| Year |
Citation |
Score |
| 2023 |
Commichaux S, Rand H, Javkar K, Molloy EK, Pettengill JB, Pightling A, Hoffmann M, Pop M, Jayeola V, Foley S, Luo Y. Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation. Bmc Genomics. 24: 165. PMID 37016310 DOI: 10.1186/s12864-023-09245-0 |
0.309 |
|
| 2023 |
Javkar K, Rand H, Strain E, Pop M. PRAWNS: compact pan-genomic features for whole-genome population genomics. Bioinformatics (Oxford, England). 39. PMID 36579850 DOI: 10.1093/bioinformatics/btac844 |
0.4 |
|
| 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 |
0.341 |
|
| 2021 |
Commichaux S, Javkar K, Ramachandran P, Nagarajan N, Bertrand D, Chen Y, Reed E, Gonzalez-Escalona N, Strain E, Rand H, Pop M, Ottesen A. Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads. Bmc Genomics. 22: 389. PMID 34039264 DOI: 10.1186/s12864-021-07702-2 |
0.423 |
|
| 2021 |
Medvedev P, Pop M. What do Eulerian and Hamiltonian cycles have to do with genome assembly? Plos Computational Biology. 17: e1008928. PMID 34014915 DOI: 10.1371/journal.pcbi.1008928 |
0.313 |
|
| 2021 |
Muralidharan HS, Shah N, Meisel JS, Pop M. Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins. Frontiers in Microbiology. 12: 638561. PMID 33717033 DOI: 10.3389/fmicb.2021.638561 |
0.407 |
|
| 2020 |
Mitchell K, Brito JJ, Mandric I, Wu Q, Knyazev S, Chang S, Martin LS, Karlsberg A, Gerasimov E, Littman R, Hill BL, Wu NC, Yang HT, Hsieh K, Chen L, ... ... Pop M, et al. Benchmarking of computational error-correction methods for next-generation sequencing data. Genome Biology. 21: 71. PMID 32183840 DOI: 10.1186/S13059-020-01988-3 |
0.423 |
|
| 2019 |
Chopyk J, Nasko DJ, Allard S, Callahan MT, Bui A, Ferelli AMC, Chattopadhyay S, Mongodin EF, Pop M, Micallef SA, Sapkota AR. Metagenomic analysis of bacterial and viral assemblages from a freshwater creek and irrigated field reveals temporal and spatial dynamics. The Science of the Total Environment. 706: 135395. PMID 31846873 DOI: 10.1016/J.Scitotenv.2019.135395 |
0.301 |
|
| 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 |
0.314 |
|
| 2019 |
Shah N, Meisel JS, Pop M. Embracing Ambiguity in the Taxonomic Classification of Microbiome Sequencing Data. Frontiers in Genetics. 10: 1022. PMID 31681437 DOI: 10.3389/Fgene.2019.01022 |
0.488 |
|
| 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 |
0.502 |
|
| 2019 |
Ghurye J, Rhie A, Walenz BP, Schmitt A, Selvaraj S, Pop M, Phillippy AM, Koren S. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. Plos Computational Biology. 15: e1007273. PMID 31433799 DOI: 10.1371/Journal.Pcbi.1007273 |
0.42 |
|
| 2019 |
Bickhart DM, Watson M, Koren S, Panke-Buisse K, Cersosimo LM, Press MO, Van Tassell CP, Van Kessel JAS, Haley BJ, Kim SW, Heiner C, Suen G, Bakshy K, Liachko I, Sullivan ST, ... ... Pop M, et al. Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation. Genome Biology. 20: 153. PMID 31375138 DOI: 10.1186/S13059-019-1760-X |
0.385 |
|
| 2019 |
Ghurye J, Pop M. Modern technologies and algorithms for scaffolding assembled genomes. Plos Computational Biology. 15: e1006994. PMID 31166948 DOI: 10.1371/Journal.Pcbi.1006994 |
0.545 |
|
| 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 |
0.42 |
|
