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Author Details

Gail L Rosen
Drexel University
2006
52
18
PMIDPaper TitleJournal TitlePublished Year
36785708Complet+: a computationally scalable method to improve completeness of large-scale protein sequence clustering.PeerJ2023
37558860Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants.ISME J2023
37095444Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing.BMC Genomics2023
35311562Mapping Data to Deep Understanding: Making the Most of the Deluge of SARS-CoV-2 Genome Sequences.mSystems2022
36552295Interpretable and Predictive Deep Neural Network Modeling of the SARS-CoV-2 Spike Protein Sequence to Predict COVID-19 Disease Severity.Biology (Basel)2022
35157026MetaMutationalSigs: comparison of mutational signature refitting results made easy.Bioinformatics2022
34550967Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network.PLoS Comput Biol2021
33868369RRM2B Is Frequently Amplified Across Multiple Tumor Types: Implications for DNA Repair, Cellular Survival, and Cancer Therapy.Front Genet2021
32140140Emerging Priorities for Microbiome Research.Front Microbiol2020
33193120Teaching Microbiome Analysis: From Design to Computation Through Inquiry.Front Microbiol2020
33126516Amino Acid <i>k</i>-mer Feature Extraction for Quantitative Antimicrobial Resistance (AMR) Prediction by Machine Learning and Model Interpretation for Biological Insights.Biology (Basel)2020
32941419Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization.PLoS Comput Biol2020
32957925Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life.BMC Bioinformatics2020
3080756716S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses.PLoS Comput Biol2019
31825995Exploring thematic structure and predicted functionality of 16S rRNA amplicon data.PLoS One2019
30953547Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.Genome Biol2019
28504951A Sequential Learning Approach for Scaling Up Filter-Based Feature Subset Selection.IEEE Trans Neural Netw Learn Syst2018
29618526Opportunities and obstacles for deep learning in biology and medicine.J R Soc Interface2018
29028210Extensions to Online Feature Selection Using Bagging and Boosting.IEEE Trans Neural Netw Learn Syst2018
28934964Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.Genome Biol2017
28938903Metagenomic characterization of ambulances across the USA.Microbiome2017
27017007Engineering Human Microbiota: Influencing Cellular and Community Dynamics for Therapeutic Applications.Int Rev Cell Mol Biol2016
28725742Nanopore sequencing in microgravity.NPJ Microgravity2016
27138046Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains.Microbiome2016
25607539A toolkit for ARB to integrate custom databases and externally built phylogenies.PLoS One2015
26538306Fizzy: feature subset selection for metagenomics.BMC Bioinformatics2015
26316190Multi-Layer and Recursive Neural Networks for Metagenomic Classification.IEEE Trans Nanobioscience2015
25861819Prokaryotic nucleotide composition is shaped by both phylogeny and the environment.Genome Biol Evol2015
25794384A bootstrap based Neyman-Pearson test for identifying variable importance.IEEE Trans Neural Netw Learn Syst2015
24198250POGO-DB--a database of pairwise-comparisons of genomes and conserved orthologous genes.Nucleic Acids Res2014
25075627Characterizing the empirical distribution of prokaryotic genome n-mers in the presence of nullomers.J Comput Biol2014
24626336WGSQuikr: fast whole-genome shotgun metagenomic classification.PLoS One2014
23261776Establishing a relationship between bacteria in the human gut and complex regional pain syndrome.Brain Behav Immun2013
24467949Selecting age-related functional characteristics in the human gut microbiome.Microbiome2013
23786768Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing.Bioinformatics2013
21844637Exploiting the functional and taxonomic structure of genomic data by probabilistic topic modeling.IEEE/ACM Trans Comput Biol Bioinform2012
22486918Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis.Mol Ecol2012
22293603NBC update: The addition of viral and fungal databases to the Naïve Bayes classification tool.BMC Res Notes2012
22403664Using the RDP classifier to predict taxonomic novelty and reduce the search space for finding novel organisms.PLoS One2012
21232129Combining gene prediction methods to improve metagenomic gene annotation.BMC Bioinformatics2011
22255310Ordering samples along environmental gradients using particle swarm optimization.Annu Int Conf IEEE Eng Med Biol Soc2011
21541181Discovering the unknown: improving detection of novel species and genera from short reads.J Biomed Biotechnol2011
21704267Information-theoretic approaches to SVM feature selection for metagenome read classification.Comput Biol Chem2011
21062764NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads.Bioinformatics2011
19908353Benchmarking blast accuracy of genus/phyla classification of metagenomic reads.Pac Symp Biocomput2010
21097156Benchmarking of gene prediction programs for metagenomic data.Annu Int Conf IEEE Eng Med Biol Soc2010
20876033Comparison of statistical methods to classify environmental genomic fragments.IEEE Trans Nanobioscience2010
19758547Implementation of a Hebbian chemoreceptor model for diffusive source localization.Biosystems2009
20436876Signal processing for metagenomics: extracting information from the soup.Curr Genomics2009
19163534An information theoretic method of microarray probe design for genome classification.Annu Int Conf IEEE Eng Med Biol Soc2008
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Collaborators

Stephen Woloszynek
Beth Israel Deaconess Medical Center
Co-authored papers 7
Christopher E Mason
Feil Family Brain and Mind Research Institute.
Co-authored papers 4
Shawn Levy
HudsonAlpha Institute for Biotechnology
Co-authored papers 3
Noah Alexander
David Geffen School of Medicine, university of california los angeles
Co-authored papers 3
David Koslicki
and the Huck Institutes of the Life Sciences, Penn State University, University Park
Co-authored papers 2
Jonathan Foox
Co-authored papers 2
Stefano Lonardi
University of California Riverside
Co-authored papers 2
Ekaterina Smirnova
Institut de Genetique et de Biologie Moleculaire et Cellulaire
Co-authored papers 1
Alexandr A Kalinin
Broad Institute of Harvard and MIT
Co-authored papers 1
Jack Lanchantin
University of Virginia
Co-authored papers 1
Brett K Beaulieu-Jones
University of Chicago
Co-authored papers 1
Anshul Kundaje
Stanford University.
Co-authored papers 1
Simina M Boca
Georgetown University Medical Center
Co-authored papers 1
David DeCaprio
Broad Institute of Harvard and MIT
Co-authored papers 1
Erica A Golemis
Co-authored papers 1
Laura K Wiley
University of Colorado Anschutz Medical Campus
Co-authored papers 1
Daniel S Himmelstein
University of Pennsylvania
Co-authored papers 1
Anthony Gitter
University of Wisconsin
Co-authored papers 1
Rob Knight
University of California
Co-authored papers 1
Evan M Cofer
Lewis-Sigler Institute for Integrative Genomics, Princeton University
Co-authored papers 1
Casey S Greene
Co-authored papers 1
Michael Zietz
University of Pennsylvania
Co-authored papers 1
Yifan Peng
National Center for Biotechnology Information, National Institutes of Health
Co-authored papers 1
Paul-Michael Agapow
Imperial College London
Co-authored papers 1
Srinivas C Turaga
Howard Hughes Medical Institute
Co-authored papers 1
Roland L Dunbrack
Fox Chase Cancer Center
Co-authored papers 1
Sanjay J Swamidass
Washington University School of Medicine
Co-authored papers 1
Avanti Shrikumar
Stanford University
Co-authored papers 1
Casey S Greene
Dartmouth College Geisel School of Medicine, Princeton University, University of Colorado Anschutz Medical Campus, University of Pennsylvania Perelman School of Medicine
Co-authored papers 1
Enrico Ferrero
Novartis Institutes for BioMedical Research
Co-authored papers 1
Release 1.2