List of works - Scott J Emrich

%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding

scientific article published in November 2017

A molecular mechanism of artemisinin resistance in Plasmodium falciparum malaria

scientific article (publication date: 30 April 2015)

A statistical approach to finding overlooked genetic associations

scientific article

A strategy for assembling the maize (Zea mays L.) genome

scientific article

A supervised learning approach to the ensemble clustering of genes

scientific article

Activation of endothelial cells by extracellular vesicles derived from Mycobacterium tuberculosis infected macrophages or mice.

scientific article published on 31 May 2018

Adjusted likelihood-ratio test for variants with unknown genotypes

scientific article published on 01 October 2018

Analysis of computational codon usage models and their association with translationally slow codons

scientific article published on 30 April 2020

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

scientific article

Assessing De Novo transcriptome assembly metrics for consistency and utility

scientific article

Author Correction: GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison

scientific article published on 10 August 2020

Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion

scientific article

Chromosomal inversions and ecotypic differentiation in Anopheles gambiae: the perspective from whole-genome sequencing

scientific article

Climate-mediated hybrid zone movement revealed with genomics, museum collection, and simulation modeling

scientific article published on 20 February 2018

Corrigendum: Whole genome analysis of a schistosomiasis-transmitting freshwater snail

scientific article published on 23 August 2017

Detecting inversions with PCA in the presence of population structure

scientific article published on 29 October 2020

Evaluation of five ab initio gene prediction programs for the discovery of maize genes

article

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

scientific article published on 02 January 2020

Examination of the genetic basis for sexual dimorphism in the Aedes aegypti (dengue vector mosquito) pupal brain

scientific article

Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow

scientific article published on 15 June 2015

Freshwater bacterial lifestyles inferred from comparative genomics

scientific article

GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison.

scientific article published on 2 November 2017

Gene discovery and annotation using LCM-454 transcriptome sequencing.

scientific article

Gene expression in closely related species mirrors local adaptation: consequences for responses to a warming world.

scientific article

Genetic characterization of a novel Iflavirus associated with vomiting disease in the Chinese oak silkmoth Antheraea pernyi

scientific article

Genetic mapping of fitness determinants across the malaria parasite Plasmodium falciparum life cycle

scientific article published on 14 October 2019

Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.

scientific article

Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection

scientific article

Geochemistry and microbial diversity of a trichloroethene-contaminated Superfund site undergoing intrinsic in situ reductive dechlorination

scientific article published in May 2002

Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.).

scientific article

HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning.

scientific article

Haplotype and minimum-chimerism consensus determination using short sequence data

scientific article

High-quality genetic mapping with ddRADseq in the non-model tree Quercus rubra.

scientific article

High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

scientific article

High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti

scientific article

High-throughput genetic mapping of mutants via quantitative single nucleotide polymorphism typing

scientific article

Highly Accurate and Efficient Data-Driven Methods For Genotype Imputation

scientific article

Leveraging evolutionary relationships to improve Anopheles genome assemblies

MIReAD, a minimum information standard for reporting arthropod abundance data

scientific article published on 25 April 2019

Mapping genomic features to functional traits through microbial whole genome sequences.

scientific article published in January 2014

Minimum Information for Reusable Arthropod Abundance Data (MIReAAD)

scholarly article published 29 September 2018

Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics

scientific article

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes

scientific article published on 27 November 2014

Nearly identical paralogs: implications for maize (Zea mays L.) genome evolution.

scientific article published on 16 November 2006

Network analysis of synonymous codon usage

scientific article published on 01 July 2020

Networks' Characteristics Matter for Systems Biology

scientific article

PROBEmer: A web-based software tool for selecting optimal DNA oligos

scientific article

PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map

publication published on 28 January 2021

Phlebotomus papatasi SP15: mRNA expression variability and amino acid sequence polymorphisms of field populations

scientific article published on 29 May 2015

Phlebotomus papatasi sand fly predicted salivary protein diversity and immune response potential based on in silico prediction in Egypt and Jordan populations

scientific article published on 13 July 2020

Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon

scientific article

Predicting Local Inversions Using Rectangle Clustering and Representative Rectangle Prediction

scientific article published on 05 June 2019

Prediction of fine-tuned promoter activity from DNA sequence

scientific article published on 11 February 2016

Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes

scientific article

RNA-Rocket: An RNA-Seq Analysis Resource for Infectious Disease Research

scholarly article published 14 August 2014

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research

scientific article published on 7 January 2015

Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes

scientific article published on 29 March 2016

Reduced-representation sequencing identifies small effective population sizes of Anopheles gambiae in the north-western Lake Victoria basin, Uganda

article

SNP Mining from Maize 454 EST Sequences ⬇️

scientific article published on 01 July 2007

SNP discovery via 454 transcriptome sequencing

scientific article

Scaling up genome annotation using MAKER and work queue

scientific article published on January 2014

Single molecule sequencing-guided scaffolding and correction of draft assemblies

scientific article published on 6 December 2017

Standardized metadata for human pathogen/vector genomic sequences

scientific article (publication date: 2014)

