A5076022537- Cancer-related molecular mechanisms research
- Explainable Artificial Intelligence (XAI)
- Computational Physics and Python Applications
- Anomaly Detection Techniques and Applications
- Machine Learning and Data Classification
- Genomics and Phylogenetic Studies
- Neurological diseases and metabolism
- Metabolomics and Mass Spectrometry Studies
- Food composition and properties
- Escherichia coli research studies
- RNA and protein synthesis mechanisms
- Single-cell and spatial transcriptomics
- Heavy metals in environment
- Machine Learning in Bioinformatics
- Antimicrobial Peptides and Activities
- Soil Carbon and Nitrogen Dynamics
- Ruminant Nutrition and Digestive Physiology
- Soil and Water Nutrient Dynamics
- Cancer Research and Treatments
- Gene Regulatory Network Analysis
- Nutrition, Genetics, and Disease
- Chemical Synthesis and Analysis
- RNA Interference and Gene Delivery
- Genetic and phenotypic traits in livestock
- Cell Image Analysis Techniques
Merck & Co., Inc., Rahway, NJ, USA (United States)
2024
Massachusetts Institute of Technology
2023-2024
Lawrence Berkeley National Laboratory
2021
University of California, Berkeley
2020-2021
University of Alberta
2011-2020
The Structural Classification of Proteins-extended (SCOPe, https://scop.berkeley.edu) knowledgebase aims to provide an accurate, detailed, and comprehensive description the structural evolutionary relationships amongst majority proteins known structure, along with resources for analyzing protein structures their sequences. Structures from PDB are divided into domains classified using a combination manual curation highly precise automated methods. In current release SCOPe, 2.08, we have...
ABSTRACT Machine learning (ML) for protein design requires large fitness datasets generated by high-throughput experiments training, fine-tuning, and benchmarking models. However, most models do not account experimental noise inherent in these datasets, harming model performance changing rankings studies. Here we develop FLIGHTED, a Bayesian method of accounting uncertainty generating probabilistic landscapes from noisy experiments. We demonstrate how FLIGHTED can improve on two categories...
Abstract Background Optimization of an RNA-Sequencing (RNA-Seq) pipeline is critical to maximize power and accuracy identify genetic variants, including SNPs, which may serve as markers select for feed efficiency, leading economic benefits beef production. This study used RNA-Seq data (GEO Accession ID: PRJEB7696 PRJEB15314) from muscle liver tissue, respectively, 12 Nellore steers selected 585 with residual intake measures (RFI; n = 6 low-RFI, high-RFI). Three pipelines were compared...
Oral delivery of peptide therapeutics is limited by degradation gut proteases like chymotrypsin. Existing databases peptidases are in size and do not enable systematic analyses protease substrate preferences, especially for non‐natural amino acids. Thus, stability optimization hit compounds time resource intensive. To accelerate the ligands, we generated large datasets chymotrypsin‐resistant peptides via mRNA display to create a predictive model sequences. Through analysis enriched motifs,...
Bovine spongiform encephalopathy (BSE) is a fatal disorder in cattle characterized by progressive neurodegeneration of the central nervous system.We investigated molecular mechanisms involved during prion infection through identification genes that are differentially expressed (DE) between experimentally infected and non-challenged cattle.Gene expression caudal medulla from control orally animals was compared microarray analysis using 24,000 bovine oligonucleotides representing 16,846...
Super-shedder cattle, which are defined as cattle shedding > 4 log of CFU Escherichia coli O157 (O157) per g feces, responsible for the majority excretion into farm environment. Colonization rectal anal junction by is integral to super shedding. The objective current study was further understand molecular mechanisms colonization during super-shedding through investigating transcriptome whole intestinal tract cattle. We hypothesized that difference in gene expression profiles between anterior...
Liver occupies a unique role in nutritional physiology of lactating dairy cows, but the effects forage source on its metabolism and function have not been well examined. This study was conducted to investigate different liver metabolites key gene functions cows using gas chromatography–time flight/mass spectrometry (GC-TOF/MS) based metabolomics RNA-seq analysis. A total 12 multiparous Holstein were fed 2 diets with source: Alfalfa hay (AH, n = 6) corn stover (CS, 6). The multivariate...
The objective was to determine the effect of maternal nutrition management during mid-gestation on skeletal muscle transcriptome in progeny using 3 dietary treatments. Spring-calving, multiparous cows (n = 25) were limit-fed a common diet at three levels intake achieve 70% NRC requirement (70%REQ; 5.2 kg DMI), 100% energy and protein requirements (REQ; 7.4 130% (130%REQ; 9.7 DMI). Diet composition included soy hulls, corn silage, alfalfa haylage. Treatment diets fed (d 88 171 gestation),...