Mihai Pop
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Mihai Popcomputer-science Degrees
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Data Science
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Computational Linguistics
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Computer Science
Mihai Pop's Degrees
- PhD Computer Science Stanford University
- Masters Computer Science Stanford University
- Bachelors Computer Science Stanford University
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(Suggest an Edit or Addition)Mihai Pop's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome (2009) (19739)
- Structure, Function and Diversity of the Healthy Human Microbiome (2012) (8630)
- Metagenomic Analysis of the Human Distal Gut Microbiome (2006) (4088)
- A framework for human microbiome research (2012) (2113)
- Evolution of genes and genomes on the Drosophila phylogeny (2007) (1992)
- The Genome Sequence of Trypanosoma cruzi, Etiologic Agent of Chagas Disease (2005) (1341)
- Differential abundance analysis for microbial marker-gene surveys (2013) (1326)
- Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples (2009) (1313)
- Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. (2002) (1301)
- ARDB—Antibiotic Resistance Genes Database (2008) (1034)
- The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria (2003) (832)
- The genome of the protist parasite Entamoeba histolytica (2005) (808)
- Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii (2002) (729)
- GAGE: A critical evaluation of genome assemblies and assembly algorithms. (2012) (702)
- Draft Genome of the Filarial Nematode Parasite Brugia malayi (2007) (639)
- Microbiome Metagenomic Analysis of the Human Distal Gut (2009) (616)
- The Dog Genome: Survey Sequencing and Comparative Analysis (2003) (556)
- Searching for SNPs with cloud computing (2009) (520)
- Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software (2017) (514)
- Bioinformatics challenges of new sequencing technology. (2008) (496)
- Sequence assembly demystified (2013) (444)
- Robust methods for differential abundance analysis in marker gene surveys (2013) (436)
- Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus anthracis (2002) (417)
- Minimus: a fast, lightweight genome assembler (2007) (417)
- Genome assembly reborn: recent computational challenges (2009) (402)
- Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease (2012) (364)
- Integrating Hi-C links with assembly graphs for chromosome-scale assembly (2018) (342)
- Genome assembly forensics: finding the elusive mis-assembly (2008) (290)
- Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition (2014) (273)
- Comparative genome assembly (2004) (251)
- Hierarchical scaffolding with Bambus. (2003) (238)
- Assembly complexity of prokaryotic genomes using short reads (2010) (235)
- Exploiting sparseness in de novo genome assembly (2012) (229)
- Scaffolding and validation of bacterial genome assemblies using optical restriction maps (2008) (214)
- Next Generation Sequence Assembly with AMOS (2011) (212)
- MetAMOS: a modular and open source metagenomic assembly and analysis pipeline (2013) (197)
- A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity (2016) (195)
- DNACLUST: accurate and efficient clustering of phylogenetic marker genes (2011) (192)
- Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences (2011) (171)
- Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation (2011) (160)
- Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering (2011) (154)
- Bambus 2: scaffolding metagenomes (2011) (146)
- Serendipitous discovery of Wolbachia genomes in multiple Drosophila species (2005) (143)
- Parametric Complexity of Sequence Assembly: Theory and Applications to Next Generation Sequencing (2009) (136)
- Scaffolding of long read assemblies using long range contact information (2016) (129)
- Genome Sequence Assembly: Algorithms and Issues (2002) (120)
- An optimized system for expression and purification of secreted bacterial proteins. (2006) (116)
- Genomic characterization of the Yersinia genus (2010) (113)
- The Theory and Practice of Genome Sequence Assembly. (2015) (113)
- Non-classical receptive field mediates switch in a sensory neuron ’ s frequency tuning (111)
- Quantitative PCR for Detection of Shigella Improves Ascertainment of Shigella Burden in Children with Moderate-to-Severe Diarrhea in Low-Income Countries (2013) (102)
- Characterization of Ehp, a Secreted Complement Inhibitory Protein from Staphylococcus aureus* (2007) (101)
- Alignment and clustering of phylogenetic markers - implications for microbial diversity studies (2010) (95)
