Bioinformatics

Low-cost metagenomic and amplicon-based sequencing has provided a snapshots of microbial communities and their surrounding environments. One of the goals for case-control studies using microbiome data is to investigate whether cases differ from controls in term of the microbiome composition of a particular body ecosystems (e.g., the gut) and which taxa are responsible for any
0 Comments
Protein sequence alignments, as an effective and intuitive way of identifying homologous regions among sequences, play a fundamental role in various biomedical researches such as database construction and query, prediction of protein structure and function, etc. [1]. Protein sequence alignments could identify regions of similarity that may reflect biological relationships among the input sequences. As
0 Comments
Cyclic peptides have attracted considerable interest from both the pharmaceutical industry and academia [1–4] for three main reasons. First, as with monoclonal antibody therapeutics, they can bind to target proteins with high affinities [5]. Second, they can interact with flat, shallow, and featureless surfaces of proteins or protein-protein interaction interfaces that are barely targeted by
0 Comments
We downloaded the MHC-I peptide datasets from the IEDB [48]. We filtered, processed, and prepared the data according to the guidelines in Vang’s work [10]. The amount of highly-binding-affinity peptides of different allele subtypes varies substantially. The 9-mer peptides of HLA-A*0201 are 13,088 while the 9-mer peptides for HLA-A*0206, HLA-B*2705, HLA-A*6802, and Mamu-A1*001:01 are only
0 Comments
Functional Magnetic Resonance Imaging (fMRI) [1, 2] provides a novel perspective for the study of brain functions, which is noninvasive and has high resolution in both space and time. Different from task-based fMRI [3, 4] that studies the brain reacting to stimulus, resting state fMRI [5, 6] studies the inner functional connectivity of brain, which
0 Comments
hoDCA is implemented in the julia language (0.6.2) [16], and depends directly on a) the ArgParse [17] module for command-line arguments and b) on the GaussDCA [18] module for performing preprocessing operations on the MSA and the implicit dependencies for those packages. A typical command-line call is julia hoDCA.jl Example.fasta Example.csv –No_A_Map=1 –Path_Map=A_Map.csv –MaxGap=0.9 –theta=0.2
0 Comments
A major challenge in systems biology is understanding the structure and function of the molecular interaction networks that regulate cellular processes. Gene regulatory networks (GRNs) are abstractions of these networks [1] in which nodes correspond to genes and edges to interactions, providing a high-level overview of the topology of gene-gene interactions and their purposes. A
0 Comments
The potential for astrocyte participation in central nervous system recovery is highlighted by in vitro experiments demonstrating their capacity to transdifferentiate into neurons. Understanding astrocyte plasticity could be advanced by comparing astrocytes with stem cells. RNA sequencing (RNA-seq) is ideal for comparing differences across cell types. However, this novel multi-stage process has the potential to
0 Comments
In this work, a multitask bi-directional RNN model is proposed for extracting entity terms from Chinese EMR. The proposed model can be divided into two parts: shared layer and task specific layer, see Fig. 1. Specifically, vector representation of each word is a concatenation of word embedding and character embedding in the proposed model, see Fig. 2.
0 Comments
The overall approach in this study includes three steps (Fig. 1). We firstly used association rule mining of FAERS indication data to obtain disease comorbidity patterns. Secondly, we constructed a disease comorbidity network (DCN) based on mined rules. Thirdly, we detected the inherent clusters of DCN and examined its correlation with disease genetics, semantic similarity and
0 Comments
The 2018 International Conference on Intelligent Biology and Medicine (ICIBM 2016) provided a multidisciplinary forum for computational scientists and experimental biologists to share their most recent findings in the field of cancer genomics, systems biology, medical informatics, big data analytics and machine learning, among others. The conference was held on June 10–12, 2018, in Los
