Arun Somwarpet Seetharam

Extensive modulation of a conserved cis-regulatory code across 589 grass species

The paper identifies a conserved cis-regulatory code across 589 grass species and finds that motif conservation declines rapidly but remains significant over evolutionary time, with adaptive changes linked to ecological transitions.

Fishing for a reelGene: evaluating gene models with evolution and machine learning

reelGene evaluates gene models using machine learning and evolutionary data, finding 28% of maize gene models are incorrectly annotated or nonfunctional.

Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize

The paper identifies genetic variants at transcription factor binding sites that explain a large portion of phenotypic heritability in maize under different water conditions.

Molecular evolution of a reproductive barrier in maize and related species

The paper investigates the molecular evolution of three reproductive barrier loci in maize and related species, identifying gene duplication, selection, and epigenetic silencing mechanisms.

Extensive genome evolution distinguishes maize within a stable tribe of grasses

The paper examines genome evolution in maize and related grasses, revealing variable outcomes of polyploidy across species.

MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.

The paper identifies bi-directionally expressed enhancers in maize with domestication signatures using integrated epigenomic and transcriptomic data from multiple tissues and inbred lines.

Maize and wild relatives show distinct patterns of genome downsizing following polyploidy

The paper compares genome fractionation patterns in maize and its wild relatives, finding distinct subgenome retention and gene loss trends between species.

A unified VCF data set from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize

The paper provides a unified VCF dataset from 1,498 maize accessions to explore genomic diversity using a standardized variant-calling pipeline.

Differences in activity and stability drive transposable element variation in tropical and temperate maize.

The paper develops a pan-TE annotation tool to analyze TE variation in maize, finding that tropical maize has more TE sequences due to active and less methylated LTR retrotransposons.

Current genomic deep learning architectures generalize across grass species but not alleles

The paper benchmarks deep learning models on genomic data across 18 grass species, finding they generalize across species but not across alleles within species.

A pan-tissue, pan-disease compendium of human orphan genes

The paper identifies thousands of human orphan genes from RNA-Seq data, validates them with single-cell RNA-seq, and provides a compendium for future research.

Foster thy young: Enhanced prediction of orphan genes in assembled genomes

The paper evaluates gene annotation pipelines for predicting orphan genes in genomes, finding that combining methods improves prediction accuracy, especially for Arabidopsis.

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

A multi-genome analysis of maize reveals previously unknown variation in gene content, genome structure, and methylation.

pyrpipe: a python package for RNA-Seq workflows

pyrpipe is a Python package that simplifies RNA-Seq analysis by enabling reproducible, flexible, and customizable pipelines through object-oriented programming and integration with existing tools.

SequelTools: A Suite of Tools for Working with PacBio Sequel Raw Sequence Data

SequelTools provides quality control, subsampling, and filtering tools for PacBio Sequel raw sequence data, offering free and platform-independent analysis.

Gapless assembly of maize chromosomes using long read technologies

The paper presents a gapless maize genome assembly using long read technologies and optical maps, achieving telomere-to-telomere assemblies for chromosomes 3 and 9.

Effect of Sequence Depth and Length in Long-read Assembly of the Maize Inbred NC358

This study evaluates the impact of sequence depth and read length on long-read assembly quality for the maize genome, finding that lower depths and shorter reads result in fragmented assemblies.

GenomeQC: A quality assessment tool for genome assemblies and gene structure annotations

GenomeQC evaluates genome assembly and gene annotation quality by integrating multiple metrics and allows benchmarking against reference genomes.

phylostratr: A framework for phylostratigraphy

The paper introduces phylostratr, an R package for phylostratigraphy, enabling automated and customizable analysis of gene evolutionary origins across species.

The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes

The paper assembles and annotates the genome of the soybean cyst nematode, revealing duplications and horizontal gene transfer events in effector genes involved in parasitism.