- Metagenomic Assembly: Overview, Challenges and Applications (2016) (94)
- Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes (2019) (94)
- Bioinformatics for the Human Microbiome Project (2012) (84)
- TIPP: taxonomic identification and phylogenetic profiling (2014) (83)
- Metastats: an improved statistical method for analysis of metagenomic data (2011) (80)
- MetaPhyler: Taxonomic profiling for metagenomic sequences (2010) (72)
- Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies (2011) (66)
- Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products (2014) (65)
- Automated ensemble assembly and validation of microbial genomes (2014) (63)
- Finishing genomes with limited resources: lessons from an ensemble of microbial genomes (2010) (63)
- Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows (2018) (61)
- Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software (2017) (58)
- Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation (2018) (57)
- Sequencing and genome assembly using next-generation technologies. (2010) (55)
- De novo likelihood-based measures for comparing genome assemblies (2013) (52)
- AGORA: Assembly Guided by Optical Restriction Alignment (2012) (51)
- Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment (2016) (50)
- Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information (2009) (49)
- Shotgun Sequence Assembly (2004) (48)
- MetaPath: identifying differentially abundant metabolic pathways in metagenomic datasets (2011) (47)
- Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies (2013) (47)
- Use and mis-use of supplementary material in science publications (2015) (39)
- Conventional wastewater treatment and reuse site practices modify bacterial community structure but do not eliminate some opportunistic pathogens in reclaimed water. (2018) (38)
- Identification of Coli Surface Antigen 23, a Novel Adhesin of Enterotoxigenic Escherichia coli (2012) (38)
- Figaro: a novel statistical method for vector sequence removal (2008) (37)
- Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection (2016) (37)
- Modern technologies and algorithms for scaffolding assembled genomes (2019) (37)
- Temporal Variations in Cigarette Tobacco Bacterial Community Composition and Tobacco-Specific Nitrosamine Content Are Influenced by Brand and Storage Conditions (2017) (36)
- Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences (2011) (36)
- Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold (2013) (35)
- Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens (2017) (32)
- Computational methods for optical mapping (2014) (32)
- Genome-Wide Analysis of Repetitive Elements in Papaya (2008) (31)
- Microbiota That Affect Risk for Shigellosis in Children in Low-Income Countries (2015) (29)
- Complete Genome Sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700 (2009) (28)
- Using the TIGR assembler in shotgun sequencing projects. (2004) (26)
- Pharmaceuticals, herbicides, and disinfectants in agricultural water sources. (2019) (26)
- Metastats: an improved statistical method for analysis of metagenomic data (2011) (26)
- Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species (2005) (26)
- Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection (2013) (23)
- We are what we eat: how the diet of infants affects their gut microbiome (2012) (21)
- Maligner: a fast ordered restriction map aligner (2016) (21)
- The Capacity to Produce Hydrogen Sulfide (H2S) via Cysteine Degradation Is Ubiquitous in the Human Gut Microbiome (2021) (20)
- MetaCompass: Reference-guided Assembly of Metagenomes (2017) (17)
- Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers (2016) (16)
- Benchmarking of computational error-correction methods for next-generation sequencing data (2020) (16)
- MetaCarvel: linking assembly graph motifs to biological variants (2019) (14)
- MetAMOS: a metagenomic assembly and analysis pipeline for AMOS (2011) (14)
- Chaperone-Usher Pili Loci of Colonization Factor-Negative Human Enterotoxigenic Escherichia coli (2017) (13)
- Outlier detection in BLAST hits (2018) (13)
- Genomic Drivers of Multidrug-Resistant Shigella Affecting Vulnerable Patient Populations in the United States and Abroad (2021) (13)
- Incidence of fecal indicator and pathogenic bacteria in reclaimed and return flow waters in Arizona, USA (2019) (13)
- Reply to: "A fair comparison" (2014) (12)
- Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications. (2019) (12)
- TIPP2: metagenomic taxonomic profiling using phylogenetic markers (2021) (12)
- A critical assessment of gene catalogs for metagenomic analysis (2021) (12)
