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1. Improving the usability and archival stability of bioinformatics software

Author:
Mangul, Serghei; Martin, Lana S.; Eskin, Eleazar; Blekhman, Ran
Source:
Genome biology 2019 v.20 no.1 pp. 47
ISSN:
1474-760X
Subject:
bioinformatics,   etc   ; computer software; genomics; product quality;     Show all 4 Subjects
Abstract:
... Implementation of bioinformatics software involves numerous unique challenges; a rigorous standardized approach is needed to examine software tools prior to their publication. ...
DOI:
10.1186/s13059-019-1649-8

2. Protein engineers turned evolutionists—the quest for the optimal starting point

Author:
Trudeau, Devin L; Tawfik, Dan S
Source:
Current opinion in biotechnology 2019 v.60 pp. 46-52
ISSN:
0958-1669
Subject:
bioinformatics,   etc   ; bioengineering; directed evolution; enzymes; phylogeny; plasticity;     Show all 6 Subjects
Abstract:
... The advent of laboratory directed evolution yielded a fruitful crosstalk between the disciplines of molecular evolution and bio-engineering. Here, we outline recent developments in both disciplines with respect to how one can identify the best starting points for directed evolution, such that highly efficient and robust tailor-made enzymes can be obtained with minimal optimization. Directed evolut ...
DOI:
10.1016/j.copbio.2018.12.002

3. The tech for the next decade: promises and challenges in genome biology

Author:
Hajirasouliha, Iman; Tilgner, Hagen U.
Source:
Genome biology 2019 v.20 no.1 pp. 86
ISSN:
1474-760X
Subject:
bioinformatics,   etc   ; gene expression; genome; genome assembly;     Show all 4 Subjects
Abstract:
... The 19th Annual Advances in Genome Biology and Technology (AGBT) meeting came back to Marco Island, Florida, and was held in the renovated venue from 27 February to 2 March 2019. The meeting showed a variety of new technology, both in wet lab and in bioinformatics. This year’s themes included single-cell technology and applications, spatially resolved gene expression measurements, new sequencing p ...
DOI:
10.1186/s13059-019-1695-2

4. A Fast Detection Strategy for Cyanobacterial blooms and associated cyanotoxins (FDSCC) reveals the occurrence of lyngbyatoxin A in campania (South Italy)

Author:
Esposito, Germana; Teta, Roberta; Marrone, Raffaele; De Sterlich, Carlo; Casazza, Marco; Anastasio, Aniello; Lega, Massimiliano; Costantino, Valeria
Source:
Chemosphere 2019 v.225 pp. 342-351
ISSN:
0045-6535
Subject:
bioinformatics,   etc   ; Bivalvia; Cyanobacteria; cyanobacterial toxins; lipophilicity; Italy;     Show all 6 Subjects
Abstract:
... Fast Detection Strategy for Cyanobacterial blooms and associated Cyanotoxins (FDSCC) is a multidisciplinary strategy that allows early detection, in 24 man-hours, of cyanobacteria and related cyanotoxins in water and bivalve samples. This approach combines the advantages of remote/proximal sensing with those of analytical/bioinformatics analyses, namely, LC-HRMS-based molecular networking. The det ...
DOI:
10.1016/j.chemosphere.2019.02.201

5. Deep learning in bioinformatics: Introduction, application, and perspective in the big data era

Author:
Li, Yu; Huang, Chao; Ding, Lizhong; Li, Zhongxiao; Pan, Yijie; Gao, Xin
Source:
Methods 2019
ISSN:
1046-2023
Subject:
bioinformatics,   etc   ; Internet; information management; neural networks; research;     Show all 5 Subjects
Abstract:
... Deep learning, which is especially formidable in handling big data, has achieved great success in various fields, including bioinformatics. With the advances of the big data era in biology, it is foreseeable that deep learning will become increasingly important in the field and will be incorporated in vast majorities of analysis pipelines. In this review, we provide both the exoteric introduction ...
DOI:
10.1016/j.ymeth.2019.04.008

