Volume 20, issue 1, December 2019
498 articles in this issue
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Alignment-free genomic sequence comparison using FCGR and signal processing
Authors
- Daniel Lichtblau
- Content type: Software
- Open Access
- Published: 30 December 2019
- Article: 742
This is part of 1 collection: -
The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa’s capacity for genomics research
Authors (first, second and last of 12)
- Judit Kumuthini
- Lyndon Zass
- as members of the Sustainability and Outreach Work Package of the H3ABioNet Consortium
- Content type: Research article
- Open Access
- Published: 30 December 2019
- Article: 741
This is part of 1 collection: -
ZDOG: zooming in on dominating genes with mutations in cancer pathways
Authors
- Rudi Alberts
- Jinyu Chen
- Louxin Zhang
- Content type: Software
- Open Access
- Published: 30 December 2019
- Article: 740
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LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation
Authors
- Emanuel Maldonado
- Agostinho Antunes
- Content type: Software
- Open Access
- Published: 30 December 2019
- Article: 739
This is part of 1 collection: -
Benchmarking the PEPOP methods for mimicking discontinuous epitopes
Authors (first, second and last of 6)
- Vincent Demolombe
- Alexandre G. de Brevern
- Violaine Moreau
- Content type: Methodology article
- Open Access
- Published: 30 December 2019
- Article: 738
This is part of 1 collection: -
Modelling TERT regulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach
Authors (first, second and last of 7)
- Alexandra M. Poos
- Theresa Kordaß
- Rainer König
- Content type: Methodology article
- Open Access
- Published: 30 December 2019
- Article: 737
This is part of 1 collection: -
Identification of infectious disease-associated host genes using machine learning techniques
Authors (first, second and last of 4)
- Ranjan Kumar Barman
- Anirban Mukhopadhyay
- Santasabuj Das
- Content type: Research article
- Open Access
- Published: 27 December 2019
- Article: 736
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Biomedical named entity recognition using deep neural networks with contextual information
Authors
- Hyejin Cho
- Hyunju Lee
- Content type: Research Article
- Open Access
- Published: 27 December 2019
- Article: 735
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Improvement of the memory function of a mutual repression network in a stochastic environment by negative autoregulation
Authors
- A. B. M. Shamim Ul Hasan
- Hiroyuki Kurata
- Sebastian Pechmann
- Content type: Research article
- Open Access
- Published: 27 December 2019
- Article: 734
This is part of 1 collection: -
ki67 nuclei detection and ki67-index estimation: a novel automatic approach based on human vision modeling
Authors (first, second and last of 7)
- Barbara Rita Barricelli
- Elena Casiraghi
- Barbara Vergani
- Content type: Methodology article
- Open Access
- Published: 27 December 2019
- Article: 733
This is part of 2 collections: -
PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets
Authors (first, second and last of 4)
- Dvir Netanely
- Neta Stern
- Ron Shamir
- Content type: Software
- Open Access
- Published: 26 December 2019
- Article: 732
This is part of 1 collection: -
ICGRM: integrative construction of genomic relationship matrix combining multiple genomic regions for big dataset
Authors (first, second and last of 5)
- Dan Jiang
- Cong Xin
- Ming Fang
- Content type: Software
- Open Access
- Published: 26 December 2019
- Article: 731
This is part of 1 collection: -
Antimicrobial peptide identification using multi-scale convolutional network
Authors (first, second and last of 5)
- Xin Su
- Jing Xu
- Han Zhang
- Content type: Research article
- Open Access
- Published: 23 December 2019
- Article: 730
This is part of 1 collection: -
perfectphyloR: An R package for reconstructing perfect phylogenies
Authors
- Charith B. Karunarathna
- Jinko Graham
- Content type: Software
- Open Access
- Published: 23 December 2019
- Article: 729
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Metabolic disassembler for understanding and predicting the biosynthetic units of natural products