- Capturing the most wanted taxa through cross-sample correlations (2016) (11)
- Erratum: Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440 (Environmental Microbiology 4:12 (799-808)) (2003) (11)
- Metagenomic analysis of bacterial and viral assemblages from a freshwater creek and irrigated field reveals temporal and spatial dynamics. (2019) (10)
- Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets (2010) (9)
- Genome Sequencing of Four Strains of Rickettsia prowazekii, the Causative Agent of Epidemic Typhus, Including One Flying Squirrel Isolate (2013) (9)
- Better Identification of Repeats in Metagenomic Scaffolding (2016) (9)
- SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning (2021) (9)
- MetAMOS: a metagenomic assembly and analysis pipeline for AMOS (2011) (8)
- SeqScreen: a biocuration platform for robust taxonomic and biological process characterization of nucleic acid sequences of interest (2019) (8)
- Characterization of Two Cryptic Plasmids Isolated in Haiti from Clinical Vibrio cholerae Non-O1/Non-O139 (2017) (8)
- SparseAssembler: de novo Assembly with the Sparse de Bruijn Graph (2011) (8)
- On using optical maps for genome assembly (2011) (8)
- Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond (2020) (7)
- Robust Parameter Estimation for Biological Systems: A Study on the Dynamics of Microbial Communities (2015) (7)
- Identification of microbiota dynamics using robust parameter estimation methods. (2017) (7)
- Inexact Local Alignment Search over Suffix Arrays (2009) (7)
- Comparison Of The Respiratory Microbiome In HIV-Infected And HIV-Uninfected Individuals (2012) (7)
- Microbiota of the Hickey Run Tributary of the Anacostia River (2019) (6)
- Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019 (2019) (6)
- What do Eulerian and Hamiltonian cycles have to do with genome assembly? (2021) (6)
- Embracing Ambiguity in the Taxonomic Classification of Microbiome Sequencing Data (2019) (5)
- SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning (2022) (5)
- Zero-Valent Iron Sand Filtration Can Reduce Human and Plant Pathogenic Bacteria While Increasing Plant Growth Promoting Bacteria in Reclaimed Water (2020) (5)
- Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads (2021) (4)
- Suppression subtractive hybridization PCR isolation of cDNAs from a Caribbean soft coral (2001) (4)
- Next Generation Sequencing (Dagstuhl Seminar 16351) (2016) (4)
- Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences (2011) (4)
- K-mulus: Strategies for BLAST in the Cloud (2013) (3)
- High-Throughput Sequencing as a Tool for Exploring the Human Microbiome (2015) (3)
- Whole-Genome Assessment of Clinical Acinetobacter baumannii Isolates Uncovers Potentially Novel Factors Influencing Carbapenem Resistance (2021) (3)
- Limitations of Current Approaches for Reference-Free, Graph-Based Variant Detection (2016) (3)
- 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 (2018) (3)
- Author ' s personal copy Bioinformatics challenges of new sequencing technology (2008) (3)
- MetagenomeScope: Web-Based Hierarchical Visualization of Metagenome Assembly Graphs (2017) (3)
- Benchmarking of computational error-correction methods for next-generation sequencing via unique molecular identifiers (2019) (2)
- Viral diversity in children with diarrhea in Gambia (2011) (2)
- Reconstructing microbial communities (2011) (2)
- ScaffViz: visualizing metagenome assemblies (2011) (2)
- De novo likelihood-based measures for comparing metagenomic assemblies (2013) (2)
- SparseAssembler2: Sparse k-mer Graph for Memory Efficient Genome Assembly (2011) (2)
- Exploiting sparseness in de novo genome assembly (2012) (2)
- Better Greedy Sequence Clustering with Fast Banded Alignment (2017) (2)
- We are what we eat: how the diet of infants affects their gut microbiome (2012) (2)
- Microbial dynamics of human obesity (2009) (2)
- Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection (2016) (1)
- Computational approaches for genome assembly validation (2009) (1)
- Statistical methods for comparing the abundances of metabolic pathways in metagenomics (2010) (1)
- from an ensemble of microbial genomes (2010) (1)
- De novo likelihood-based measures for comparing genome assemblies (2013) (1)
- Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins (2021) (1)
- Invited: Challenges in metagenomic assembly (2011) (1)
- Benchmarking of computational error-correction methods for next-generation sequencing data (2020) (1)
- Optimizing source tracking of Listeria monocytogenes with quasimetagenomics and integrated long and short read sequencing (2020) (1)
- MetaCarvel: linking assembly graph motifs to biological variants (2019) (1)