| 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, ... ... Pop M, 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 |
0.408 |
|
| 2018 |
Shah N, Altschul SF, Pop M. Outlier detection in BLAST hits. Algorithms For Molecular Biology : Amb. 13: 7. PMID 29588650 DOI: 10.1186/S13015-018-0126-3 |
0.449 |
|
| 2017 |
Ceccarelli D, Garriss G, Choi SY, Hasan NA, Stepanauskas R, Pop M, Huq A, Colwell RR. Characterization of Two Cryptic Plasmids Isolated in Haiti from Clinical Vibrio cholerae Non-O1/Non-O139. Frontiers in Microbiology. 8: 2283. PMID 29218035 DOI: 10.3389/Fmicb.2017.02283 |
0.339 |
|
| 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 |
0.521 |
|
| 2017 |
Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, ... ... Pop M, et al. Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software. Nature Methods. PMID 28967888 DOI: 10.1038/Nmeth.4458 |
0.427 |
|
| 2017 |
Ghurye J, Pop M, Koren S, Bickhart D, Chin CS. Scaffolding of long read assemblies using long range contact information. Bmc Genomics. 18: 527. PMID 28701198 DOI: 10.1186/S12864-017-3879-Z |
0.372 |
|
| 2017 |
Chopyk J, Chattopadhyay S, Kulkarni P, Claye E, Babik KR, Reid MC, Smyth EM, Hittle LE, Paulson JN, Cruz-Cano R, Pop M, Buehler SS, Clark PI, Sapkota AR, Mongodin EF. Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens. Microbiome. 5: 22. PMID 28202080 DOI: 10.1186/S40168-017-0235-0 |
0.385 |
|
| 2017 |
Ghurye J, Pop M, Koren S, Bickhart D, Chin C. Chromosome scale de novo assembly of genomes using chromatin interaction data F1000research. 6. DOI: 10.7490/F1000Research.1114160.1 |
0.391 |
|
| 2017 |
Olson ND, Hill CM, Cepeda-Espinoza V, Ghurye J, Koren S, Treangen TJ, Pop M. Metagenomic assembly through the lens of validation: a review of recent advances in assessing and improving the quality of genes and genomes assembled from metagenomes. Briefings in Bioinformatics. DOI: 10.1002/Https://Doi.Org/10.1093/Bib/Bbx098 |
0.432 |
|
| 2016 |
Nguyen NP, Warnow T, Pop M, White B. A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity. Npj Biofilms and Microbiomes. 2: 16004. PMID 28721243 DOI: 10.1038/npjbiofilms.2016.4 |
0.363 |
|
| 2016 |
Del Canto F, O'Ryan M, Pardo M, Torres A, Gutiérrez D, Cádiz L, Valdés R, Mansilla A, Martínez R, Hernández D, Caro B, Levine MM, Rasko DA, Hill CM, Pop M, et al. Chaperone-Usher Pili Loci of Colonization Factor-Negative Human Enterotoxigenic Escherichia coli. Frontiers in Cellular and Infection Microbiology. 6: 200. PMID 28111618 DOI: 10.3389/Fcimb.2016.00200 |
0.316 |
|
| 2016 |
Ghurye JS, Cepeda-Espinoza V, Pop M. Metagenomic Assembly: Overview, Challenges and Applications. The Yale Journal of Biology and Medicine. 89: 353-362. PMID 27698619 |
0.408 |
|
| 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 |
0.416 |
|
| 2016 |
Almeida M, Pop M, Le Chatelier E, Prifti E, Pons N, Ghozlane A, Ehrlich SD. Capturing the most wanted taxa through cross-sample correlations. The Isme Journal. PMID 26943627 DOI: 10.1038/Ismej.2016.35 |
0.556 |
|
| 2015 |
Mendelowitz LM, Schwartz DC, Pop M. Maligner: a fast ordered restriction map aligner. Bioinformatics (Oxford, England). PMID 26637292 DOI: 10.1093/Bioinformatics/Btv711 |
0.427 |
|
| 2015 |
