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01:57 EDT 2nd April 2020 | BioPortfolio

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Showing PubMed Articles 1–25 of 183 from Journal of computational biology : a journal of computational molecular cell biology

Identification of Selective Inhibitors of DHFR Enzyme Using Pharmacoinformatic Methods.

Dihydrofolate reductase (DHFR) is a well-known enzyme of the folate metabolic pathway and it is a validated drug target for leishmaniasis. However, only a few leads are reported against DHFR (DHFR), and thus, there is a need to identify new inhibitors. In this article, pharmacoinformatic tools such as molecular docking, virtual screening, absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiling, and molecular dynamics (MD) simulations were utilized to identify potential DHFR inhibito...

Identification of Prognosis Biomarkers of Prostatic Cancer in a Cohort of 498 Patients from TCGA, by Chen Z, Hu H. (J Comput Biol Dec 2019: epub ahead of print; DOI: 10.1089/cmb.2019.0224).

Integrated Survival Analysis of mRNA and microRNA Signature of Patients with Breast Cancer Based on Cox Model.

Conditional Random Fields with Least Absolute Shrinkage and Selection Operator to Classifying the Barley Genes Based on Expression Level Affected by the Fungal Infection.

Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data.

Characterizing intratumor heterogeneity (ITH) is crucial to understanding cancer development, but it is hampered by limits of available data sources. Bulk DNA sequencing is the most common technology to assess ITH, but involves the analysis of a mixture of many genetically distinct cells in each sample, which must then be computationally deconvolved. Single-cell sequencing is a promising alternative, but its limitations-for example, high noise, difficulty scaling to large populations, technical artifacts, a...

Efficient Construction of a Complete Index for Pan-Genomics Read Alignment.

Matching Reads to Many Genomes with the -Index.

The -index is a tool for compressed indexing of genomic databases for exact pattern matching, which can be used to completely align reads that perfectly match some part of a genome in the database or to find seeds for reads that do not. This article shows how to download and install the programs ri-buildfasta and ri-align; how to call ri-buildfasta on an FASTA file to build an -index for that file; and how to query that index with ri-align.

De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality Value-Based Algorithm.

An Efficient, Scalable, and Exact Representation of High-Dimensional Color Information Enabled Using de Bruijn Graph Search.

MethCP: Differentially Methylated Region Detection with Change Point Models.

PyGTED: Python Application for Computing Graph Traversal Edit Distance.

Designing RNA Secondary Structures Is Hard.

A Nested 2-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in .

Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data.

Preface Special Issue: RECOMB 2018.

AptaBlocks Online: A Web-Based Toolkit for the In Silico Design of Oligonucleotide Sticky Bridges.

Comparison of Pseudoknotted RNA Secondary Structures by Topological Centroid Identification and Tree Edit Distance.

Graph Traversal Edit Distance and Extensions.

A Practicable Method of Tuning the Noise Intensity at Protein Level.

Context-Specific Nested Effects Models.

A Unifying Framework for Imputing Summary Statistics in Genome-Wide Association Studies.

Methods to impute missing data are routinely used to increase power in genome-wide association studies. There are two broad classes of imputation methods. The first class imputes genotypes at the untyped variants, given those at the typed variants, and then performs a statistical test of association at the imputed variants. The second class, summary statistic imputation (SSI), directly imputes association statistics at the untyped variants, given the association statistics observed at the typed variants. Th...

Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models.

ChExMix: A Method for Identifying and Classifying Protein-DNA Interaction Subtypes.

Regulatory proteins can employ multiple direct and indirect modes of interaction with the genome. The ChIP-exo mixture model (ChExMix) provides a principled approach to detecting multiple protein-DNA interaction modes in a single ChIP-exo experiment. ChExMix discovers and characterizes binding event subtypes in ChIP-exo data by leveraging both protein-DNA cross-linking signatures and DNA motifs. In this study, we present a summary of the major features and applications of ChExMix. We demonstrate that ChExMi...

Loss-Function Learning for Digital Tissue Deconvolution.

Reverse de Bruijn: Utilizing Reverse Peptide Synthesis to Cover All Amino Acid -mers.

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