Mihai Pop - Publications

Affiliations: 
Computer Science University of Maryland, College Park, College Park, MD 
Area:
Bioinformatics and Computational Biology

101 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
2021 Commichaux S, Shah N, Ghurye J, Stoppel A, Goodheart JA, Luque GG, Cummings MP, Pop M. A critical assessment of gene catalogs for metagenomic analysis. Bioinformatics (Oxford, England). PMID 33792639 DOI: 10.1093/bioinformatics/btab216  0.4
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  0.48
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  0.48
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  0.76
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  0.76
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  0.4
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  0.92
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  0.92
2018 Kulkarni P, Olson ND, Paulson JN, Pop M, Maddox C, Claye E, Rosenberg Goldstein RE, Sharma M, Gibbs SG, Mongodin EF, Sapkota AR. Conventional wastewater treatment and reuse site practices modify bacterial community structure but do not eliminate some opportunistic pathogens in reclaimed water. The Science of the Total Environment. 639: 1126-1137. PMID 29929281 DOI: 10.1016/J.Scitotenv.2018.05.178  0.4
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  0.92
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  0.64
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  0.48
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  0.48
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  0.4
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  0.92
2016 Pop M, Paulson JN, Chakraborty S, Astrovskaya I, Lindsay BR, Li S, Bravo HC, Harro C, Parkhill J, Walker AW, Walker RI, Sack DA, Stine OC. Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment. Bmc Genomics. 17: 440. PMID 27277524 DOI: 10.1186/S12864-016-2777-0  0.32
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  1
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  1
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  1
2014 Mandoiu I, Pop M, Rajasekaran S, Spouge JL. This special issue includes a selection of papers presented at the 2nd IEEE International Conference. Introduction. International Journal of Bioinformatics Research and Applications. 10: 341-4. PMID 25715438  1
2014 Mendelowitz L, Pop M. Computational methods for optical mapping. Gigascience. 3: 33. PMID 25671093 DOI: 10.1186/2047-217X-3-33  1
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  1
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  1
2014 Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, Hossain MA, Oundo J, Tamboura B, Mai V, Astrovskaya I, Corrada Bravo H, Rance R, Stares M, Levine MM, Panchalingam S, et al. Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. Genome Biology. 15: R76. PMID 24995464 DOI: 10.1186/Gb-2014-15-6-R76  1
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  1
2014 Paulson JN, Bravo HC, Pop M. Reply to: "a fair comparison". Nature Methods. 11: 359-60. PMID 24681718 DOI: 10.1038/Nmeth.2898  1
2014 Almeida M, Pop M. High-Throughput Sequencing as a Tool for Exploring the Human Microbiome Metagenomics For Microbiology. 55-66. DOI: 10.1016/B978-0-12-410472-3.00004-X  1
2014 Hill CM, Albach CH, Angel SG, Pop M. K-mulus: Strategies for BLAST in the cloud Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8385: 237-246. DOI: 10.1007/978-3-642-55195-6_22  1
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  1
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  1
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  1
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  1
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  0.64
2013 Lindsay B, Ochieng JB, Ikumapayi UN, Toure A, Ahmed D, Li S, Panchalingam S, Levine MM, Kotloff K, Rasko DA, Morris CR, Juma J, Fields BS, Dione M, Malle D, ... ... Pop M, et al. Quantitative PCR for detection of Shigella improves ascertainment of Shigella burden in children with moderate-to-severe diarrhea in low-income countries. Journal of Clinical Microbiology. 51: 1740-6. PMID 23536399 DOI: 10.1128/Jcm.02713-12  1
2013 Nagarajan N, Pop M. Sequence assembly demystified. Nature Reviews. Genetics. 14: 157-67. PMID 23358380 DOI: 10.1038/Nrg3367  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2012 Del Canto F, Botkin DJ, Valenzuela P, Popov V, Ruiz-Perez F, Nataro JP, Levine MM, Stine OC, Pop M, Torres AG, Vidal R. Identification of Coli Surface Antigen 23, a novel adhesin of enterotoxigenic Escherichia coli. Infection and Immunity. 80: 2791-801. PMID 22645287 DOI: 10.1128/Iai.00263-12  1
2012 Pop M. We are what we eat: how the diet of infants affects their gut microbiome. Genome Biology. 13: 152. PMID 22546514 DOI: 10.1186/Gb-2012-13-4-152  1
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  1
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  1
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  1
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  1
2012 Mandoiu I, Pop M, Spouge J. Message from the program chairs 2012 Ieee 2nd International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2012. DOI: 10.1109/ICCABS.2012.6182613  1
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.  1
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/Gb-2011-12-S1-P11  1
2011 Koren S, Treangen TJ, Pop M. Bambus 2: scaffolding metagenomes. Bioinformatics (Oxford, England). 27: 2964-71. PMID 21926123 DOI: 10.1093/Bioinformatics/Btr520  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2011 Mai V, Pop M, Schell M. Metagenomic analysis of human gut microbiota Metagenomics and Its Applications in Agriculture, Biomedicine and Environmental Studies. 255-276.  1
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  1
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  1
2010 Navlakha S, White J, Nagarajan N, Pop M, Kingsford C. Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 503-16. PMID 20377460 DOI: 10.1089/Cmb.2009.0173  1
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  1
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  1
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  1
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  1
2010 Liu B, Pop M. Identifying differentially abundant metabolic pathways in metagenomic datasets Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6053: 101-112. DOI: 10.1007/978-3-642-13078-6_12  1
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  1
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  1
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  1
2009 Pop M. Genome assembly reborn: recent computational challenges. Briefings in Bioinformatics. 10: 354-66. PMID 19482960 DOI: 10.1093/Bib/Bbp026  1
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  1
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  1
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  1
2009 Liu B, Pop M. ARDB--Antibiotic Resistance Genes Database. Nucleic Acids Research. 37: D443-7. PMID 18832362 DOI: 10.1093/Nar/Gkn656  1
2009 White JR, Pop M. Microbial dynamics of human obesity Proceedings - 2009 Ieee International Conference On Bioinformatics and Biomedicine Workshops, Bibmw 2009. 352. DOI: 10.1109/BIBMW.2009.5332071  1
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  1
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  1
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  1
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  1
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  1
2007 Hammel M, Sfyroera G, Pyrpassopoulos S, Ricklin D, Ramyar KX, Pop M, Jin Z, Lambris JD, Geisbrecht BV. Characterization of Ehp, a secreted complement inhibitory protein from Staphylococcus aureus. The Journal of Biological Chemistry. 282: 30051-61. PMID 17699522 DOI: 10.1074/Jbc.M704247200  1
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  1
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  1
2006 Geisbrecht BV, Bouyain S, Pop M. An optimized system for expression and purification of secreted bacterial proteins. Protein Expression and Purification. 46: 23-32. PMID 16260150 DOI: 10.1016/J.Pep.2005.09.003  1
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  1
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  1
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  1
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  1
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  1
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  1
2004 Pop M, Kosack DS, Salzberg SL. Hierarchical scaffolding with Bambus. Genome Research. 14: 149-59. PMID 14707177 DOI: 10.1101/Gr.1536204  1
2004 Pop M. Shotgun Sequence Assembly Advances in Computers. 60: 193-248. DOI: 10.1016/S0065-2458(03)60006-9  1
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  1
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  1
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  1
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  1
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  1
2002 Pop M, Salzberg SL, Shumway M. Genome sequence assembly: Algorithms and issues Computer. 35: 47-54+9. DOI: 10.1109/Mc.2002.1016901  1
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