Pop M, Salzberg SL. Use and mis-use of supplementary material in science publications. Bmc Bioinformatics. 16: 237. PMID 26525146 DOI: 10.1186/S12859-015-0668-Z |
0.474 |
|
| 2015 |
Simpson JT, Pop M. The Theory and Practice of Genome Sequence Assembly. Annual Review of Genomics and Human Genetics. 16: 153-72. PMID 25939056 DOI: 10.1146/Annurev-Genom-090314-050032 |
0.575 |
|
| 2015 |
Lindsay B, Oundo J, Hossain MA, Antonio M, Tamboura B, Walker AW, Paulson JN, Parkhill J, Omore R, Faruque AS, Das SK, Ikumapayi UN, Adeyemi M, Sanogo D, Saha D, ... ... Pop M, et al. Microbiota that affect risk for shigellosis in children in low-income countries. Emerging Infectious Diseases. 21: 242-50. PMID 25625766 DOI: 10.3201/Eid2101.140795 |
0.318 |
|
| 2014 |
Mendelowitz L, Pop M. Computational methods for optical mapping. Gigascience. 3: 33. PMID 25671093 DOI: 10.1186/2047-217X-3-33 |
0.384 |
|
| 2014 |
Almeida M, Hébert A, Abraham AL, Rasmussen S, Monnet C, Pons N, Delbès C, Loux V, Batto JM, Leonard P, Kennedy S, Ehrlich SD, Pop M, Montel MC, Irlinger F, et al. Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products. Bmc Genomics. 15: 1101. PMID 25496341 DOI: 10.1186/1471-2164-15-1101 |
0.512 |
|
| 2014 |
Nguyen NP, Mirarab S, Liu B, Pop M, Warnow T. TIPP: taxonomic identification and phylogenetic profiling. Bioinformatics (Oxford, England). 30: 3548-55. PMID 25359891 DOI: 10.1093/Bioinformatics/Btu721 |
0.364 |
|
| 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 |
0.545 |
|
| 2013 |
Paulson JN, Stine OC, Bravo HC, Pop M. Differential abundance analysis for microbial marker-gene surveys. Nature Methods. 10: 1200-2. PMID 24076764 DOI: 10.1038/Nmeth.2658 |
0.319 |
|
| 2013 |
Nijkamp JF, Pop M, Reinders MJ, de Ridder D. Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold. Bioinformatics (Oxford, England). 29: 2826-34. PMID 24058058 DOI: 10.1093/Bioinformatics/Btt502 |
0.488 |
|
| 2013 |
Ghodsi M, Hill CM, Astrovskaya I, Lin H, Sommer DD, Koren S, Pop M. De novo likelihood-based measures for comparing genome assemblies. Bmc Research Notes. 6: 334. PMID 23965294 DOI: 10.1186/1756-0500-6-334 |
0.768 |
|
| 2013 |
Lindsay B, Pop M, Antonio M, Walker AW, Mai V, Ahmed D, Oundo J, Tamboura B, Panchalingam S, Levine MM, Kotloff K, Li S, Magder LS, Paulson JN, Liu B, et al. Survey of culture, goldengate assay, universal biosensor assay, and 16S rRNA Gene sequencing as alternative methods of bacterial pathogen detection. Journal of Clinical Microbiology. 51: 3263-9. PMID 23884998 DOI: 10.1128/Jcm.01342-13 |
0.327 |
|
| 2013 |
Bishop-Lilly KA, Ge H, Butani A, Osborne B, Verratti K, Mokashi V, Nagarajan N, Pop M, Read TD, Richards AL. Genome Sequencing of Four Strains of Rickettsia prowazekii, the Causative Agent of Epidemic Typhus, Including One Flying Squirrel Isolate. Genome Announcements. 1. PMID 23814035 DOI: 10.1128/Genomea.00399-13 |
0.445 |
|
| 2013 |
Nagarajan N, Pop M. Sequence assembly demystified. Nature Reviews. Genetics. 14: 157-67. PMID 23358380 DOI: 10.1038/Nrg3367 |
0.541 |
|
| 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 |
0.482 |
|
| 2013 |
Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M. Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Briefings in Bioinformatics. 14: 213-24. PMID 22199379 DOI: 10.1093/Bib/Bbr074 |