- Sequence analysis TIPP: taxonomic identification and phylogenetic profiling (2014) (1)
- On using optical maps for genome assembly (2011) (1)
- AGORA: Assembly Guided by Optical Restriction Alignment (2012) (1)
- You can't always sequence your way out of a tight spot (2018) (1)
- nsemble assembly and validation of microbial genomes (2014) (1)
- Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products (2014) (1)
- Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond (2020) (0)
- 23 : 2 Outlier Detection in BLAST Hits 1 Introduction (2017) (0)
- Metamorphic Testing in Bioinformatics Software: A Case Study on Metagenomic Assembly (2022) (0)
- 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 (2018) (0)
- OMICS DAY Schedule 8 : 30 Registration and Coffee 9 : 00 (2012) (0)
- MetAMOS: a modular and open source metagenomic assembly and analysis pipeline (2013) (0)
- Viral diversity in children with diarrhea in Gambia (2011) (0)
- Reconstructing microbial communities (2011) (0)
- Chromosome scale de novo assembly of genomes using chromatin interaction data (2017) (0)
- Paraoxonase and acylated homoserine lactones in urine from patients with urinary tract infections-- relationship to microbial diversity by 16S rRNA gene sequencing (2021) (0)
- Algorithms that can assemble millions of small DNA fragments into gene sequences underlie the current revolution in biotechnology, helping researchers build the growing database of complete genomes. (2002) (0)
- Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation (2023) (0)
- Reference-guided Assembly of Metagenomic Sequences (2016) (0)
- Workshop: Can you assemble whole genomes from next generation sequencing data? (2011) (0)
- Impact of conventional wastewater treatment and reuse site practices on the bacterial community structure of reclaimed water (2018) (0)
- 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. (2017) (0)
- Outlier detection in BLAST hits (2018) (0)
- Gut Microbiome–Wide Search for Bacterial Azoreductases Reveals Potentially Uncharacterized Azoreductases Encoded in the Human Gut Microbiome (2022) (0)
- Automated ensemble assembly and validation of microbial genomes (2014) (0)
- Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment (2016) (0)
- Protein Folding: Computational Challenges (1996) (0)
- Use and mis-use of supplementary material in science publications (2015) (0)
- SCRAPT: an iterative algorithm for clustering large 16S rRNA gene data sets. (2023) (0)
- Robust statistical methods for differential abundance analysis of metagenomics data (2011) (0)
- Scaffolding of long read assemblies using long range contact information (2017) (0)
- Genome Assembly Forensics: Metrics for Assessing Assembly Correctness (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time) (2011) (0)
- stRainy: assembly-based metagenomic strain phasing using long reads (2023) (0)
- Computational challenges in microbiome research (2015) (0)
- Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads (2021) (0)
- K-mulus : A Database-Clustering Approach to Protein BLAST in the Cloud (2011) (0)
- PRAWNS: compact pan-genomic features for whole-genome population genomics (2022) (0)
- Lower odds of moderate-to-severe diarrhea among children co-infected with Cryptosporidium spp . and Shigella spp . or other pathogens compared to children with single infections (2016) (0)
- ACM-BCB 2018 Program Chairs' Welcome (2018) (0)
- TaxaTarget: Fast, Sensitive, and Precise Classification of Microeukaryotes in Metagenomic Data (2021) (0)
- Workshop: Comparative assembly of metagenomic sequences (2012) (0)
- Counting k-mers A novel method for contig abundance estimation in metagenomic sample (2015) (0)
- Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation (2019) (0)
- Next Generation Sequencing – Algorithms , and Software For Biomedical Applications (2016) (0)
- Device and method of electrochemical corrosion potential (2007) (0)
- Eddy current method for characterizing the blockage of an evacuated tube support plate (2010) (0)
- Procedure and analysis tool impurities of a boiling water reactor and pressurized water reactor in situ (2005) (0)
- Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens (2017) (0)
- Procedure for positive identification of an inner surface and an outer surface of sample flakes (2007) (0)
- Variations in Bacterial Communities and Antibiotic Resistance Genes Across Diverse Recycled and Surface Water Irrigation Sources in the Mid-Atlantic and Southwest United States: A CONSERVE Two-Year Field Study (2022) (0)
- ScaffViz: visualizing metagenome assemblies (2011) (0)
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