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Comparative Genomic Analysis of Bacterial Data in BV-BRC: An Example Exploring Antimicrobial Resistance
As genomic and related data continue to expand, research biologists are often hampered by the computational hurdles required to analyze their data. The National Institute of Allergy and Infectious Diseases (NI...
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Open AccessAI-accelerated protein-ligand docking for SARS-CoV-2 is 100-fold faster with no significant change in detection
Protein-ligand docking is a computational method for identifying drug leads. The method is capable of narrowing a vast library of compounds down to a tractable size for downstream simulation or experimental te...
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Open AccessPublisher Correction: Converting tabular data into images for deep learning with convolutional neural networks
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Open AccessConverting tabular data into images for deep learning with convolutional neural networks
Convolutional neural networks (CNNs) have been successfully used in many applications where important information about data is embedded in the order of features, such as speech and imaging. However, most tabu...
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Open AccessLearning curves for drug response prediction in cancer cell lines
Motivated by the size and availability of cell line drug sensitivity data, researchers have been develo** machine learning (ML) models for predicting drug response to advance cancer treatment. As drug sensit...
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Open AccessEnsemble transfer learning for the prediction of anti-cancer drug response
Transfer learning, which transfers patterns learned on a source dataset to a related target dataset for constructing prediction models, has been shown effective in many applications. In this paper, we investig...
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Open AccessCANDLE/Supervisor: a workflow framework for machine learning applied to cancer research
Current multi-petaflop supercomputers are powerful systems, but present challenges when faced with problems requiring large machine learning workflows. Complex algorithms running at system scale, often with di...
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Open AccessPredicting tumor cell line response to drug pairs with deep learning
The National Cancer Institute drug pair screening effort against 60 well-characterized human tumor cell lines (NCI-60) presents an unprecedented resource for modeling combinational drug activity.
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Open AccessDevelo** an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae
Antimicrobial resistant infections are a serious public health threat worldwide. Whole genome sequencing approaches to rapidly identify pathogens and predict antibiotic resistance phenotypes are becoming more ...
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Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center
In the “big data” era, research biologists are faced with analyzing new types that usually require some level of computational expertise. A number of programs and pipelines exist, but acquiring the expertise t...
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Open AccessAntimicrobial Resistance Prediction in PATRIC and RAST
The emergence and spread of antimicrobial resistance (AMR) mechanisms in bacterial pathogens, coupled with the dwindling number of effective antibiotics, has created a global health crisis. Being able to ident...
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Open AccessRASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic ...
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Open AccessComplete genome sequence of Arthrobacter sp. strain FB24
Arthrobacter sp. strain FB24 is a species in the genus Arthrobacter Conn and Dimmick 1947, in the family Micrococcaceae and class Actinobacteria. A number of Arthrobacter genome sequences have been completed beca...
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Open AccessComplete genome sequence of Thauera aminoaromatica strain MZ1T
Thauera aminoaromatica strain MZ1T, an isolate belonging to genus Thauera, of the family Rhodocyclaceae and the class the Betaproteobacteria, has been characterized for its ability to produce abundant exopolysacc...
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Open AccessComplete genome sequence of Polynucleobacter necessariussubsp. asymbioticus type strain (QLW-P1DMWA-1T)
Polynucleobacter necessarius subsp. asymbioticus strain QLW-P1DMWA-1T is a planktonic freshwater bacterium affiliated with the family Burkholderiaceae (class Betaproteobacteria). This strain is of interest becaus...
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Open AccessComplete genome sequence of Paenibacillus sp. strain JDR-2
Paenibacillus sp. strain JDR-2, an aggressively xylanolytic bacterium isolated from sweetgum (Liquidambar styraciflua) wood, is able to efficiently depolymerize, assimilate and metabolize 4-O-methylglucuronoxylan...
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Open AccessComplete genome sequence of the halophilic and highly halotolerant Chromohalobacter salexigens type strain (1H11T)
Chromohalobacter salexigens is one of nine currently known species of the genus Chromohalobacter in the family Halomonadaceae. It is the most halotolerant of the so-called ‘moderately halophilic bacteria’ current...
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Open AccessComplete genome sequence of Parvibaculum lavamentivorans type strain (DS-1T)
Parvibaculum lavamentivorans DS-1T is the type species of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Alphaproteobacteria. Strain DS-1T ...
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Open AccessComplete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95T)
Herpetosiphon aurantiacus Holt and Lewin 1968 is the type species of the genus Herpetosiphon, which in turn is the type genus of the family Herpetosiphonaceae, type family of the order Herpetosiphonales in the ph...
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Open AccessComplete genome sequence of Ferroglobus placidus AEDII12DO
Ferroglobus placidus belongs to the order Archaeoglobales within the archaeal phylum Euryarchaeota. Strain AEDII12DO is the type strain of the species and was isolated from a shallow marine hydrothermal system at...