0 Comments
DLAD4U showed better performance in discovering gene-disease associations and drug/chemical-disease associations compared with COREMINE and CTD_inferred. COREMINE is a concept-oriented application for mining existing biomedical literature to build disease lists [10]. The application attempts to build the relationship between publications and concepts (including diseases) through text mining tools. CTD_inferred predicts new relationships using a “guilt-by-association”
0 Comments
Citation: Brown AV, Campbell JD, Assefa T, Grant D, Nelson RT, Weeks NT, et al. (2018) Ten quick tips for sharing open genomic data. PLoS Comput Biol 14(12): e1006472. https://doi.org/10.1371/journal.pcbi.1006472 Editor: Francis Ouellette, Genome Quebec, CANADA Published: December 27, 2018 This is an open access article, free of all copyright, and may be freely reproduced,
0 Comments
Abstract Several key transcription factors have unusually short half-lives compared to other cellular proteins. Here, we explore the utility of active degradation in shaping how the multiple antibiotic resistance activator MarA coordinates its downstream targets. MarA controls a variety of stress response genes in Escherichia coli. We modify its half-life either by knocking down the
0 Comments
Abstract An ongoing challenge in protein chemistry is to identify the underlying interaction energies that capture protein dynamics. The traditional trade-off in biomolecular simulation between accuracy and computational efficiency is predicated on the assumption that detailed force fields are typically well-parameterized, obtaining a significant fraction of possible accuracy. We re-examine this trade-off in the more
0 Comments
Citation: Jumper JM, Faruk NF, Freed KF, Sosnick TR (2018) Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics. PLoS Comput Biol 14(12): e1006342. https://doi.org/10.1371/journal.pcbi.1006342 Editor: Roland L. Dunbrack Jr., Fox Chase Cancer Center, UNITED STATES Received: September 1, 2017; Accepted: June 21, 2018; Published: December 27, 2018 Copyright:
0 Comments
Citation: B. George A, Korolev KS (2018) Chirality provides a direct fitness advantage and facilitates intermixing in cellular aggregates. PLoS Comput Biol 14(12): e1006645. https://doi.org/10.1371/journal.pcbi.1006645 Editor: Herbert Levine, Rice University, UNITED STATES Received: May 7, 2018; Accepted: November 15, 2018; Published: December 27, 2018 Copyright: © 2018 B. George, Korolev. This is an open access
0 Comments
Posted by: RNA-Seq Blog in Jobs 5 hours ago 121 Views Emeryville, CA R&D Life Sciences Full-time Berkeley Lights: The power of engineering, brought to life. Berkeley Lights, Inc. is enabling precise cell by cell selection and manipulation to empower: cell line development, antibody discovery and engineering, and manufacturing of personalized cellular therapies. Founded in
0 Comments
BE-designer overview BE-Designer is a sgRNA designing tool for CRISPR base editors. BE-Designer rapidly provides a list of all possible sgRNA sequences from a given input DNA sequence along with useful information: possible editable sequences in a target window, relative target positions, GC content, and potential off-target sites. Basically, the interface of BE-Designer was developed
0 Comments
Strand-specific false priming and amplification at the poly(T/a) sites When the SMART protocol (or kit) is applied to prepare NGS libraries from DNA fragments, such as those from chromatin immunoprecipitation (IP), there are five steps, 1) 3′ T-tailing, 2) annealing of DNA SMART poly(dA) primer to the T-tails, 3) primer extension by the SMARTScribe™ reverse
0 Comments
1. Homet Moreno, B. & Ribas, A. Anti-programmed cell death protein-1/ligand-1 therapy in different cancers. Br. J. Cancer 112, 1421–1427 (2015). 2. Pardoll, D. M. The blockade of immune checkpoints in cancer immunotherapy. Nat. Rev. Cancer 12, 252–264 (2012). 3. Dong, H. et al. Tumor-associated B7-H1 promotes T-cell apoptosis: a potential mechanism of immune evasion.
