Mihai's publications
2009
N Nagarajan, M Pop Parametric complexity of sequence assembly: theory and applications to next generation sequencing. J Comput Biol, 16:897-908 2009 More details »
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L. Salzberg Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biology, 10:R25 2009 More details »
M. Ghodsi, M. Pop Inexact local alignment search over suffix arrays Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 83-87 2009 PDF More details »
Mihai Pop Genome assembly reborn: recent computational challenges Briefings in Bioinformatics, 10:354-366 2009 More details »
Saket Navlakha, James White, Niranjan Nagarajan, Mihai Pop, Carl Kingsford Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information RECOMB '09: Proceedings of 14th Annual International Conference on Research in Computational Molecular Biology, 2009 More details »
MP Di Bonaventura, R DeSalle, M Pop, N Nagarajan, DH Figurski, DH Fine, JB Kaplan, PJ Planet Complete genome sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700. J Bacteriol, 191:4693-4 2009 More details »
James R. White, Niranjan Nagarajan, Mihai Pop Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples PLoS Computational Biology, 5:e1000352 2009 More details »
Bo Liu, Mihai Pop ARDB - Antibiotic Resistance Genes Database Nucleic Acids Research, 37:D443-D447 2009 More details »
Ben Langmead, Michael C. Schatz, Jimmy Lin, Mihai Pop, Steven L. Salzberg Searching for SNPs with cloud computing Genome Biology, 10:R134 2009 More details »
2008
Niranjan Nagarajan, Timothy D. Read, Mihai Pop Scaffolding and validation of bacterial genome assemblies using optical restriction maps Bioinformatics, 24:1229-1235 2008 More details »
JR White, M Roberts, JA Yorke, M Pop Figaro: a novel statistical method for vector sequence removal. Bioinformatics, 24:462-7 2008 More details »
Niranjan Nagarajan, Rafael Navajas-Perez, Mihai Pop, Maqsudul Alam, Steven L. Salzberg, Ray Ming, Andrew H. Paterson Genome-Wide Analysis of Repetitive Elements in Papaya Tropical Plant Biology, 2008 More details »
AM Phillippy, MC Schatz, M Pop Genome assembly forensics: finding the elusive mis-assembly. Genome Biol, 9:R55 2008 More details »
M Pop, SL Salzberg Bioinformatics challenges of new sequencing technology. Trends Genet, 24:142-9 2008 More details »
2007
AG Clark, MB Eisen, DR Smith, CM Bergman, B Oliver, TA Markow, TC Kaufman, M Kellis, W Gelbart, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450:203-18 2007 More details »
DD Sommer, AL Delcher, SL Salzberg, M Pop Minimus: a fast, lightweight genome assembler. BMC Bioinformatics, 8:64 2007 More details »
M Hammel, G Sfyroera, S Pyrpassopoulos, D Ricklin, KX Ramyar, M Pop, Z Jin, JD Lambris, BV Geisbrecht Characterization of Ehp, a secreted complement inhibitory protein from Staphylococcus aureus. J Biol Chem, 282:30051-61 2007 More details »
E Ghedin, S Wang, D Spiro, E Caler, Q Zhao, J Crabtree, JE Allen, AL Delcher, DB Guiliano, et al. Draft genome of the filarial nematode parasite Brugia malayi. Science, 317:1756-60 2007 More details »
2006 and earlier
SR Gill, M Pop, RT Deboy, PB Eckburg, PJ Turnbaugh, BS Samuel, JI Gordon, DA Relman, CM Fraser-Liggett, et al. Metagenomic analysis of the human distal gut microbiome. Science, 312:1355-9 2006 More details »
M. Pop, M. Pop DNA sequence assembly algorithms. Yearbook of Science and Technology, 2006 More details »
NM El-Sayed, PJ Myler, DC Bartholomeu, D Nilsson, G Aggarwal, AN Tran, E Ghedin, EA Worthey, AL Delcher, et al. The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science, 309:409-15 2005 More details »
B Loftus, I Anderson, R Davies, UC Alsmark, J Samuelson, P Amedeo, P Roncaglia, M Berriman, RP Hirt, et al. The genome of the protist parasite Entamoeba histolytica. Nature, 433:865-8 2005 More details »
SL Salzberg, JC Hotopp, AL Delcher, M Pop, DR Smith, MB Eisen, WC Nelson Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biology, 6:R23 2005 More details »
M. Pop Shotgun Sequence Assembly Advances in Computers. Elsevier, Academic Press, 193-248 2004 More details »
M Pop, A Phillippy, AL Delcher, SL Salzberg Comparative genome assembly. Brief Bioinform, 5:237-48 2004 More details »
M Pop, DS Kosack, SL Salzberg Hierarchical scaffolding with Bambus. Genome Res, 14:149-59 2004 More details »
M Pop, D Kosack Using the TIGR assembler in shotgun sequencing projects. Methods Mol Biol, 255:279-94 2004 More details »
TD Read, SN Peterson, N Tourasse, LW Baillie, IT Paulsen, KE Nelson, H Tettelin, DE Fouts, JA Eisen, et al. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature, 423:81-6 2003 More details »
EF Kirkness, V Bafna, AL Halpern, S Levy, K Remington, DB Rusch, AL Delcher, M Pop, W Wang, et al. The dog genome: survey sequencing and comparative analysis. Science, 301:1898-903 2003 More details »
M. Pop, S.L. Salzberg, M. Shumway Genome sequence assembly: Algorithms and issues Computer, 35:47-54 2002 More details »
KE Nelson, C Weinel, IT Paulsen, RJ Dodson, H Hilbert, VA Martins dos Santos, DE Fouts, SR Gill, M Pop, et al. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol, 4:799-808 2002 More details »
TD Read, SL Salzberg, M Pop, M Shumway, L Umayam, L Jiang, E Holtzapple, JD Busch, KL Smith, et al. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science, 296:2028-33 2002 More details »
JM Carlton, SV Angiuoli, BB Suh, TW Kooij, M Pertea, JC Silva, MD Ermolaeva, JE Allen, JD Selengut, et al. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature, 419:512-9 2002 More details »