Mihai Pop
Publications
2013
2013. Differential abundance analysis for microbial marker-gene surveys. Nature methods. 10
2013. Genome sequencing of four strains of Rickettsia prowazekii, the causative agent of epidemic typhus, including one flying squirrel isolate. Genome announcementsGenome announcements. 1
2013. Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Briefings in bioinformaticsBriefings in bioinformatics. 14
2013. Sequence assembly demystified. Nature Reviews GeneticsNature Reviews Genetics. 14
2013. Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold. Bioinformatics (Oxford, England)Bioinformatics (Oxford, England). 29
2013. K-mulus: Strategies for BLAST in the cloud. 10th International Conference on Parallel Processing and Applied Mathematics (PPAM).
2013. Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection. Journal of Clinical MicrobiologyJournal of Clinical Microbiology. 51
2013. De novo likelihood-based measures for comparing genome assemblies. BMC research notes. 6
2013. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome BiolGenome Biol. 14
2012
2012. AGORA: Assembly Guided by Optical Restriction Alignment. BMC bioinformaticsBMC Bioinformatics. 13
2012. We are what we eat: how the diet of infants affects their gut microbiome. Genome BiologyGenome Biology. 13
2012. Bioinformatics for the Human Microbiome Project. PLOS Computational BiologyPLOS Computational Biology. 8
2012. Exploiting sparseness in de novo genome assembly. BMC bioinformaticsBMC Bioinformatics. 13
2012. Identification of Coli Surface Antigen 23, a Novel Adhesin of Enterotoxigenic Escherichia coli. Infection and immunityInfection and immunity. 80
2012. A framework for human microbiome research. NatureNature. 486
2012. Gene Prediction with Glimmer for Metagenomic Sequences Augmented by Classification and Clustering. Nucleic Acids ResearchNucl. Acids Res.Nucleic Acids ResearchNucl. Acids Res.. 40
2011
2011. DNACLUST: accurate and efficient clustering of phylogenetic marker genes. BMC BioinformaticsBMC Bioinformatics. 12
2011. Next Generation Sequence Assembly with AMOS. Current Protocols in BioinformaticsCurrent Protocols in Bioinformatics. 11
2011. Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. BMC bioinformaticsBMC Bioinformatics. 12
2011. Bambus 2: Scaffolding Metagenomes. Bioinformatics. 27
2011. Suppression subtractive hybridization PCR isolation of cDNAs from a Caribbean soft coral. Electronic Journal of BiotechnologyElectronic Journal of Biotechnology. 14
2011. Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC GenomicsBMC Genomics. 12
2011. MetaPath: identifying differentially abundant metabolic pathways in metagenomic datasets. BMC ProceedingsBMC Proceedings. 5
2010
2010. MetaPhyler: Taxonomic profiling for metagenomic sequences. 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
2010. Alignment and clustering of phylogenetic markers - implications for microbial diversity studies. BMC BioinformaticsBMC Bioinformatics. 11
2010. Assembly complexity of prokaryotic genomes using short reads. BMC bioinformaticsBMC Bioinformatics. 11
2010. Genomic characterization of the Yersinia genus. Genome BiologyGenome Biology. 11
2010. Sequencing and genome assembly using next-generation technologies. Methods Mol. BiolMethods Mol. Biol. 673
2010. Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets. Bioinformatics Research and ApplicationsBioinformatics Research and Applications. 6053
2010. Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information. Journal of Computational BiologyJournal of Computational Biology. 17
2010. Finishing genomes with limited resources: lessons from an ensemble of microbial genomes. BMC GenomicsBMC Genomics. 11