6. Optimization of DamID for use in primary cultures of mouse hepatocytes

Author:
Gatticchi, Leonardo; de las Heras, Jose I.; Roberti, Rita; Schirmer, Eric C.
Source:
Methods 2019 v.157 pp. 88-99
ISSN:
1046-2023
Subject:
bioinformatics,   etc   ; DNA; genome; hepatocytes; mice; tissue culture;     Show all 6 Subjects
Abstract:
... DamID, a method to identify DNA associating with a particular protein, was originally developed for use in immortalized tissue culture lines. The power of this technique has led to its adaptation for a number of additional systems. Here we report adaptations for its use in primary cells isolated from rodents with emphasis on the challenges this presents. Specifically, we present several modificati ...
DOI:
10.1016/j.ymeth.2018.11.005

7. BEL2ABM: agent-based simulation of static models in Biological Expression Language

Author:
Gündel, Michaela; Hoyt, Charles Tapley; Hofmann-Apitius, Martin
Source:
Bioinformatics 2018 v.34 no.13 pp. 2316-2318
ISSN:
1460-2059
Subject:
bioinformatics,   etc   ; computer software; models;     Show all 3 Subjects
Abstract:
... While cause-and-effect knowledge assembly models encoded in Biological Expression Language are able to support generation of mechanistic hypotheses, they are static and limited in their ability to encode temporality. Here, we present BEL2ABM, a software for producing continuous, dynamic, executable agent-based models from BEL templates. The tool has been developed in Java and NetLogo. Code, data a ...
DOI:
10.1093/bioinformatics/bty107

8. Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies

Author:
Peng, Yisu; Jiang, Yuxiang; Radivojac, Predrag
Source:
Bioinformatics 2018 v.34 no.13 pp. i313
ISSN:
1460-2059
Subject:
bioinformatics,   etc   ; algorithms; genes; graphs;     Show all 4 Subjects
Abstract:
... Modern problems of concept annotation associate an object of interest (gene, individual, text document) with a set of interrelated textual descriptors (functions, diseases, topics), often organized in concept hierarchies or ontologies. Most ontology can be seen as directed acyclic graphs (DAGs), where nodes represent concepts and edges represent relational ties between these concepts. Given an ont ...
DOI:
10.1093/bioinformatics/bty268

9. IWTomics: testing high-resolution sequence-based ‘Omics’ data at multiple locations and scales

Author:
Cremona, Marzia A; Pini, Alessia; Cumbo, Fabio; Makova, Kateryna D; Chiaromonte, Francesca; Vantini, Simone
Source:
Bioinformatics 2018 v.34 no.13 pp. 2289-2291
ISSN:
1460-2059
Subject:
bioinformatics,   etc   ; Internet; genomics;     Show all 3 Subjects
Abstract:
... With increased generation of high-resolution sequence-based ‘Omics’ data, detecting statistically significant effects at different genomic locations and scales has become key to addressing several scientific questions. IWTomics is an R/Bioconductor package (integrated in Galaxy) that, exploiting sophisticated Functional Data Analysis techniques (i.e. statistical techniques that deal with the analy ...
DOI:
10.1093/bioinformatics/bty090

10. SearchGUI: A Highly Adaptable Common Interface for Proteomics Search and de Novo Engines

Author:
Barsnes, Harald; Vaudel, Marc
Source:
Journal of proteome research 2018 v.17 no.7 pp. 2552-2555
ISSN:
1535-3907
Subject:
bioinformatics,   etc   ; proteins; proteome; proteomics;     Show all 4 Subjects
Abstract:
... Mass-spectrometry-based proteomics has become the standard approach for identifying and quantifying proteins. A vital step consists of analyzing experimentally generated mass spectra to identify the underlying peptide sequences for later mapping to the originating proteins. We here present the latest developments in SearchGUI, a common open-source interface for the most frequently used freely avai ...
DOI:
10.1021/acs.jproteome.8b00175

