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Todd Treangen - Publications

Affiliations: 
2010-2012 Computer Science University of Maryland, College Park, College Park, MD 
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49 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 Scalzo PL, Marshall A, Soriano S, Curry K, Dulay M, Hodics T, Quigley EM, Treangen TJ, Piskorz MM, Villapol S. Gut microbiome dysbiosis and immune activation correlate with somatic and neuropsychiatric symptoms in COVID-19 patients. Medrxiv : the Preprint Server For Health Sciences. PMID 39606341 DOI: 10.1101/2024.11.18.24317428  0.586
2024 Wu CT, Shropshire WC, Bhatti MM, Cantu S, Glover IK, Anand SS, Liu X, Kalia A, Treangen TJ, Chemaly RF, Spallone A, Shelburne S. Rapid Whole Genome Characterization of High-Risk Pathogens Using Long-Read Sequencing to Identify Potential Healthcare Transmission. Medrxiv : the Preprint Server For Health Sciences. PMID 39228727 DOI: 10.1101/2024.08.19.24312266  0.303
2024 Amaral WZ, Kokroko N, Treangen TJ, Villapol S, Gomez-Pinilla F. Probiotic therapy modulates the brain-gut-liver microbiota axis in a mouse model of traumatic brain injury. Biochimica Et Biophysica Acta. Molecular Basis of Disease. 1870: 167483. PMID 39209236 DOI: 10.1016/j.bbadis.2024.167483  0.636
2024 Wang MX, Lou EG, Sapoval N, Kim E, Kalvapalle P, Kille B, Elworth RAL, Liu Y, Fu Y, Stadler LB, Treangen TJ. Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens. Nature Communications. 15: 6306. PMID 39060254 DOI: 10.1038/s41467-024-49957-9  0.35
2024 Flinn H, Marshall A, Holcomb M, Cruz L, Soriano S, Treangen TJ, Villapol S. Antibiotic treatment induces microbiome dysbiosis and reduction of neuroinflammation following traumatic brain injury in mice. Research Square. PMID 38946944 DOI: 10.21203/rs.3.rs-4475195/v1  0.698
2024 Curry KD, Yu FB, Vance SE, Segarra S, Bhaya D, Chikhi R, Rocha EPC, Treangen TJ. Reference-free structural variant detection in microbiomes via long-read co-assembly graphs. Bioinformatics (Oxford, England). 40: i58-i67. PMID 38940156 DOI: 10.1093/bioinformatics/btae224  0.333
2024 Sapoval N, Liu Y, Curry KD, Kille B, Huang W, Kokroko N, Nute MG, Tyshaieva A, Dilthey A, Molloy EK, Treangen TJ. Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet. Biorxiv : the Preprint Server For Biology. PMID 38895276 DOI: 10.1101/2024.06.01.596961  0.313
2024 Kille B, Nute MG, Huang V, Kim E, Phillippy AM, Treangen TJ. Parsnp 2.0: Scalable Core-Genome alignment for massive microbial datasets. Bioinformatics (Oxford, England). PMID 38724243 DOI: 10.1093/bioinformatics/btae311  0.612
2024 Agustinho DP, Fu Y, Menon VK, Metcalf GA, Treangen TJ, Sedlazeck FJ. Unveiling microbial diversity: harnessing long-read sequencing technology. Nature Methods. PMID 38689099 DOI: 10.1038/s41592-024-02262-1  0.334
2024 Holcomb M, Marshall A, Flinn H, Lozano M, Soriano S, Gomez-Pinilla F, Treangen TJ, Villapol S. Probiotic treatment causes sex-specific neuroprotection after traumatic brain injury in mice. Research Square. PMID 38645104 DOI: 10.21203/rs.3.rs-4196801/v1  0.708
2024 Curry KD, Soriano S, Nute MG, Villapol S, Dilthey A, Treangen TJ. Microbial Community Profiling Protocol with Full-length 16S rRNA Sequences and Emu. Current Protocols. 4: e978. PMID 38511467 DOI: 10.1002/cpz1.978  0.652
2024 Curry KD, Yu FB, Vance SE, Segarra S, Bhaya D, Chikhi R, Rocha EPC, Treangen TJ. Reference-free Structural Variant Detection in Microbiomes via Long-read Coassembly Graphs. Biorxiv : the Preprint Server For Biology. PMID 38352454 DOI: 10.1101/2024.01.25.577285  0.365
2024 Kille B, Nute MG, Huang V, Kim E, Phillippy AM, Treangen TJ. Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets. Biorxiv : the Preprint Server For Biology. PMID 38352342 DOI: 10.1101/2024.01.30.577458  0.612
2023 Kille B, Garrison E, Treangen TJ, Phillippy AM. Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation. Bioinformatics (Oxford, England). 39. PMID 37603771 DOI: 10.1093/bioinformatics/btad512  0.545
2023 Kille B, Garrison E, Treangen TJ, Phillippy AM. Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation. Biorxiv : the Preprint Server For Biology. PMID 37325780 DOI: 10.1101/2023.05.16.540882  0.545