0.668 |
|
| 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 |
0.407 |
|
| 2012 |
Gevers D, Pop M, Schloss PD, Huttenhower C. Bioinformatics for the Human Microbiome Project. Plos Computational Biology. 8: e1002779. PMID 23209389 DOI: 10.1371/Journal.Pcbi.1002779 |
0.356 |
|
| 2012 |
Lin HC, Goldstein S, Mendelowitz L, Zhou S, Wetzel J, Schwartz DC, Pop M. AGORA: Assembly Guided by Optical Restriction Alignment. Bmc Bioinformatics. 13: 189. PMID 22856673 DOI: 10.1186/1471-2105-13-189 |
0.454 |
|
| 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 |
0.373 |
|
| 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 |
0.704 |
|
| 2012 |
Ye C, Ma ZS, Cannon CH, Pop M, Yu DW. Exploiting sparseness in de novo genome assembly. Bmc Bioinformatics. 13: S1. PMID 22537038 DOI: 10.1186/1471-2105-13-S6-S1 |
0.451 |
|
| 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 |
0.695 |
|
| 2012 |
Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL. Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Research. 40: e9. PMID 22102569 DOI: 10.1093/Nar/Gkr1067 |
0.614 |
|
| 2012 |
Liu B, Pop M. Workshop: Comparative assembly of metagenomic sequences 2012 Ieee 2nd International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2012. DOI: 10.1109/ICCABS.2012.6182671 |
0.477 |
|
| 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 (2012) 22 (557-567)) Genome Research. 22: 1196. |
0.37 |
|
| 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 |
0.734 |
|
| 2011 |
Koren S, Treangen TJ, Pop M. Bambus 2: scaffolding metagenomes. Bioinformatics (Oxford, England). 27: 2964-71. PMID 21926123 DOI: 10.1093/Bioinformatics/Btr520 |
0.439 |
|
| 2011 |
Ghodsi M, Liu B, Pop M. DNACLUST: Accurate and efficient clustering of phylogenetic marker genes Bmc Bioinformatics. 12. PMID 21718538 DOI: 10.1186/1471-2105-12-271 |
0.69 |
|
| 2011 |
Liu B, Pop M. MetaPath: identifying differentially abundant metabolic pathways in metagenomic datasets. Bmc Proceedings. 5: S9. PMID 21554767 DOI: 10.1186/1753-6561-5-S2-S9 |
0.383 |
|
| 2011 |
Wetzel J, Kingsford C, Pop M. Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. Bmc Bioinformatics. 12: 95. PMID 21486487 DOI: 10.1186/1471-2105-12-95 |
0.52 |
|
| 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 |
0.48 |
|
| 2011 |
Rasko DA, Worsham PL, Abshire TG, Stanley ST, Bannan JD, Wilson MR, Langham RJ, Decker RS, Jiang L, Read TD, Phillippy AM, Salzberg SL, Pop M, Van Ert MN, Kenefic LJ, et al. Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proceedings of the National Academy of Sciences of the United States of America. 108: 5027-32. PMID 21383169 DOI: 10.1073/Pnas.1016657108 |
0.653 |
|
| 2011 |
Ye C, Cannon CH, Ma ZS, Yu DW, Pop M. SparseAssembler2: Sparse k-mer Graph for Memory Efficient Genome Assembly F1000research. 2. DOI: 10.7490/F1000Research.1089342.1 |
0.353 |
|
| 2011 |
Lopez JV, Ledger A, Santiago-Vázquez LZ, Pop M, Sommer DD, Ranzer LK, Feldman RA, Kerr RG. Suppression subtractive hybridization PCR isolation of cDNAs from a Caribbean soft coral Electronic Journal of Biotechnology. 14. DOI: 10.2225/Vol14-Issue1-Fulltext-3 |
0.441 |
|
| 2011 |