0 Comments
Abstract There are a huge number of pathogens with multi-component transmission cycles, involving amplifier hosts, vectors or complex pathogen life cycles. These complex systems present challenges in terms of modeling and policy development. A lethal tick-borne infectious disease, the Brazilian Spotted Fever (BSF), is a relevant example of that. The current increase of human cases
0 Comments
Abstract This paper presents a variational framework for dense diffeomorphic atlas-mapping onto high-throughput histology stacks at the 20 μm meso-scale. The observed sections are modelled as Gaussian random fields conditioned on a sequence of unknown section by section rigid motions and unknown diffeomorphic transformation of a three-dimensional atlas. To regularize over the high-dimensionality of our
0 Comments
Citation: Lu J, Cao X, Zhong S (2018) A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome. PLoS Comput Biol 14(12): e1006673. https://doi.org/10.1371/journal.pcbi.1006673 Editor: Joshua G. Schraiber, Temple University, UNITED STATES Received: May 26, 2018; Accepted: November 26, 2018; Published: December 26, 2018 Copyright: © 2018 Lu et al. This is
0 Comments
Abstract Research on human motor adaptation has often focused on how people adapt to self-generated or externally-influenced errors. Trial-by-trial adaptation is a person’s response to self-generated errors. Externally-influenced errors applied as catch-trial perturbations are used to calculate a person’s perturbation adaptation rate. Although these adaptation rates are sometimes compared to one another, we show through
0 Comments
I can directly use msms by biopython’s script on windows10’s cmd shell and it runs well. However,if i run the same code on Spyder. It shows “AssertionError: Failed to generate surface file using command:” https://imgur.com/GqmkHzP Is there any solvation on this situation? The code is here from Bio.PDB import * pdb_code = “1d3z” pdb_filename =
0 Comments
Coherent differential expression In this section, we make our concept of coherence precise and describe our procedure, Coherent Network Expression (CoNE), for identifying coherent subnetworks. Let G be a network with gene set V(G) and link set E(G), and let S⊆G be the coherent subnetwork corresponding to differentially expressed genes. The genes in the gene
0 Comments
fastText yielded good results with very low training times for both unsupervised and semi-supervised training. While we introduced a simple pre-proces5sing algorithm for utilizing sentence sequence information, it is noteworthy that fastText functioned well without much additional pre-processing (e.g., rare words and numbers were not removed from the corpora, resulting in a very high number
0 Comments
The algorithmic part of FELLA has already been discussed and validated in [12]. The usage of FELLA is hereby demonstrated on three public human studies on epithelial cells [17], ovarian cancer cells [18] and febrile illnesses [19]. The examples guide the user on how to build the database, format the input data, complete the enrichment
0 Comments
RNA sequencing (RNA-seq) has become a widely used technology for analyzing global gene-expression changes during certain biological processes. It is generally acknowledged that RNA-seq data displays equidispersion and overdispersion characteristics; therefore, most RNA-seq analysis methods were developed based on a negative binomial model capable of capturing both equidispersed and overdispersed data. Researchers from Hebei Normal
0 Comments
Understanding how plants respond to microgravity is critical to providing fresh food during space exploration initiatives. Researchers compared two methods – RNA-Seq and microarray — of analyzing which genes are expressed (the ‘transcriptome’) in plant tissue, specifically in the root tip. The results reveal how plants adapt to the microgravity space environment and can help
0 Comments
Serological surveillance for trachoma is being considered to help programmes undertake post-validation surveillance. Prior analyses of the potential utility of serology have used only single-study-site data, with few studies taking a quantitative modelling approach14,18. In all settings evaluated, our modelling suggested transmission of trachoma had declined over time, either through a step-change in transmission, or
0 Comments
The Surveillance, Epidemiology, and End Result (SEER) collects and curates cancer patient data from electronic pathology (e-path) reports. Those data are used for population-based research on cancer trends to develop cancer treatment and screening policy recommendations. That information is extracted manually by experts, which is labor intensive. This limits the geographical coverage of the database,
0 Comments
Images of tumor biopsies have a long history in oncology, and remain an important component of cancer diagnosis and treatment; they also provide promising opportunities for the application of machine learning to human health. Identifying the genetic signatures of cancer is an active area of research (reviewed in [1]); we examined a dataset [2] where
0 Comments
As the drive towards precision medicine has accelerated, enabled by an ever-increasing abundance of new data and information, the opportunities and challenges in applying computational approaches in cancer research and clinical applications are also growing dramatically. The onset of exascale computing together with the rapid rise of deep learning as an enabling technology and its
0 Comments
I first organize related notations and models. Then, I address details on the six candidate α-diversity metrics, Richness, Shannon17, Simpson18, PD19, PE20 and PQE21,22. Finally, I delineate the test statistic and microbial diversity effect score of aMiAD and the residual permutation-based computational algorithm. While the application of aMiAD can be much broader (e.g., extendable to
0 Comments
Expression landscape of tRNAs across 31 cancer types We obtained tRNA annotations from the UCSC genome browser (http://genome.ucsc.edu/), including 604 tRNA transcripts, 62 codons, and 21 amino acids. We then mapped those reads obtained from miRNA-seq to tRNA annotation to infer the relative expression level of tRNAs. The tRNA expression data were merged to the
0 Comments
Animals All IMPC centers maintain strict ethical review licensing and accrediting bodies that are reflective of their national legislation (Institutional Animal Care and Usage Committees, Regierung von Oberbayern, Com’Eth, Animal Welfare and Ethical Review Bodies, RIKEN Tsukuba Animal Experiments Committee, and Animal Care Committee). Phenotyping procedures consortium-wide were assessed routinely for animal welfare and refined
0 Comments