Mihai Pop

PLoS Comput. Biol., 2024

2023

PRAWNS: compact pan-genomic features for whole-genome population genomics.

[BibT_eX]

[DOI]

Bioinform., January, 2023

2022

Metamorphic Testing in Bioinformatics Software: A Case Study on Metagenomic Assembly.

[BibT_eX]

[DOI]

Proceedings of the IEEE/ACM 7th International Workshop on Metamorphic Testing, 2022

Probabilistic Petri Nets Model for Assessing Temporal Variations of the Number of Bikes in Bike-Sharing Stations.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Conference on Automation, 2022

2021

What do Eulerian and Hamiltonian cycles have to do with genome assembly?

[BibT_eX]

[DOI]

Paul Medvedev

PLoS Comput. Biol., 2021

TIPP2: metagenomic taxonomic profiling using phylogenetic markers.

[BibT_eX]

[DOI]

Bioinform., 2021

A critical assessment of gene catalogs for metagenomic analysis.

[BibT_eX]

[DOI]

Bioinform., 2021

2020

Benchmarking of computational error-correction methods for next-generation sequencing data.

[BibT_eX]

[DOI]

Proceedings of the BCB '20: 11th ACM International Conference on Bioinformatics, 2020

Similarity measure for station clustering in bike sharing systems.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Conference on Automation, 2020

2019

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

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2019

Modern technologies and algorithms for scaffolding assembled genomes.

[BibT_eX]

[DOI]

Jay Ghurye

PLoS Comput. Biol., 2019

Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows.

[BibT_eX]

[DOI]

Bioinform., 2019

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

[BibT_eX]

[DOI]

Nathan D. Olson

Victoria Cepeda-Espinoza

Jay Ghurye

Sergey Koren

Briefings Bioinform., 2019

SeqScreen: a biocuration platform for robust taxonomic and biological process characterization of nucleic acid sequences of interest.

[BibT_eX]

[DOI]

Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

2018

Outlier detection in BLAST hits.

[BibT_eX]

[DOI]

Nidhi Shah

Stephen F. Altschul

Algorithms Mol. Biol., 2018

2017

Better Greedy Sequence Clustering with Fast Banded Alignment.

[BibT_eX]

[DOI]

Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017

Gesture-based Visual Analytics in Virtual Reality.

[BibT_eX]

[DOI]

Adrian Sabou

Proceedings of the 14th International Conference on Human Computer Interaction, 2017

Events based advanced control strategy for urban street lighting.

[BibT_eX]

[DOI]

Proceedings of the International Conference on Engineering, Technology and Innovation, 2017

2016

Next Generation Sequencing (Dagstuhl Seminar 16351).

[BibT_eX]

[DOI]

Dagstuhl Reports, 2016

Maligner: a fast ordered restriction map aligner.

[BibT_eX]

[DOI]

Lee Mendelowitz

David C. Schwartz

Bioinform., 2016

Better Identification of Repeats in Metagenomic Scaffolding.

[BibT_eX]

[DOI]

Jay Ghurye

Proceedings of the Algorithms in Bioinformatics - 16th International Workshop, 2016

Limitations of Current Approaches for Reference-Free, Graph-Based Variant Detection.

[BibT_eX]

[DOI]

Amelia Bateman

Proceedings of the 7th ACM International Conference on Bioinformatics, 2016

Two stage scheduling method of touristic transport in multimodal networks.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Conference on Automation, 2016

2015

Use and mis-use of supplementary material in science publications.

[BibT_eX]

[DOI]

Steven Salzberg

BMC Bioinform., 2015

Computational challenges in microbiome research.

[BibT_eX]

[DOI]

Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

2014

Automated ensemble assembly and validation of microbial genomes.

[BibT_eX]

[DOI]

Sergey Koren

Adam M. Phillippy

BMC Bioinform., 2014

TIPP: taxonomic identification and phylogenetic profiling.

[BibT_eX]

[DOI]

Bioinform., 2014

2013

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

[BibT_eX]

[DOI]

Jurgen F. Nijkamp

Marcel J. T. Reinders

Dick de Ridder

Bioinform., 2013

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

[BibT_eX]

[DOI]

Briefings Bioinform., 2013

K-mulus: Strategies for BLAST in the Cloud.

[BibT_eX]

[DOI]

Carl H. Albach

Sebastian Angel

Proceedings of the Parallel Processing and Applied Mathematics, 2013

De novo likelihood-based measures for comparing metagenomic assemblies.