Lin H, Pop M. On using optical maps for genome assembly Genome Biology. 12: P41. DOI: 10.1186/Gb-2011-12-S1-P41 |
0.393 |
|
| 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 |
0.348 |
|
| 2011 |
Paulson JN, Pop M, Bravo HC. Metastats: an improved statistical method for analysis of metagenomic data Genome Biology. 12. DOI: 10.1186/Gb-2011-12-S1-P17 |
0.341 |
|
| 2011 |
Pop M. Reconstructing microbial communities Genome Biology. 12: I13. DOI: 10.1186/Gb-2011-12-S1-I13 |
0.381 |
|
| 2011 |
Pop M. Invited: Challenges in metagenomic assembly 2011 Ieee 1st International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2011. 9. DOI: 10.1109/ICCABS.2011.5729950 |
0.4 |
|
| 2011 |
Pop M. Workshop: Can you assemble whole genomes from next generation sequencing data? 2011 Ieee 1st International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2011. 273. DOI: 10.1109/ICCABS.2011.5729927 |
0.468 |
|
| 2010 |
Nagarajan N, Pop M. Sequencing and genome assembly using next-generation technologies. Methods in Molecular Biology (Clifton, N.J.). 673: 1-17. PMID 20835789 DOI: 10.1007/978-1-60761-842-3_1 |
0.46 |
|
| 2010 |
Nagarajan N, Cook C, Di Bonaventura M, Ge H, Richards A, Bishop-Lilly KA, DeSalle R, Read TD, Pop M. Finishing genomes with limited resources: lessons from an ensemble of microbial genomes. Bmc Genomics. 11: 242. PMID 20398345 DOI: 10.1186/1471-2164-11-242 |
0.567 |
|
| 2010 |
White JR, Navlakha S, Nagarajan N, Ghodsi MR, Kingsford C, Pop M. Alignment and clustering of phylogenetic markers--implications for microbial diversity studies. Bmc Bioinformatics. 11: 152. PMID 20334679 DOI: 10.1186/1471-2105-11-152 |
0.71 |
|
| 2010 |
Kingsford C, Schatz MC, Pop M. Assembly complexity of prokaryotic genomes using short reads. Bmc Bioinformatics. 11: 21. PMID 20064276 DOI: 10.1186/1471-2105-11-21 |
0.467 |
|
| 2010 |
Chen PE, Cook C, Stewart AC, Nagarajan N, Sommer DD, Pop M, Thomason B, Thomason MP, Lentz S, Nolan N, Sozhamannan S, Sulakvelidze A, Mateczun A, Du L, Zwick ME, et al. Genomic characterization of the Yersinia genus. Genome Biology. 11: R1. PMID 20047673 DOI: 10.1186/Gb-2010-11-1-R1 |
0.535 |
|
| 2010 |
Liu B, Pop M. Statistical methods for comparing the abundances of metabolic pathways in metagenomics Genome Biology. 11. DOI: 10.1186/Gb-2010-11-S1-O7 |
0.35 |
|
| 2010 |
Liu B, Gibbons T, Ghodsi M, Pop M. MetaPhyler: Taxonomic profiling for metagenomic sequences Proceedings - 2010 Ieee International Conference On Bioinformatics and Biomedicine, Bibm 2010. 95-100. DOI: 10.1109/BIBM.2010.5706544 |
0.716 |
|
| 2009 |
Ghodsi M, Pop M. Inexact Local Alignment Search over Suffix Arrays. Proceedings. Ieee International Conference On Bioinformatics and Biomedicine. 2009: 83-97. PMID 21278916 DOI: 10.1109/BIBM.2009.25 |
0.652 |
|
| 2009 |
Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computing. Genome Biology. 10: R134. PMID 19930550 DOI: 10.1186/Gb-2009-10-11-R134 |
0.569 |
|
| 2009 |
Nagarajan N, Pop M. Parametric complexity of sequence assembly: theory and applications to next generation sequencing. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 897-908. PMID 19580519 DOI: 10.1089/Cmb.2009.0005 |
0.519 |
|
| 2009 |
