Mihai Pop | Academic Influence

Mihai Pop's AcademicInfluence.com Rankings

Mihai Pop

Computer Science

#5666

World Rank

#5984

Historical Rank

Data Science

#96

World Rank

#98

Historical Rank

Computational Linguistics

#849

World Rank

#862

Historical Rank

Machine Learning

#1590

World Rank

#1612

Historical Rank

computer-science Degrees

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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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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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