11. CytoCtrlAnalyser: a Cytoscape app for biomolecular network controllability analysis

Author:
Wu, Lin; Li, Min; Wang, Jianxin; Wu, Fang-Xiang
Source:
Bioinformatics 2018 v.34 no.8 pp. 1428-1430
ISSN:
1460-2059
Subject:
bioinformatics,   etc   ; algorithms; drugs; topology;     Show all 4 Subjects
Abstract:
... Studying the controllability of biomolecular networks can result in profound knowledge about molecular biological systems. However, there is no comprehensive and easy-to-use platform for analyzing controllability of biomolecular networks although various algorithms for analyzing complex network controllability have been proposed recently. In this application note, we develop the CytoCtrlAnalyser w ...
DOI:
10.1093/bioinformatics/btx764

12. Efficiently counting all orbits of graphlets of any order in a graph using autogenerated equations

Author:
Melckenbeeck, Ine; Audenaert, Pieter; Colle, Didier; Pickavet, Mario
Source:
Bioinformatics 2018 v.34 no.8 pp. 1372-1380
ISSN:
1460-2059
Subject:
bioinformatics,   etc   ; algorithms; equations; graphs;     Show all 4 Subjects
Abstract:
... Graphlets are a useful tool to determine a graph’s small-scale structure. Finding them is exponentially hard with respect to the number of nodes in each graphlet. Therefore, equations can be used to reduce the size of graphlets that need to be enumerated to calculate the number of each graphlet touching each node. Hočevar and Demšar first introduced such equations, which were derived manually, and ...
DOI:
10.1093/bioinformatics/btx758

13. Reactome diagram viewer: data structures and strategies to boost performance

Author:
Fabregat, Antonio; Sidiropoulos, Konstantinos; Viteri, Guilherme; Marin-Garcia, Pablo; Ping, Peipei; Stein, Lincoln; D’Eustachio, Peter; Hermjakob, Henning
Source:
Bioinformatics 2018 v.34 no.7 pp. 1208-1214
ISSN:
1460-2059
Subject:
bioinformatics,   etc   ; Internet; algorithms;     Show all 3 Subjects
Abstract:
... Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. For web-based pathway visualization, Reactome uses a custom pathway diagram viewer that has been evolved over the past years. Here, we present comprehensive enhancements in usability and performance based on extensive usability testing sessions and technology developments, aiming to optimi ...
DOI:
10.1093/bioinformatics/btx752

14. MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool

Author:
Lochovsky, Lucas; Zhang, Jing; Gerstein, Mark
Source:
Bioinformatics 2018 v.34 no.6 pp. 1031-1033
ISSN:
1460-2059
Subject:
bioinformatics,   etc   ; genomics; mutation; neoplasms;     Show all 4 Subjects
Abstract:
... Identifying genomic regions with higher than expected mutation count is useful for cancer driver detection. Previous parametric approaches require numerous cell-type-matched covariates for accurate background mutation rate (BMR) estimation, which is not practical for many situations. Non-parametric, permutation-based approaches avoid this issue but usually suffer from considerable compute-time cos ...
DOI:
10.1093/bioinformatics/btx700

15. PESTO: Parameter EStimation TOolbox

Author:
Stapor, Paul; Weindl, Daniel; Ballnus, Benjamin; Hug, Sabine; Loos, Carolin; Fiedler, Anna; Krause, Sabrina; Hroß, Sabrina; Fröhlich, Fabian; Hasenauer, Jan
Source:
Bioinformatics 2018 v.34 no.4 pp. 705-707
ISSN:
1460-2059
Subject:
bioinformatics,   etc   ; algorithms; uncertainty;     Show all 3 Subjects
Abstract:
... PESTO is a widely applicable and highly customizable toolbox for parameter estimation in MathWorks MATLAB. It offers scalable algorithms for optimization, uncertainty and identifiability analysis, which work in a very generic manner, treating the objective function as a black box. Hence, PESTO can be used for any parameter estimation problem, for which the user can provide a deterministic objectiv ...
DOI:
10.1093/bioinformatics/btx676