2010. Computational Approaches for Genome Assembly Validation. Biological Data MiningBiological Data Mining.
2009
2009. Genome Assembly Reborn: Recent Computational Challenges. Briefings in BioinformaticsBrief BioinformBriefings in BioinformaticsBrief Bioinform. 10
2009. ARDB--Antibiotic Resistance Genes Database. Nucleic Acids ResearchNucleic Acids Research. 37
2009. Parametric Complexity of Sequence Assembly: Theory and Applications to Next Generation Sequencing. Journal of Computational BiologyJournal of Computational Biology. 16
2009. Searching for SNPs with cloud computing. Genome BiologyGenome Biology. 10
2009. Finding Biologically Accurate Clusterings in Hierarchical Decompositions Using the Variation of Information. Lecture Notes in Computer Science: Research in Computational Molecular BiologyLecture Notes in Computer Science: Research in Computational Molecular Biology. 5541
2009. Inexact Local Alignment Search over Suffix Arrays. IEEE International Conference on Bioinformatics and Biomedicine, 2009. BIBM '09.
2009. Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples. PLoS Comput BiologyPLoS Comput BiolPLoS Comput BiologyPLoS Comput Biol. 5
2009. Complete Genome Sequence of Aggregatibacter (Haemophilus) Aphrophilus NJ8700. Journal of BacteriologyJ. Bacteriol.Journal of BacteriologyJ. Bacteriol.. 191
2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome BiologyGenome Biology. 10
2008
2008. Genome-wide analysis of repetitive elements in papaya. Tropical Plant BiologyTropical Plant Biology. 1
2008. Scaffolding and Validation of Bacterial Genome Assemblies Using Optical Restriction Maps. BioinformaticsBioinformaticsBioinformaticsBioinformatics. 24
2008. Bioinformatics challenges of new sequencing technology. Trends in GeneticsTrends in Genetics. 24
2008. Figaro: A Novel Statistical Method for Vector Sequence Removal. BioinformaticsBioinformaticsBioinformaticsBioinformatics. 24
2008. Genome assembly forensics: finding the elusive mis-assembly. Genome BiologyGenome Biology. 9
2007
2007. Minimus: a fast, lightweight genome assembler. BMC bioinformaticsBMC Bioinformatics. 8
2007. Evolution of genes and genomes on the Drosophila phylogeny. NatureNature. 450
2007. Characterization of Ehp, a Secreted Complement Inhibitory Protein from Staphylococcus aureus. Journal of Biological ChemistryJournal of Biological Chemistry. 282
2006
2006. An optimized system for expression and purification of secreted bacterial proteins. Protein Expression and PurificationProtein Expression and Purification. 46
2006. Metagenomic Analysis of the Human Distal Gut Microbiome. ScienceScienceScienceScience. 312
2005
2005. Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome BiologyGenome Biology. 6
2004
2004. Using the TIGR assembler in shotgun sequencing projects. METHODS IN MOLECULAR BIOLOGY-CLIFTON THEN TOTOWA-METHODS IN MOLECULAR BIOLOGY-CLIFTON THEN TOTOWA-. 255
2004. Hierarchical Scaffolding With Bambus. Genome ResearchGenome Research. 14
2004. Comparative Genome Assembly. Briefings in BioinformaticsBrief BioinformBriefings in BioinformaticsBrief Bioinform. 5
2004. Shotgun Sequence Assembly. Advances in ComputersAdvances in Computers. Volume 60
2003
2003. The dog genome: survey sequencing and comparative analysis. ScienceScience. 301
2003. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. NatureNature. 423
2003. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environmental MicrobiologyEnvironmental Microbiology. 5
2002
2002. Genome sequence assembly: Algorithms and issues. ComputerComputer. 35
2002. Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus Anthracis. ScienceScienceScienceScience. 296
2001
2001. Efficient perspective-accurate silhouette computation and applications. Proceedings of the seventeenth annual symposium on Computational geometry.
2000
1998
1998. Drawing of Two-Dimensional Irregular Meshes. Graph DrawingGraph Drawing. 1547
1998. De-amortization of Algorithms. Computing and CombinatoricsComputing and Combinatorics. 1449
1995
1995. Unsupervised learning of disambiguation rules for part of speech tagging. Proceedings of the third workshop on very large corporaProceedings of the third workshop on very large corpora. 30