2023 Wang MX, Lou EG, Sapoval N, Kim E, Kalvapalle P, Kille B, Elworth RAL, Liu Y, Fu Y, Stadler LB, Treangen TJ. Olivar: fully automated and variant aware primer design for multiplex tiled amplicon sequencing of pathogen genomes. Biorxiv : the Preprint Server For Biology. PMID 36824759 DOI: 10.1101/2023.02.11.528155  0.776
2022 Park SH, Cao M, Pan Y, Davis TH, Saxena L, Deshmukh H, Fu Y, Treangen T, Sheehan VA, Bao G. Comprehensive analysis and accurate quantification of unintended large gene modifications induced by CRISPR-Cas9 gene editing. Science Advances. 8: eabo7676. PMID 36269834 DOI: 10.1126/sciadv.abo7676  0.763
2022 Walker K, Kalra D, Lowdon R, Chen G, Molik D, Soto DC, Dabbaghie F, Khleifat AA, Mahmoud M, Paulin LF, Raza MS, Pfeifer SP, Agustinho DP, Aliyev E, Avdeyev P, ... ... Treangen T, et al. The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms. F1000research. 11: 530. PMID 36262335 DOI: 10.12688/f1000research.110194.1  0.762
2022 Kille B, Balaji A, Sedlazeck FJ, Nute M, Treangen TJ. Multiple genome alignment in the telomere-to-telomere assembly era. Genome Biology. 23: 182. PMID 36038949 DOI: 10.1186/s13059-022-02735-6  0.323
2022 Balaji A, Sapoval N, Seto C, Leo Elworth RA, Fu Y, Nute MG, Savidge T, Segarra S, Treangen TJ. KOMB: K-core based de novo characterization of copy number variation in microbiomes. Computational and Structural Biotechnology Journal. 20: 3208-3222. PMID 35832621 DOI: 10.1016/j.csbj.2022.06.019  0.76
2022 Curry KD, Wang Q, Nute MG, Tyshaieva A, Reeves E, Soriano S, Wu Q, Graeber E, Finzer P, Mendling W, Savidge T, Villapol S, Dilthey A, Treangen TJ. Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data. Nature Methods. PMID 35773532 DOI: 10.1038/s41592-022-01520-4  0.665
2022 Soriano S, Curry K, Wang Q, Chow E, Treangen TJ, Villapol S. Fecal Microbiota Transplantation Derived from Alzheimer's Disease Mice Worsens Brain Trauma Outcomes in Wild-Type Controls. International Journal of Molecular Sciences. 23. PMID 35562867 DOI: 10.3390/ijms23094476  0.635
2022 Soriano S, Curry K, Sadrameli SS, Wang Q, Nute M, Reeves E, Kabir R, Wiese J, Criswell A, Schodrof S, Britz GW, Gadhia R, Podell K, Treangen T, Villapol S. Alterations to the gut microbiome after sport-related concussion in a collegiate football players cohort: A pilot study. Brain, Behavior, & Immunity - Health. 21: 100438. PMID 35284846 DOI: 10.1016/j.bbih.2022.100438  0.631
2021 Godbold GD, Kappell AD, LeSassier DS, Treangen TJ, Ternus KL. Categorizing sequences of concern by function to better assess mechanisms of microbial pathogenesis. Infection and Immunity. IAI0033421. PMID 34780277 DOI: 10.1128/IAI.00334-21  0.319
2021 Fu Y, Mahmoud M, Muraliraman VV, Sedlazeck FJ, Treangen TJ. Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment. Gigascience. 10. PMID 34561697 DOI: 10.1093/gigascience/giab063  0.766
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  0.573
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  0.644
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  0.635
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  0.324
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  0.321
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  0.654
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  0.563
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  0.307
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  0.664
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  0.578
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  0.548
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  0.628
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  0.558
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  0.598
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  0.618
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  0.622
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  0.589
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  0.525
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  0.785
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  0.535
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  0.414
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  0.529
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  0.334
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  0.337
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