Pop M. Genome assembly reborn: recent computational challenges. Briefings in Bioinformatics. 10: 354-66. PMID 19482960 DOI: 10.1093/Bib/Bbp026 |
0.554 |
|
| 2009 |
Di Bonaventura MP, DeSalle R, Pop M, Nagarajan N, Figurski DH, Fine DH, Kaplan JB, Planet PJ. Complete genome sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700. Journal of Bacteriology. 191: 4693-4. PMID 19447908 DOI: 10.1128/Jb.00447-09 |
0.478 |
|
| 2009 |
White JR, Nagarajan N, Pop M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. Plos Computational Biology. 5: e1000352. PMID 19360128 DOI: 10.1371/Journal.Pcbi.1000352 |
0.364 |
|
| 2009 |
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology. 10: R25. PMID 19261174 DOI: 10.1186/Gb-2009-10-3-R25 |
0.634 |
|
| 2009 |
Liu B, Pop M. ARDB--Antibiotic Resistance Genes Database. Nucleic Acids Research. 37: D443-7. PMID 18832362 DOI: 10.1093/Nar/Gkn656 |
0.335 |
|
| 2008 |
Nagarajan N, Read TD, Pop M. Scaffolding and validation of bacterial genome assemblies using optical restriction maps. Bioinformatics (Oxford, England). 24: 1229-35. PMID 18356192 DOI: 10.1093/Bioinformatics/Btn102 |
0.525 |
|
| 2008 |
Phillippy AM, Schatz MC, Pop M. Genome assembly forensics: finding the elusive mis-assembly. Genome Biology. 9: R55. PMID 18341692 DOI: 10.1186/Gb-2008-9-3-R55 |
0.479 |
|
| 2008 |
Pop M, Salzberg SL. Bioinformatics challenges of new sequencing technology. Trends in Genetics : Tig. 24: 142-9. PMID 18262676 DOI: 10.1016/J.Tig.2007.12.006 |
0.647 |
|
| 2008 |
White JR, Roberts M, Yorke JA, Pop M. Figaro: a novel statistical method for vector sequence removal. Bioinformatics (Oxford, England). 24: 462-7. PMID 18202027 DOI: 10.1093/Bioinformatics/Btm632 |
0.499 |
|
| 2008 |
Nagarajan N, Navajas-Pérez R, Pop M, Alam M, Ming R, Paterson AH, Salzberg SL. Genome-Wide Analysis of Repetitive Elements in Papaya Tropical Plant Biology. 1: 191-201. DOI: 10.1007/S12042-008-9015-0 |
0.53 |
|
| 2007 |
Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, ... ... Pop M, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341 |
0.657 |
|
| 2007 |
Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, Delcher AL, Guiliano DB, Miranda-Saavedra D, Angiuoli SV, Creasy T, Amedeo P, Haas B, El-Sayed NM, ... ... Pop M, et al. Draft genome of the filarial nematode parasite Brugia malayi. Science (New York, N.Y.). 317: 1756-60. PMID 17885136 DOI: 10.1126/Science.1145406 |
0.633 |
|
| 2007 |
Sommer DD, Delcher AL, Salzberg SL, Pop M. Minimus: a fast, lightweight genome assembler. Bmc Bioinformatics. 8: 64. PMID 17324286 DOI: 10.1186/1471-2105-8-64 |
0.655 |
|
| 2006 |
Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE. Metagenomic analysis of the human distal gut microbiome. Science (New York, N.Y.). 312: 1355-9. PMID 16741115 DOI: 10.1126/Science.1124234 |
0.49 |
|
| 2005 |
El-Sayed NM, Myler PJ, Bartholomeu DC, Nilsson D, Aggarwal G, Tran AN, Ghedin E, Worthey EA, Delcher AL, Blandin G, Westenberger SJ, Caler E, Cerqueira GC, Branche C, Haas B, ... ... Pop M, et al. The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science (New York, N.Y.). 309: 409-15. PMID 16020725 DOI: 10.1126/Science.1112631 |
0.656 |
|
| 2005 |
