List of works by Mihai Pop

A framework for human microbiome research

scientific article

A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity

scientific article published on 20 April 2016

AGORA: Assembly Guided by Optical Restriction Alignment

scientific article

ARDB--Antibiotic Resistance Genes Database

scientific article published on 02 October 2008

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

scientific article

Algorithms in Bioinformatics

Alignment and clustering of phylogenetic markers--implications for microbial diversity studies

scientific article

An optimized system for expression and purification of secreted bacterial proteins

scientific article published on 4 October 2005

Assembly complexity of prokaryotic genomes using short reads

scientific article

Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies ⬇️

scientific article

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

scientific article published on 02 August 2019

Automated ensemble assembly and validation of microbial genomes

scientific article

Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation

scientific article

Bambus 2: scaffolding metagenomes

scientific article

Better Identification of Repeats in Metagenomic Scaffolding

Bioinformatics challenges of new sequencing technology

scientific article published on 11 February 2008

Bioinformatics for the Human Microbiome Project

scientific article

Capturing the most wanted taxa through cross-sample correlations

scientific article published on 04 March 2016

Chaperone-Usher Pili Loci of Colonization Factor-Negative Human Enterotoxigenic Escherichia coli

scientific article published on January 2016

Characterization of Ehp, a secreted complement inhibitory protein from Staphylococcus aureus

scientific article

Comparative genome assembly.

scientific article published in September 2004

Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis

scientific article (publication date: 14 June 2002)

Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440

scientific article

Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440

article by K. E. Nelson et al published July 2003 in Environmental Microbiology

Complete genome sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700.

scientific article published on 15 May 2009

Computational methods for optical mapping

scientific article

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

scientific article published on 2 October 2017

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

scientific article published on 5 November 2018

DNACLUST: accurate and efficient clustering of phylogenetic marker genes

scientific article

De novo likelihood-based measures for comparing genome assemblies

scientific article

Deep sequencing of the oral microbiome reveals signatures of periodontal disease

scientific article

Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition

scientific article

Differential abundance analysis for microbial marker-gene surveys

scientific article

Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers

scientific article

Draft genome of the filarial nematode parasite Brugia malayi

scientific article

Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads

scientific article published on 26 May 2021

Evolution of genes and genomes on the Drosophila phylogeny

scientific article

Exploiting sparseness in de novo genome assembly

scientific article

Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold

scientific article

Figaro: a novel statistical method for vector sequence removal

scientific article

Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information

article

Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information.

scientific article published in March 2010

Finishing genomes with limited resources: lessons from an ensemble of microbial genomes

scientific article

GAGE: A critical evaluation of genome assemblies and assembly algorithms

scientific article published on 6 January 2012

Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering

scientific article

Genome Sequencing of Four Strains of Rickettsia prowazekii, the Causative Agent of Epidemic Typhus, Including One Flying Squirrel Isolate

scientific article

Genome assembly forensics: finding the elusive mis-assembly

scientific article

Genome assembly reborn: recent computational challenges

scientific article

Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii

scientific article

Genome sequence assembly: algorithms and issues

scholarly article by Mihai Pop et al published July 2002 in Computer

Genomic characterization of the Yersinia genus

scientific article

Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies

scientific article published on 23 December 2011

Hierarchical scaffolding with Bambus

scientific article

Identification of Coli Surface Antigen 23, a novel adhesin of enterotoxigenic Escherichia coli

scientific article published on 29 May 2012

Identification of microbiota dynamics using robust parameter estimation methods

scientific article published on 10 October 2017

Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets

article published in 2010

Incidence of fecal indicator and pathogenic bacteria in reclaimed and return flow waters in Arizona, USA

scientific article published on 01 December 2018

Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment

scientific article

Inexact Local Alignment Search over Suffix Arrays

scientific article published on November 2009

Integrating Hi-C links with assembly graphs for chromosome-scale assembly

scientific article published on 21 August 2019

Invited: Challenges in metagenomic assembly

Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection

scientific article published on 08 July 2016

Maligner: a fast ordered restriction map aligner

scientific article published on 3 December 2015

Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens

scientific article published on 15 February 2017

Messages from the Chairs

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

scientific article

MetaCarvel: linking assembly graph motifs to biological variants

scientific article published on 26 August 2019

MetaPath: identifying differentially abundant metabolic pathways in metagenomic datasets

scientific article

MetaPhyler: Taxonomic profiling for metagenomic sequences

Metagenomic analysis of the human distal gut microbiome

scientific article

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes

scientific article

Microbial dynamics of human obesity

article

Microbiota of the Hickey Run Tributary of the Anacostia River

scientific article published on 21 March 2019

Microbiota that affect risk for shigellosis in children in low-income countries

scientific article

Minimus: a fast, lightweight genome assembler

scientific article

Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows

scientific article published on 01 May 2019

Modern technologies and algorithms for scaffolding assembled genomes

scientific article published on 05 June 2019

Next generation sequence assembly with AMOS.

scientific article

Outlier detection in BLAST hits.

scientific article published on 22 March 2018

Parametric complexity of sequence assembly: theory and applications to next generation sequencing

scientific article

Pharmaceuticals, herbicides, and disinfectants in agricultural water sources

scientific article published on 17 April 2019

Quantitative PCR for detection of Shigella improves ascertainment of Shigella burden in children with moderate-to-severe diarrhea in low-income countries

scientific article

Reply to: "a fair comparison".

scientific article published in April 2014

Scaffolding and validation of bacterial genome assemblies using optical restriction maps

scientific article

Scaffolding of long read assemblies using long range contact information

scientific article

Searching for SNPs with cloud computing

scientific article

Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

scientific article published on 28 October 2020

SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning

scientific article published in 2022

Sequence assembly demystified

scientific article

Sequencing and genome assembly using next-generation technologies

scientific article published on January 2010

Serendipitous discovery of Wolbachia genomes in multiple Drosophila species

scientific article

Shotgun Sequence Assembly

article

Statistical methods for detecting differentially abundant features in clinical metagenomic samples

scientific article

Structure, function and diversity of the healthy human microbiome

scientific article

Suppression subtractive hybridization PCR isolation of cDNAs from a Caribbean soft coral

Survey of culture, goldengate assay, universal biosensor assay, and 16S rRNA Gene sequencing as alternative methods of bacterial pathogen detection

scientific article

TIPP: taxonomic identification and phylogenetic profiling

scientific article

Temporal Variations in Cigarette Tobacco Bacterial Community Composition and Tobacco-Specific Nitrosamine Content Are Influenced by Brand and Storage Conditions

scientific article published on 07 March 2017

The Genome Sequence of Trypanosoma cruzi, Etiologic Agent of Chagas Disease

scientific article

The Theory and Practice of Genome Sequence Assembly

scientific article published on 22 April 2015

The dog genome: survey sequencing and comparative analysis

scientific article

The genome of the protist parasite Entamoeba histolytica

scientific article

The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria

scientific article

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

scientific article

We are what we eat: how the diet of infants affects their gut microbiome

scientific article

Workshop: Can you assemble whole genomes from next generation sequencing data?

Workshop: Comparative assembly of metagenomic sequences

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

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