[BibT_eX]

[DOI]

Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

2012

Review of parallel algorithms by Henri Casanova, Arnaud Legrand, and Yves Robert.

[BibT_eX]

[DOI]

SIGACT News, 2012

Bioinformatics for the Human Microbiome Project.

[BibT_eX]

[DOI]

PLoS Comput. Biol., 2012

Exploiting sparseness in de novo genome assembly.

[BibT_eX]

[DOI]

BMC Bioinform., 2012

AGORA: Assembly Guided by Optical Restriction Alignment.

[BibT_eX]

[DOI]

BMC Bioinform., 2012

Workshop: Comparative assembly of metagenomic sequences.

[BibT_eX]

[DOI]

Proceedings of the IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, 2012

2011

SparseAssembler2: Sparse k-mer Graph for Memory Efficient Genome Assembly

[BibT_eX]

[DOI]

CoRR, 2011

SparseAssembler: de novo Assembly with the Sparse de Bruijn Graph

[BibT_eX]

[DOI]

CoRR, 2011

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

[BibT_eX]

[DOI]

Joshua L. Wetzel

Carl Kingsford

BMC Bioinform., 2011

DNACLUST: accurate and efficient clustering of phylogenetic marker genes.

[BibT_eX]

[DOI]

Mohammadreza Ghodsi

BMC Bioinform., 2011

Bambus 2: scaffolding metagenomes.

[BibT_eX]

[DOI]

Sergey Koren

Bioinform., 2011

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

[BibT_eX]

[DOI]

Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011

Invited: Challenges in metagenomic assembly.

[BibT_eX]

[DOI]

Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011

2010

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

[BibT_eX]

[DOI]

J. Comput. Biol., 2010

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

[BibT_eX]

[DOI]

BMC Bioinform., 2010

Assembly complexity of prokaryotic genomes using short reads.

[BibT_eX]

[DOI]

Carl Kingsford

Michael C. Schatz

BMC Bioinform., 2010

Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets.

[BibT_eX]

[DOI]

Proceedings of the Bioinformatics Research and Applications, 6th International Symposium, 2010

MetaPhyler: Taxonomic profiling for metagenomic sequences.

[BibT_eX]

[DOI]

Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010

2009

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples.

[BibT_eX]

[DOI]

James Robert White

Niranjan Nagarajan

PLoS Comput. Biol., 2009

ARDB - Antibiotic Resistance Genes Database.

[BibT_eX]

[DOI]

Nucleic Acids Res., 2009

Parametric Complexity of Sequence Assembly: Theory and Applications to Next Generation Sequencing.

[BibT_eX]

[DOI]

Niranjan Nagarajan

J. Comput. Biol., 2009

Genome assembly reborn: recent computational challenges.

[BibT_eX]

[DOI]

Briefings Bioinform., 2009

Inexact Local Alignment Search over Suffix Arrays.

[BibT_eX]

[DOI]

Mohammadreza Ghodsi

Proceedings of the 2009 IEEE International Conference on Bioinformatics and Biomedicine, 2009

2008

Figaro: a novel statistical method for vector sequence removal.

[BibT_eX]

[DOI]

Bioinform., 2008

Scaffolding and validation of bacterial genome assemblies using optical restriction maps.

[BibT_eX]

[DOI]

Niranjan Nagarajan

Timothy D. Read

Bioinform., 2008

2007

Minimus: a fast, lightweight genome assembler.

[BibT_eX]

[DOI]

BMC Bioinform., 2007

2004

Comparative genome assembly.

[BibT_eX]

[DOI]

Briefings Bioinform., 2004

Shotgun Sequence Assembly.

[BibT_eX]

[DOI]

Adv. Comput., 2004

2002

Genome Sequence Assembly: Algorithms and Issues.

[BibT_eX]

[DOI]

Steven Salzberg

Martin Shumway

Computer, 2002

2001

Efficient perspective-accurate silhouette computation and applications.

[BibT_eX]

[DOI]

Proceedings of the Seventeenth Annual Symposium on Computational Geometry, 2001

1999

Efficient Perspective-Accurate Silhouette Computation.

[BibT_eX]

[DOI]

Proceedings of the Fifteenth Annual Symposium on Computational Geometry, 1999

1998

Drawing of Two-Dimensional Irregular Meshes.

[BibT_eX]

[DOI]

Alok Aggarwal

S. Rao Kosaraju

Proceedings of the Graph Drawing, 6th International Symposium, 1998

De-amortization of Algorithms.

[BibT_eX]

[DOI]

S. Rao Kosaraju