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List of works by Rick Stevens

A Comprehensive Investigation of Active Learning Strategies for Conducting Anti-Cancer Drug Screening

scholarly article

A communal catalogue reveals Earth's multiscale microbial diversity

scientific article published in November 2017

AI Meets Exascale Computing: Advancing Cancer Research With Large-Scale High Performance Computing

scientific article published on 02 October 2019

AI-accelerated protein-ligand docking for SARS-CoV-2 is 100-fold faster with no significant change in detection

scientific article published in 2023

Accessing the SEED genome databases via Web services API: tools for programmers

scientific article

Antimicrobial Resistance Prediction in PATRIC and RAST.

scientific article published on 14 June 2016

Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center

scientific article

Building the blueprint of life ⬇️

scientific article published on July 1, 2010

Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model.

scientific article published on 29 October 2012

CANDLE/Supervisor: a workflow framework for machine learning applied to cancer research

scholarly article by Justin M Wozniak et al published 21 December 2018 in BMC Bioinformatics

Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation

scientific article

Connecting genotype to phenotype in the era of high-throughput sequencing.

scientific article published on 21 March 2011

Consent insufficient for data release-Response

scientific article published on 01 May 2019

Deep learning methods for drug response prediction in cancer: Predominant and emerging trends

scientific article published in 2023

Detecting operons in bacterial genomes via visual representation learning

scientific article published on 22 January 2021

Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae

scientific article published on 11 January 2018

Enhanced Co-Expression Extrapolation (COXEN) Gene Selection Method for Building Anti-Cancer Drug Response Prediction Models

scientific article published on 11 September 2020

Ensemble transfer learning for the prediction of anti-cancer drug response

scientific article published on 22 October 2020

Essential genes on metabolic maps.

scientific article

Functional metagenomic profiling of nine biomes

scientific article (publication date: 3 April 2008)

Functional metagenomic profiling of nine biomes

scientific article published in Nature

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains

scientific article published in August 2014

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

scientific article

High-throughput generation, optimization and analysis of genome-scale metabolic models

scientific article

IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads

scientific article published on 05 October 2021

Identifying genomic islands with deep neural networks

scientific article published on 02 June 2021

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

scientific article

KBase: The United States Department of Energy Systems Biology Knowledgebase

article

Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project

scientific article

Modeling central metabolism and energy biosynthesis across microbial life

scientific article

National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics

scientific article

PATRIC as a unique resource for studying antimicrobial resistance.

scientific article published on 31 July 2017

PATRIC, the bacterial bioinformatics database and analysis resource

scientific article

Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers

scientific article published in 2021

Performance, Energy, and Scalability Analysis and Improvement of Parallel Cancer Deep Learning CANDLE Benchmarks

scientific article published on 25 July 2019

Predicting tumor cell line response to drug pairs with deep learning

scientific article published on 21 December 2018

RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

scientific article

Real time metagenomics: using k-mers to annotate metagenomes

scientific article

SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models

scientific article

Scalable HPC & AI infrastructure for COVID-19 therapeutics

scientific article published on 26 August 2021

Standardized metadata for human pathogen/vector genomic sequences

scientific article (publication date: 2014)

The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010.

scientific article

The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011.

scientific article published on 22 November 2011

The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes

scientific article

The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation

scientific article published on December 2006

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

scientific article published on 01 January 2020

The RAST Server: rapid annotations using subsystems technology

scientific article

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).

scientific article

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

scientific article

Toward unrestricted use of public genomic data:

scientific article

Trillion Parameter AI Serving Infrastructure for Scientific Discovery: A Survey and Vision

scientific article published on 03 April 2024

Unlocking the potential of metagenomics through replicated experimental design

scientific article published on 7 June 2012

Using machine learning to predict antimicrobial minimum inhibitory concentrations and associated genomic features for nontyphoidal

scientific article published on 30 January 2019

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

scientific article published on 25 June 2009

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