Scott Emrich

Functional genomic signatures predict microbial culturability across the tree of life

The paper identifies genomic signatures predictive of microbial culturability using MAGs from the GEM catalog, finding that cultured microbes have more conserved metabolic pathways.

Evaluation and optimization of sequence-based gene regulatory deep learning models

The paper evaluates and optimizes sequence-based gene regulatory deep learning models using a DREAM Challenge dataset, showing improvements through architectural and training strategy refinements.

Profiling Expression Strategies for a Type III Polyketide Synthase in a Lysate-Based, Cell-free System

This paper improves the expression of a type III polyketide synthase in cell-free systems by optimizing codon usage and promoters, showing better results than traditional codon optimization.

Genomic Analysis of Two Phlebotomine Sand Fly Vectors of Leishmania from the New and Old World

The paper sequences and annotates the genomes of two sand fly species, identifying genes related to vector biology and population structure to aid in leishmaniasis control.

Synonymous codon substitutions regulate transcription and translation of an upstream gene

The paper shows that synonymous codon substitutions in E. coli can upregulate an upstream gene through cryptic transcription, challenging the view that synonymous mutations have no phenotypic effects.

Whole genome comparisons reveal panmixia among fall armyworm (Spodoptera frugiperda) from diverse locations

The paper analyzes whole genome sequences of fall armyworm samples from multiple locations to show panmixia, with minor gene flow reduction between two host strains in the USA.

Detecting Inversions with PCA in the Presence of Population Structure

The paper applies PCA-based inversion detection to simulated and real insect data, showing its robustness in complex scenarios with multiple inversions or populations.

Phlebotomus papatasi sand fly salivary protein diversity and immune response potential in Egypt and Jordan populations

The paper analyzes genetic variability and immune response potential of salivary proteins in Phlebotomus papatasi sand flies from Egypt and Jordan.

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

The paper evaluates five computational codon usage models for their ability to predict translational slowdowns using ribosome footprint data from S. cerevisiae, finding strong associations but also highlighting inconsistencies in RFP data.

Surprising variation in the outcome of two malaria genetic crosses using humanized mice: implications for genetic mapping and malaria biology

The paper reports two new genetic crosses of Plasmodium falciparum in humanized mice, showing significant variation in marker segregation and demonstrating improved power for genetic mapping of malaria traits.

Functional genomics of the stable fly, Stomoxys calcitrans, reveals mechanisms underlying reproduction, host interactions, and novel targets for pest control

This study provides insights into the biology of the stable fly by combining genome sequencing, microbiome analysis, and RNA-seq to identify genes related to reproduction, host interactions, and pest control.

Improved bacteria population structure analysis on thousands of genomes using unsupervised methods

The paper applies unsupervised clustering to analyze population structure in thousands of bacterial genomes, showing improved identification of mixed genomes and inter-related groups.

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

HECIL improves long read error correction using iterative learning and short read alignments, outperforming existing methods on multiple datasets.

Methods in Description and Validation of Local Metagenetic Microbial Communities

The paper compares MinHash and NMF methods for metagenetic sample similarity and evaluates clustering quality using ecological metadata.

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

RNA-Rocket provides RNA-Seq and ChIP-Seq analysis tools for infectious disease research, offering pre-indexed genomes, educational resources, and integration with bioinformatics platforms.