
|
| 2015 |
Nobu MK, Dodsworth JA, Murugapiran SK, Rinke C, Gies EA, Webster G, Schwientek P, Kille P, Parkes RJ, Sass H, Jørgensen BB, Weightman AJ, Liu WT, Hallam SJ, Tsiamis G, et al. Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics. The Isme Journal. PMID 26090992 DOI: 10.1038/Ismej.2015.97 |
0.435 |
|
| 2015 |
Youssef NH, Farag IF, Rinke C, Hallam SJ, Woyke T, Elshahed MS. In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3). Plos One. 10: e0127499. PMID 26039074 DOI: 10.1371/Journal.Pone.0127499 |
0.338 |
|
| 2015 |
Chow CE, Winget DM, White RA, Hallam SJ, Suttle CA. Combining genomic sequencing methods to explore viral diversity and reveal potential virus-host interactions. Frontiers in Microbiology. 6: 265. PMID 25914678 DOI: 10.3389/Fmicb.2015.00265 |
0.37 |
|
| 2015 |
Labonté JM, Swan BK, Poulos B, Luo H, Koren S, Hallam SJ, Sullivan MB, Woyke T, Eric Wommack K, Stepanauskas R. Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton. The Isme Journal. PMID 25848873 DOI: 10.1038/Ismej.2015.48 |
0.325 |
|
| 2015 |
Baldwin SA, Khoshnoodi M, Rezadehbashi M, Taupp M, Hallam S, Mattes A, Sanei H. The microbial community of a passive biochemical reactor treating arsenic, zinc, and sulfate-rich seepage. Frontiers in Bioengineering and Biotechnology. 3: 27. PMID 25798439 DOI: 10.3389/Fbioe.2015.00027 |
0.373 |
|
| 2015 |
Roux S, Hallam SJ, Woyke T, Sullivan MB. Viral dark matter and virus–host interactions resolved from publicly available microbial genomes Elife. 4. DOI: 10.7554/eLife.08490.001 |
0.33 |
|
| 2014 |
Gies EA, Konwar KM, Beatty JT, Hallam SJ. Illuminating microbial dark matter in meromictic Sakinaw Lake. Applied and Environmental Microbiology. 80: 6807-18. PMID 25172853 DOI: 10.1128/AEM.01774-14 |
0.403 |
|
| 2014 |
Wright JJ, Mewis K, Hanson NW, Konwar KM, Maas KR, Hallam SJ. Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle. The Isme Journal. 8: 455-68. PMID 24030600 DOI: 10.1038/ismej.2013.152 |
0.311 |
|
| 2013 |
Garrity GM, Banfield J, Eisen J, van der Lelie N, McMahon T, Rusch D, Delong E, Moran MA, Currie C, Furhman J, Hallam S, Hugenholtz P, Moran N, Nelson K, Roberts R, et al. Prokaryotic Super Program Advisory Committee DOE Joint Genome Institute, Walnut Creek, CA, March 27, 2013. Standards in Genomic Sciences. 8: 561-70. PMID 24501639 DOI: 10.4056/Sigs.4638348 |
0.523 |
|
| 2013 |
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, ... ... Hallam SJ, et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature. 499: 431-7. PMID 23851394 DOI: 10.1038/Nature12352 |
0.413 |
|
| 2013 |
Swan BK, Tupper B, Sczyrba A, Lauro FM, Martinez-Garcia M, González JM, Luo H, Wright JJ, Landry ZC, Hanson NW, Thompson BP, Poulton NJ, Schwientek P, Acinas SG, Giovannoni SJ, ... ... Hallam SJ, et al. Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proceedings of the National Academy of Sciences of the United States of America. 110: 11463-8. PMID 23801761 DOI: 10.1073/Pnas.1304246110 |
0.423 |
|
| 2013 |
Solonenko SA, Ignacio-Espinoza JC, Alberti A, Cruaud C, Hallam S, Konstantinidis K, Tyson G, Wincker P, Sullivan MB. Sequencing platform and library preparation choices impact viral metagenomes. Bmc Genomics. 14: 320. PMID 23663384 DOI: 10.1186/1471-2164-14-320 |
0.689 |
|
| 2012 |
Chen HP, Zhu SH, Casabon I, Hallam SJ, Crocker FH, Mohn WW, Indest KJ, Eltis LD. Genomic and transcriptomic studies of an RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine)-degrading actinobacterium. Applied and Environmental Microbiology. 78: 7798-800. PMID 22923396 DOI: 10.1128/Aem.02120-12 |
0.339 |
|
| 2012 |