Salzberg SL, Dunning Hotopp JC, Delcher AL, Pop M, Smith DR, Eisen MB, Nelson WC. Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biology. 6: 402. PMID 15998463 DOI: 10.1186/Gb-2005-6-7-402 |
0.616 |
|
| 2005 |
Salzberg SL, Dunning Hotopp JC, Delcher AL, Pop M, Smith DR, Eisen MB, Nelson WC. Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biology. 6: R23. PMID 15774024 DOI: 10.1186/Gb-2005-6-3-R23 |
0.695 |
|
| 2005 |
Loftus B, Anderson I, Davies R, Alsmark UC, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP, Mann BJ, Nozaki T, Suh B, Pop M, Duchene M, Ackers J, et al. The genome of the protist parasite Entamoeba histolytica. Nature. 433: 865-8. PMID 15729342 DOI: 10.1038/Nature03291 |
0.46 |
|
| 2004 |
Pop M, Phillippy A, Delcher AL, Salzberg SL. Comparative genome assembly. Briefings in Bioinformatics. 5: 237-48. PMID 15383210 DOI: 10.1093/Bib/5.3.237 |
0.698 |
|
| 2004 |
Pop M, Kosack D. Using the TIGR assembler in shotgun sequencing projects. Methods in Molecular Biology (Clifton, N.J.). 255: 279-94. PMID 15020832 DOI: 10.1385/1-59259-752-1:279 |
0.421 |
|
| 2004 |
Pop M, Kosack DS, Salzberg SL. Hierarchical scaffolding with Bambus. Genome Research. 14: 149-59. PMID 14707177 DOI: 10.1101/Gr.1536204 |
0.675 |
|
| 2004 |
Pop M. Shotgun Sequence Assembly Advances in Computers. 60: 193-248. DOI: 10.1016/S0065-2458(03)60006-9 |
0.521 |
|
| 2003 |
Kirkness EF, Bafna V, Halpern AL, Levy S, Remington K, Rusch DB, Delcher AL, Pop M, Wang W, Fraser CM, Venter JC. The dog genome: survey sequencing and comparative analysis. Science (New York, N.Y.). 301: 1898-903. PMID 14512627 DOI: 10.1126/Science.1086432 |
0.545 |
|
| 2003 |
Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, ... ... Pop M, et al. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature. 423: 81-6. PMID 12721629 DOI: 10.1038/Nature01586 |
0.602 |
|
| 2003 |
Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, Martins dos Santos VAP, Fouts DE, Gill SR, Pop M, Holmes M, Brinkac L, Beanan M, DeBoy RT, Daugherty S, Kolonay J, et al. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440 Environmental Microbiology. 5: 630-630. DOI: 10.1046/J.1462-2920.2003.00480.X |
0.52 |
|
| 2002 |
Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, Martins dos Santos VA, Fouts DE, Gill SR, Pop M, Holmes M, Brinkac L, Beanan M, DeBoy RT, Daugherty S, Kolonay J, et al. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environmental Microbiology. 4: 799-808. PMID 12534463 DOI: 10.1046/J.1462-2920.2002.00366.X |
0.5 |
|
| 2002 |
Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut JD, Koo HL, Peterson JD, Pop M, Kosack DS, Shumway MF, Bidwell SL, et al. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature. 419: 512-9. PMID 12368865 DOI: 10.1038/Nature01099 |
0.625 |
|
| 2002 |
Read TD, Salzberg SL, Pop M, Shumway M, Umayam L, Jiang L, Holtzapple E, Busch JD, Smith KL, Schupp JM, Solomon D, Keim P, Fraser CM. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science (New York, N.Y.). 296: 2028-33. PMID 12004073 DOI: 10.1126/Science.1071837 |
0.675 |
|
| 2002 |
Pop M, Salzberg SL, Shumway M. Genome sequence assembly: Algorithms and issues Computer. 35: 47-54+9. DOI: 10.1109/Mc.2002.1016901 |
0.689 |
|
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