| Year |
Citation |
Score |
| 2024 |
Selvaraj Anand S, Wu CT, Bremer J, Bhatti M, Treangen TJ, Kalia A, Shelburne SA, Shropshire WC. Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant causing invasive infections in the USA. Microbial Genomics. 10. PMID 38407244 DOI: 10.1099/mgen.0.001201 |
0.334 |
|
| 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 |
0.509 |
|
| 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 |
0.69 |
|
| 2024 |
Sapoval N, Tanevski M, Treangen TJ. KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 29: 506-520. PMID 38160303 |
0.301 |
|
| 2023 |
Trovao NS, Pan V, Goel C, Gallego-García P, Liu Y, Barbara C, Borg R, Briffa M, Cilia C, Grech L, Vassallo M, Treangen TJ, Posada D, Beheshti A, Borg J, et al. Evolutionary and spatiotemporal analyses reveal multiple introductions and cryptic transmission of SARS-CoV-2 VOC/VOI in Malta. Microbiology Spectrum. e0153923. PMID 37800925 DOI: 10.1128/spectrum.01539-23 |
0.339 |
|
| 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 |
0.589 |
|
| 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 |
0.586 |
|
| 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 |
0.754 |
|
| 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 |
0.759 |
|
| 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 |
0.494 |
|
| 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 |
0.748 |
|
| 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 |
0.387 |
|
| 2022 |
Balaji A, Kille B, Kappell AD, Godbold GD, Diep M, Elworth RAL, Qian Z, Albin D, Nasko DJ, Shah N, Pop M, Segarra S, Ternus KL, Treangen TJ. SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning. Genome Biology. 23: 133. PMID 35725628 DOI: 10.1186/s13059-022-02695-x |
0.34 |
|
| 2022 |
Gallego-García P, Varela N, Estévez-Gómez N, De Chiara L, Fernández-Silva I, Valverde D, Sapoval N, Treangen TJ, Regueiro B, Cabrera-Alvargonzález JJ, Del Campo V, Pérez S, Posada D. Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters. Virus Evolution. 8: veac008. PMID 35242361 DOI: 10.1093/ve/veac008 |
0.429 |
|
| 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 |
0.434 |
|
| 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 |
0.765 |
|
| 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 |
0.404 |
|
| 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 |
0.305 |
|
| 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 |
0.34 |
|
| 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 |
0.306 |
|
| 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 |
0.459 |
|
| 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 |
0.475 |
|
| 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 |
0.302 |
|
| 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 |
0.607 |
|
| 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 |
0.443 |
|
| 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 |
0.68 |
|
| 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 |
0.301 |
|
| 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 |
0.64 |
|
| 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 |
0.589 |
|
| 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 |
0.716 |
|
| 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 |
0.607 |
|
| 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 |
0.681 |
|
| 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 |
0.707 |
|
| 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 |
0.678 |
|
| 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 |
0.661 |
|
| 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 |
0.451 |
|
| 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 |
0.571 |
|
| 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 |
0.784 |
|
| 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 |
0.611 |
|
| 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 |
0.497 |
|
| 2011 |
Koren S, Treangen TJ, Pop M. Bambus 2: scaffolding metagenomes. Bioinformatics (Oxford, England). 27: 2964-71. PMID 21926123 DOI: 10.1093/Bioinformatics/Btr520 |
0.358 |
|
| 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 |
0.554 |
|
| 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 |
0.415 |
|
| 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 |
0.414 |
|
| 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 |
0.482 |
|
| 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 |
0.341 |
|
| 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 |
0.429 |
|
| 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 |
0.495 |
|
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