Sauter LM, Latypova E, Smalley NE, Lidstrom ME, Hallam S, Kalyuzhnaya MG. Methanotrophic communities of Saanich Inlet: a microcosm perspective. Systematic and Applied Microbiology. 35: 198-203. PMID 22406542 DOI: 10.1016/J.Syapm.2011.10.006 |
0.366 |
|
| 2009 |
Lee S, Hallam SJ. Extraction of high molecular weight genomic DNA from soils and sediments. Journal of Visualized Experiments : Jove. PMID 19904232 DOI: 10.3791/1569 |
0.309 |
|
| 2006 |
Hallam SJ, Konstantinidis KT, Putnam N, Schleper C, Watanabe Y, Sugahara J, Preston C, de la Torre J, Richardson PM, DeLong EF. Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proceedings of the National Academy of Sciences of the United States of America. 103: 18296-301. PMID 17114289 DOI: 10.1073/Pnas.0608549103 |
0.795 |
|
| 2006 |
Yoshinari S, Itoh T, Hallam SJ, DeLong EF, Yokobori S, Yamagishi A, Oshima T, Kita K, Watanabe Y. Archaeal pre-mRNA splicing: a connection to hetero-oligomeric splicing endonuclease. Biochemical and Biophysical Research Communications. 346: 1024-32. PMID 16781672 DOI: 10.1016/J.Bbrc.2006.06.011 |
0.468 |
|
| 2006 |
Hallam SJ, Mincer TJ, Schleper C, Preston CM, Roberts K, Richardson PM, DeLong EF. Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. Plos Biology. 4: e95. PMID 16533068 DOI: 10.1371/Journal.Pbio.0040095 |
0.757 |
|
| 2006 |
DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard NU, Martinez A, Sullivan MB, Edwards R, Brito BR, Chisholm SW, Karl DM. Community genomics among stratified microbial assemblages in the ocean's interior. Science (New York, N.Y.). 311: 496-503. PMID 16439655 DOI: 10.1126/Science.1120250 |
0.737 |
|
| 2006 |
DeLong E, Hallam S, Mincer T, Schleper C, Preston C, Roberts K, Richardson P. Correction: Pathways of Carbon Assimilation and Ammonia Oxidation Suggested by Environmental Genomic Analyses of Marine Crenarchaeota Plos Biology. 4: e437. DOI: 10.1371/journal.pbio.0040437 |
0.77 |
|
| 2005 |
Cubonová L, Sandman K, Hallam SJ, Delong EF, Reeve JN. Histones in crenarchaea. Journal of Bacteriology. 187: 5482-5. PMID 16030242 DOI: 10.1128/Jb.187.15.5482-5485.2005 |
0.444 |
|
| 2004 |
Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D, Richardson PM, DeLong EF. Reverse methanogenesis: testing the hypothesis with environmental genomics. Science (New York, N.Y.). 305: 1457-62. PMID 15353801 DOI: 10.1126/Science.1100025 |
0.765 |
|
| 2003 |
Hallam SJ, Girguis PR, Preston CM, Richardson PM, DeLong EF. Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. Applied and Environmental Microbiology. 69: 5483-91. PMID 12957937 DOI: 10.1128/Aem.69.9.5483-5491.2003 |
0.787 |
|
| 2003 |
Girguis PR, Orphan VJ, Hallam SJ, DeLong EF. Growth and methane oxidation rates of anaerobic methanotrophic archaea in a continuous-flow bioreactor. Applied and Environmental Microbiology. 69: 5472-82. PMID 12957936 DOI: 10.1128/Aem.69.9.5472-5482.2003 |
0.731 |
|
| 2003 |
Goffredi SK, Hurtado LA, Hallam S, Vrijenhoek RC. Evolutionary relationships of deep-sea vent and cold seep clams (Mollusca: Vesicomyidae) of the "pacifica/lepta" species complex Marine Biology. 142: 311-320. DOI: 10.1007/S00227-002-0941-3 |
0.333 |
|
| 2002 |
Hallam SJ, Goncharov A, McEwen J, Baran R, Jin Y. SYD-1, a presynaptic protein with PDZ, C2 and rhoGAP-like domains, specifies axon identity in C. elegans. Nature Neuroscience. 5: 1137-46. PMID 12379863 DOI: 10.1038/Nn959 |
0.455 |
|
| 1998 |
Hallam SJ, Jin Y. lin-14 regulates the timing of synaptic remodelling in Caenorhabditis elegans. Nature. 395: 78-82. PMID 9738501 DOI: 10.1038/25757 |
0.478 |
|
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