Todd Treangen - Publications

Affiliations: 
2010-2012 Computer Science University of Maryland, College Park, College Park, MD 

28/48 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
2019 Chopyk J, Nasko DJ, Allard S, Bui A, Treangen T, Pop M, Mongodin EF, Sapkota AR. Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications. Water Research. 169: 115250. PMID 31726395 DOI: 10.1016/J.Watres.2019.115250  0.64
2019 Ghurye J, Treangen T, Fedarko M, Hervey WJ, Pop M. MetaCarvel: linking assembly graph motifs to biological variants. Genome Biology. 20: 174. PMID 31451112 DOI: 10.1186/S13059-019-1791-3  0.64
2018 Treangen TJ, Pop M. You can't always sequence your way out of a tight spot: Next-generation sequencing holds great promise for pathogen detection, but the devil is in the details. Embo Reports. PMID 30467235 DOI: 10.15252/Embr.201847036  0.64
2018 Meisel JS, Nasko DJ, Brubach B, Cepeda-Espinoza V, Chopyk J, Corrada-Bravo H, Fedarko M, Ghurye J, Javkar K, Olson ND, Shah N, Allard SM, Bazinet AL, Bergman NH, Brown A, ... ... Treangen TJ, et al. Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018. Microbiome. 6: 197. PMID 30396371 DOI: 10.1186/S40168-018-0582-5  0.64
2018 Nasko DJ, Koren S, Phillippy AM, Treangen TJ. RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification. Genome Biology. 19: 165. PMID 30373669 DOI: 10.1186/S13059-018-1554-6  0.76
2017 Olson ND, Treangen TJ, Hill CM, Cepeda-Espinoza V, Ghurye J, Koren S, Pop M. Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes. Briefings in Bioinformatics. PMID 28968737 DOI: 10.1093/Bib/Bbx098  0.64
2017 Venkateswaran K, Checinska Sielaff A, Ratnayake S, Pope RK, Blank TE, Stepanov VG, Fox GE, van Tongeren SP, Torres C, Allen J, Jaing C, Pierson D, Perry J, Koren S, Phillippy A, ... ... Treangen TJ, et al. Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains, Isolated from the International Space Station. Genome Announcements. 5. PMID 28798168 DOI: 10.1128/Genomea.00680-17  0.76
2016 Davison M, Treangen TJ, Koren S, Pop M, Bhaya D. Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers. Plos One. 11: e0160574. PMID 27611571 DOI: 10.1371/Journal.Pone.0160574  0.64
2016 Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biology. 17: 132. PMID 27323842 DOI: 10.1186/S13059-016-0997-X  0.72
2016 Treangen TJ, Schoeler G, Phillippy AM, Bergman NH, Turell MJ. Identification and Genomic Analysis of a Novel Group C Orthobunyavirus Isolated from a Mosquito Captured near Iquitos, Peru. Plos Neglected Tropical Diseases. 10: e0004440. PMID 27074162 DOI: 10.1371/Journal.Pntd.0004440  0.76
2014 Treangen TJ, Ondov BD, Koren S, Phillippy AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biology. 15: 524. PMID 25410596 DOI: 10.1186/S13059-014-0524-X  0.76
2014 Treangen TJ, Maybank RA, Enke S, Friss MB, Diviak LF, Karaolis DK, Koren S, Ondov B, Phillippy AM, Bergman NH, Rosovitz MJ. Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp. aureus ATCC 25923. Genome Announcements. 2. PMID 25377701 DOI: 10.1128/Genomea.01110-14  0.76
2014 Zimin AV, Cornish AS, Maudhoo MD, Gibbs RM, Zhang X, Pandey S, Meehan DT, Wipfler K, Bosinger SE, Johnson ZP, Tharp GK, Marçais G, Roberts M, Ferguson B, Fox HS, ... Treangen T, et al. A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biology Direct. 9: 20. PMID 25319552 DOI: 10.1186/1745-6150-9-20  0.72
2014 Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM. Automated ensemble assembly and validation of microbial genomes. Bmc Bioinformatics. 15: 126. PMID 24884846 DOI: 10.1186/1471-2105-15-126  0.72
2013 Harrington R, Ondov BD, Radune D, Friss MB, Klubnik J, Diviak L, Hnath J, Cendrowski SR, Blank TE, Karaolis D, Friedlander AM, Burans JP, Rosovitz MJ, Treangen T, Phillippy AM, et al. Genome Sequence of the Attenuated Carbosap Vaccine Strain of Bacillus anthracis. Genome Announcements. 1. PMID 23405332 DOI: 10.1128/Genomea.00067-12  0.4
2013 Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biology. 14: R2. PMID 23320958 DOI: 10.1186/Gb-2013-14-1-R2  0.72