16. graphkernels: R and Python packages for graph comparison

Author:
Sugiyama, Mahito; Ghisu, M Elisabetta; Llinares-López, Felipe; Borgwardt, Karsten
Source:
Bioinformatics 2018 v.34 no.3 pp. 530-532
ISSN:
1460-2059
Subject:
bioinformatics,   etc   ; computer software; graphs;     Show all 3 Subjects
Abstract:
... Measuring the similarity of graphs is a fundamental step in the analysis of graph-structured data, which is omnipresent in computational biology. Graph kernels have been proposed as a powerful and efficient approach to this problem of graph comparison. Here we provide graphkernels, the first R and Python graph kernel libraries including baseline kernels such as label histogram based kernels, class ...
DOI:
10.1093/bioinformatics/btx602

17. TROVE: a user-friendly tool for visualizing and analyzing cancer hallmarks in signaling networks

Author:
Chua, Huey Eng; Bhowmick, Sourav S; Zheng, Jie
Source:
Bioinformatics 2018 v.34 no.2 pp. 314-316
ISSN:
1460-2059
Subject:
bioinformatics,   etc   ; computer software; neoplasms;     Show all 3 Subjects
Abstract:
... Cancer hallmarks, a concept that seeks to explain the complexity of cancer initiation and development, provide a new perspective of studying cancer signaling which could lead to a greater understanding of this complex disease. However, to the best of our knowledge, there is currently a lack of tools that support such hallmark-based study of the cancer signaling network, thereby impeding the gain o ...
DOI:
10.1093/bioinformatics/btx600

18. SMLocalizer, a GPU accelerated ImageJ plugin for single molecule localization microscopy

Author:
Bernhem, Kristoffer; Brismar, Hjalmar
Source:
Bioinformatics 2018 v.34 no.1 pp. 137-138
ISSN:
1460-2059
Subject:
bioinformatics,   etc   ; microscopy; Fiji;     Show all 3 Subjects
Abstract:
... SMLocalizer combines the availability of ImageJ with the power of GPU processing for fast and accurate analysis of single molecule localization microscopy data. Analysis of 2D and 3D data in multiple channels is supported. Plugin freely available for Fiji and ImageJ2.0 through https://sourceforge.net/projects/smlocalizer/. Plugin also available for continuous updates through ImageJ update system, ...
DOI:
10.1093/bioinformatics/btx553

19. Bioinformatic Analysis Reveals Conservation of Intrinsic Disorder in the Linker Sequences of Prokaryotic Dual-family Immunophilin Chaperones

Author:
Barik, Sailen
Source:
Computational and Structural Biotechnology Journal 2018 v.16 pp. 6-14
ISSN:
2001-0370
Subject:
bioinformatics,   etc   ; biotechnology; cyclophilins; models;     Show all 4 Subjects
Abstract:
... The two classical immunophilin families, found essentially in all living cells, are: cyclophilin (CYN) and FK506-binding protein (FKBP). We previously reported a novel class of immunophilins that are natural chimera of these two, which we named dual-family immunophilin (DFI). The DFIs were found in either of two conformations: CYN-linker-FKBP (CFBP) or FKBP-3TPR-CYN (FCBP). While the 3TPR domain c ...
DOI:
10.1016/j.csbj.2017.12.002

20. Beyond bulk: a review of single cell transcriptomics methodologies and applications

Author:
Kulkarni, Ashwinikumar; Anderson, Ashley G.; Merullo, Devin P.; Konopka, Genevieve
Source:
Current opinion in biotechnology 2019 v.58 pp. 129-136
ISSN:
0958-1669
Subject:
bioinformatics,   etc   ; brain; gene expression; neurophysiology; sequence analysis; transcriptome; transcriptomics;     Show all 7 Subjects
Abstract:
... Single-cell RNA sequencing (scRNA-seq) is a promising approach to study the transcriptomes of individual cells in the brain and the central nervous system (CNS). This technology acts as a bridge between neuroscience, computational biology, and systems biology, enabling an unbiased and novel understanding of the cellular composition of the brain and CNS. Gene expression at the single cell resolutio ...
DOI:
10.1016/j.copbio.2019.03.001