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MOTIVATION: Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end librarie...

IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have con...

The simultaneous measurement of multiple modalities represents an exciting frontier for single-cell genomics and necessitates computational methods that can define cellular states based on multimodal data. Here, we intro...

Kyoto Encyclopedia of Genes and Genomes (KEGG) is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules. The major component of KEGG is the PATHWAY database that consi...

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information. The genomic information is stored in the...

BACKGROUND: In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reporte...

UNLABELLED: The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been we...

A new implementation of the conductor-like screening solvation model (COSMO) in the GAUSSIAN94 package is presented. It allows Hartree−Fock (HF), density functional (DF) and post-HF energy, and HF and DF gradient calcu...

Abstract In this article we discuss our experience designing and implementing a statistical computing language. In developing this new language, we sought to combine what we felt were useful features from two existing co...

Convolutional networks are at the core of most state of-the-art computer vision solutions for a wide variety of tasks. Since 2014 very deep convolutional networks started to become mainstream, yielding substantial gains ...

Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information ...

Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated ...

Cellular life depends on a complex web of functional associations between biomolecules. Among these associations, protein-protein interactions are particularly important due to their versatility, specificity and adaptabi...

Much of the complexity within cells arises from functional and regulatory interactions among proteins. The core of these interactions is increasingly known, but novel interactions continue to be discovered, and the infor...

The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific Biosciences and Oxford Nanopore Technologies DNA sequencing platfor...

Abstract CHARMM ( C hemistry at HAR vard M acromolecular M echanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build struct...

We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redoc...

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagen...

Abstract ORCA is a general‐purpose quantum chemistry program package that features virtually all modern electronic structure methods (density functional theory, many‐body perturbation and coupled cluster theories, an...

BACKGROUND: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de fa...

By decomposing the image formation process into a sequential application of denoising autoencoders, diffusion models (DMs) achieve state-of-the-art synthesis results on image data and beyond. Additionally, their formulat...

Abstract Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort 1–4 , the structures of around 100,000 un...

We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assist...

Agents repesent a new paradigm for developing software applications. In spite of the interest of this particular way of looking at problems, there is considerable discrepancy on exactly what is an agent and which are the...