2013 Hill CM, Astrovskaya I, Huang H, Koren S, Memon A, Treangen TJ, Pop M. De novo likelihood-based measures for comparing metagenomic assemblies Proceedings - 2013 Ieee International Conference On Bioinformatics and Biomedicine, Ieee Bibm 2013. 94-98. DOI: 10.1109/BIBM.2013.6732469  0.72
2012 Treangen TJ, Phillippy AM. Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone. Genome Biology. 13: 181. PMID 23270611 DOI: 10.1186/gb-2012-13-12-181  0.76
2012 Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, Stine OC, Hasturk H, Kasif S, Segrè D, Pop M, et al. Deep sequencing of the oral microbiome reveals signatures of periodontal disease Plos One. 7. PMID 22675498 DOI: 10.1371/Journal.Pone.0037919  0.72
2012 Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Research. 22: 557-67. PMID 22147368 DOI: 10.1101/Gr.131383.111  0.72
2012 Treangen TJ, Salzberg SL. Repetitive DNA and next-generation sequencing: Computational challenges and solutions Nature Reviews Genetics. 13: 36-46. PMID 22124482 DOI: 10.1038/nrg3117  0.72
2011 Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M. Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences Bmc Genomics. 12. PMID 21989143 DOI: 10.1186/1471-2164-12-S2-S4  0.72
2011 Koren S, Treangen TJ, Pop M. Bambus 2: scaffolding metagenomes. Bioinformatics (Oxford, England). 27: 2964-71. PMID 21926123 DOI: 10.1093/Bioinformatics/Btr520  0.72
2011 Enk J, Devault A, Debruyne R, King CE, Treangen T, O'Rourke D, Salzberg SL, Fisher D, MacPhee R, Poinar H. Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths. Genome Biology. 12: R51. PMID 21627792 DOI: 10.1186/Gb-2011-12-5-R51  0.72
2011 Treangen TJ, Sommer DD, Angly FE, Koren S, Pop M. Next generation sequence assembly with AMOS. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 11.8. PMID 21400694 DOI: 10.1002/0471250953.Bi1108S33  0.72
2009 Treangen TJ, Darling AE, Achaz G, Ragan MA, Messeguer X, Rocha EP. A novel heuristic for local multiple alignment of interspersed DNA repeats. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 6: 180-9. PMID 19407343 DOI: 10.1109/Tcbb.2009.9  0.72
2008 Treangen TJ, Darling AE, Ragan MA, Messeguer X. Gapped extension for local multiple alignment of interspersed DNA repeats Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4983: 74-86. DOI: 10.1007/978-3-540-79450-9_8  0.72
2007 Darling AE, Treangen TJ, Messeguer X, Perna NT. Analyzing patterns of microbial evolution using the mauve genome alignment system. Methods in Molecular Biology (Clifton, N.J.). 396: 135-52. PMID 18025691 DOI: 10.1007/978-1-59745-515-2_10  0.32
Low-probability matches
2012 Treangen TJ, Salzberg SL. Erratum: Repetitive DNA and next-generation sequencing: computational challenges and solutions Nature Reviews Genetics. 13: 146-146. DOI: 10.1038/NRG3164  0.28
2011 Treangen TJ, Rocha EP. Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. Plos Genetics. 7: e1001284. PMID 21298028 DOI: 10.1371/journal.pgen.1001284  0.04
2021 Kille B, Liu Y, Sapoval N, Nute M, Rauchwerger L, Amato N, Treangen TJ. Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets. Arxiv. PMID 33972927  0.01
2021 McDonald JT, Enguita FJ, Taylor D, Griffin RJ, Priebe W, Emmett MR, McGrath M, Sajadi MM, Harris AD, Clement J, Dybas JM, Aykin-Burns N, Guarnieri JW, Singh LN, Grabham P, ... ... Treangen TJ, et al. The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection. Biorxiv : the Preprint Server For Biology. PMID 33948587 DOI: 10.1101/2021.04.23.441024  0.01
2021 Molino S, Pisarevsky A, Mingorance FL, Vega P, Stefanolo JP, Repetti J, Ludueña G, Pepa P, Olmos JI, Fermepin MR, Uehara T, Villapol S, Savidge T, Treangen T, Viciani E, et al. Natural tannin extracts supplementation for COVID-19 patients (TanCOVID): a structured summary of a study protocol for a randomized controlled trial. Trials. 22: 310. PMID 33910614 DOI: 10.1186/s13063-021-05281-x  0.01