The B73 Maize Genome: Complexity, Diversity, and Dynamics

scientific article

The evolution of the Anopheles 16 genomes project

scientific article published on 08 July 2013

Tools and Methods from the Anopheles 16 Genome Project

Uncovering Effects from the Structure of Metabarcode Sequences for Metagenetic and Microbiome Analysis

scientific article published on 12 March 2020

VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases

scientific article

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics

scientific article

Whole genome analysis of a schistosomiasis-transmitting freshwater snail.

scientific article published on 16 May 2017

Whole-Genome Shotgun Sequencing of Two β-Proteobacterial Species in Search of the Bulgecin Biosynthetic Cluster.

scientific article published on 22 September 2017

Widespread position-specific conservation of synonymous rare codons within coding sequences.

scientific article

List of works by Scott J Emrich

%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding

A molecular mechanism of artemisinin resistance in Plasmodium falciparum malaria

A statistical approach to finding overlooked genetic associations

A strategy for assembling the maize (Zea mays L.) genome

A supervised learning approach to the ensemble clustering of genes

Activation of endothelial cells by extracellular vesicles derived from Mycobacterium tuberculosis infected macrophages or mice.

Adjusted likelihood-ratio test for variants with unknown genotypes

Analysis of computational codon usage models and their association with translationally slow codons

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Assessing De Novo transcriptome assembly metrics for consistency and utility

Author Correction: GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison

Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion

Chromosomal inversions and ecotypic differentiation in Anopheles gambiae: the perspective from whole-genome sequencing

Climate-mediated hybrid zone movement revealed with genomics, museum collection, and simulation modeling

Corrigendum: Whole genome analysis of a schistosomiasis-transmitting freshwater snail

Detecting inversions with PCA in the presence of population structure

Evaluation of five ab initio gene prediction programs for the discovery of maize genes

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

Examination of the genetic basis for sexual dimorphism in the Aedes aegypti (dengue vector mosquito) pupal brain

Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow

Freshwater bacterial lifestyles inferred from comparative genomics

GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison.

Gene discovery and annotation using LCM-454 transcriptome sequencing.

Gene expression in closely related species mirrors local adaptation: consequences for responses to a warming world.

Genetic characterization of a novel Iflavirus associated with vomiting disease in the Chinese oak silkmoth Antheraea pernyi

Genetic mapping of fitness determinants across the malaria parasite Plasmodium falciparum life cycle

Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.

Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection

Geochemistry and microbial diversity of a trichloroethene-contaminated Superfund site undergoing intrinsic in situ reductive dechlorination

Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.).

HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning.

Haplotype and minimum-chimerism consensus determination using short sequence data

High-quality genetic mapping with ddRADseq in the non-model tree Quercus rubra.

High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti

High-throughput genetic mapping of mutants via quantitative single nucleotide polymorphism typing

Highly Accurate and Efficient Data-Driven Methods For Genotype Imputation

Leveraging evolutionary relationships to improve Anopheles genome assemblies

MIReAD, a minimum information standard for reporting arthropod abundance data

Mapping genomic features to functional traits through microbial whole genome sequences.

Minimum Information for Reusable Arthropod Abundance Data (MIReAAD)

Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes

Nearly identical paralogs: implications for maize (Zea mays L.) genome evolution.

Network analysis of synonymous codon usage

Networks' Characteristics Matter for Systems Biology

PROBEmer: A web-based software tool for selecting optimal DNA oligos

PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map

Phlebotomus papatasi SP15: mRNA expression variability and amino acid sequence polymorphisms of field populations

Phlebotomus papatasi sand fly predicted salivary protein diversity and immune response potential based on in silico prediction in Egypt and Jordan populations

Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon

Predicting Local Inversions Using Rectangle Clustering and Representative Rectangle Prediction

Prediction of fine-tuned promoter activity from DNA sequence

Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes

RNA-Rocket: An RNA-Seq Analysis Resource for Infectious Disease Research

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research

Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes

Reduced-representation sequencing identifies small effective population sizes of Anopheles gambiae in the north-western Lake Victoria basin, Uganda

SNP Mining from Maize 454 EST Sequences ⬇️

SNP discovery via 454 transcriptome sequencing

Scaling up genome annotation using MAKER and work queue

Single molecule sequencing-guided scaffolding and correction of draft assemblies

Standardized metadata for human pathogen/vector genomic sequences

The B73 Maize Genome: Complexity, Diversity, and Dynamics

The evolution of the Anopheles 16 genomes project

Tools and Methods from the Anopheles 16 Genome Project

Uncovering Effects from the Structure of Metabarcode Sequences for Metagenetic and Microbiome Analysis

VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics

Whole genome analysis of a schistosomiasis-transmitting freshwater snail.

Whole-Genome Shotgun Sequencing of Two β-Proteobacterial Species in Search of the Bulgecin Biosynthetic Cluster.

Widespread position-specific conservation of synonymous rare codons within coding sequences.