2021 Wang Q, Kille B, Liu TR, Elworth RAL, Treangen TJ. PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment. Nature Communications. 12: 1167. PMID 33637701 DOI: 10.1038/s41467-021-21180-w  0.01
2021 Sapoval N, Mahmoud M, Jochum M, Liu Y, Elworth RAL, Wang Q, Albin D, Ogilvie H, Lee MD, Villapol S, Hernandez K, Maljkovic Berry I, Foox J, Beheshti A, Ternus K, ... ... Treangen TJ, et al. Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission. Genome Research. PMID 33602693 DOI: 10.1101/gr.268961.120  0.01
2020 da Silveira WA, Fazelinia H, Rosenthal SB, Laiakis EC, Kim MS, Meydan C, Kidane Y, Rathi KS, Smith SM, Stear B, Ying Y, Zhang Y, Foox J, Zanello S, Crucian B, ... ... Treangen T, et al. Comprehensive Multi-omics Analysis Reveals Mitochondrial Stress as a Central Biological Hub for Spaceflight Impact. Cell. 183: 1185-1201.e20. PMID 33242417 DOI: 10.1016/j.cell.2020.11.002  0.01
2020 Elworth RAL, Diaz C, Yang J, de Figueiredo P, Ternus K, Treangen T. Synthetic DNA and biosecurity: Nuances of predicting pathogenicity and the impetus for novel computational approaches for screening oligonucleotides. Plos Pathogens. 16: e1008649. PMID 32760120 DOI: 10.1371/journal.ppat.1008649  0.01
2020 Sapoval N, Mahmoud M, Jochum MD, Liu Y, Leo Elworth RA, Wang Q, Albin D, Ogilvie H, Lee MD, Villapol S, Hernandez KM, Berry IM, Foox J, Beheshti A, Ternus K, ... ... Treangen TJ, et al. Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission. Biorxiv : the Preprint Server For Biology. PMID 32637955 DOI: 10.1101/2020.07.02.184481  0.01
2020 Elworth RAL, Wang Q, Kota PK, Barberan CJ, Coleman B, Balaji A, Gupta G, Baraniuk RG, Shrivastava A, Treangen TJ. To Petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics. Nucleic Acids Research. PMID 32338745 DOI: 10.1093/Nar/Gkaa265  0.01
2020 Mahmoud M, Gener AR, Khayat MM, English AC, Balaji A, Zhou A, Hehn A, Fungtammasan A, Chrisman BS, Chin C, Lin C, Lo C, Liao C, Carvalho CMB, Diesh C, ... ... Treangen TJ, et al. Methods developed during the first National Center for Biotechnology Information Structural Variation Codeathon at Baylor College of Medicine F1000research. 9: 1141. DOI: 10.12688/F1000Research.23773.1  0.01
2018 Treangen TJ, Wagner J, Burns MP, Villapol S. Traumatic Brain Injury in Mice Induces Acute Bacterial Dysbiosis Within the Fecal Microbiome. Frontiers in Immunology. 9: 2757. PMID 30546361 DOI: 10.3389/Fimmu.2018.02757  0.01
2012 Methé BA, Nelson KE, Pop M, Creasy HH, Giglio MG, Huttenhower C, Gevers D, Petrosino JF, Abubucker S, Badger JH, Chinwalla AT, Earl AM, Fitzgerald MG, Fulton RS, Hallsworth-Pepin K, et al. A framework for human microbiome research Nature. 486: 215-221. PMID 22699610 DOI: 10.1038/Nature11209  0.01
2012 Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, Creasy HH, Earl AM, Fitzgerald MG, Fulton RS, Giglio MG, Hallsworth-Pepin K, Lobos EA, Madupu R, Magrini V, et al. Structure, function and diversity of the healthy human microbiome Nature. 486: 207-214. PMID 22699609 DOI: 10.1038/Nature11234  0.01
2011 Koren S, Treangen T, Pop M. ScaffViz: visualizing metagenome assemblies Genome Biology. 12: P8. DOI: 10.1186/Gb-2011-12-S1-P8  0.01
2011 Treangen TJ, Koren S, Astrovskaya I, Sommer D, Liu B, Pop M. MetAMOS: a metagenomic assembly and analysis pipeline for AMOS Genome Biology. 12: P25. DOI: 10.1186/Gb-2011-12-S1-P25  0.01
2009 Treangen TJ, Abraham AL, Touchon M, Rocha EP. Genesis, effects and fates of repeats in prokaryotic genomes. Fems Microbiology Reviews. 33: 539-71. PMID 19396957 DOI: 10.1111/j.1574-6976.2009.00169.x  0.01
2008 Treangen TJ, Ambur OH, Tonjum T, Rocha EP. The impact of the neisserial DNA uptake sequences on genome evolution and stability. Genome Biology. 9: R60. PMID 18366792 DOI: 10.1186/gb-2008-9-3-r60  0.01
2006 Treangen TJ, Messeguer X. M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. Bmc Bioinformatics. 7: 433. PMID 17022809 DOI: 10.1186/1471-2105-7-433  0.01
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