Authors (first, second and last of 5)
- Kohei Amano
- Tsubasa Matsumoto
- Masaaki Kotera
- Content type: Methodology article
- Open Access
- Published: 23 December 2019
- Article: 728
This is part of 1 collection: -
Correction to: Detailed prediction of protein sub-nuclear localization
Authors (first, second and last of 5)
- Maria Littmann
- Tatyana Goldberg
- Burkhard Rost
- Content type: Correction
- Open Access
- Published: 20 December 2019
- Article: 727
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Evaluation of knowledge graph embedding approaches for drug-drug interaction prediction in realistic settings
Authors (first, second and last of 6)
- Remzi Celebi
- Huseyin Uyar
- Michel Dumontier
- Content type: Research Article
- Open Access
- Published: 18 December 2019
- Article: 726
This is part of 1 collection: -
Deriving a Boolean dynamics to reveal macrophage activation with in vitro temporal cytokine expression profiles
Authors (first, second and last of 7)
- Ricardo Ramirez
- Allen Michael Herrera
- Yu-Fang Jin
- Content type: Research article
- Open Access
- Published: 18 December 2019
- Article: 725
This is part of 1 collection: -
Wound area measurement with 3D transformation and smartphone images
Authors (first, second and last of 6)
- Chunhui Liu
- Xingyu Fan
- Yan Xu
- Content type: Methodology Article
- Open Access
- Published: 18 December 2019
- Article: 724
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Modeling aspects of the language of life through transfer-learning protein sequences
Authors (first, second and last of 7)
- Michael Heinzinger
- Ahmed Elnaggar
- Burkhard Rost
- Content type: Research article
- Open Access
- Published: 17 December 2019
- Article: 723
This is part of 2 collections: -
Correction to: Recommendations for performance optimizations when using GATK3.8 and GATK4
Authors (first, second and last of 15)
- Jacob R. Heldenbrand
- Saurabh Baheti
- Liudmila S. Mainzer
- Content type: Correction
- Open Access
- Published: 17 December 2019
- Article: 722
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shinyBN: an online application for interactive Bayesian network inference and visualization
Authors (first, second and last of 9)
- Jiajin Chen
- Ruyang Zhang
- Feng Chen
- Content type: Software
- Open Access
- Published: 16 December 2019
- Article: 711
This is part of 1 collection: -
EvoFreq: visualization of the Evolutionary Frequencies of sequence and model data
Authors (first, second and last of 4)
- Chandler D. Gatenbee
- Ryan O. Schenck
- Alexander R. A. Anderson
- Content type: Software
- Open Access
- Published: 16 December 2019
- Article: 710
This is part of 1 collection: -
Benchmarking machine learning models for late-onset alzheimer’s disease prediction from genomic data
Authors (first, second and last of 5)
- Javier De Velasco Oriol
- Edgar E. Vallejo
- The Alzheimer’s Disease Neuroimaging Initiative
- Content type: Research Article
- Open Access
- Published: 16 December 2019
- Article: 709
This is part of 2 collections: -
Base-pair ambiguity and the kinetics of RNA folding
Authors
- Guangyao Zhou
- Jackson Loper
- Stuart Geman
- Content type: Research Article
- Open Access
- Published: 12 December 2019
- Article: 666
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DeepSV: accurate calling of genomic deletions from high-throughput sequencing data using deep convolutional neural network
Authors
- Lei Cai
- Yufeng Wu
- Jingyang Gao
- Content type: Research article
- Open Access
- Published: 12 December 2019
- Article: 665
This is part of 1 collection: -
uap: reproducible and robust HTS data analysis
Authors (first, second and last of 8)
- Christoph Kämpf
- Michael Specht
- Jörg Hackermüller
- Content type: Software
- Open Access
- Published: 12 December 2019
- Article: 664
This is part of 1 collection: -
Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads
Authors (first, second and last of 4)
- Iñigo Prada-Luengo
- Anders Krogh
- Birgitte Regenberg
- Content type: Software
- Open Access
- Published: 12 December 2019
- Article: 663
This is part of 1 collection: -
A pan-cancer somatic mutation embedding using autoencoders
Authors
- Martin Palazzo
- Pierre Beauseroy
- Patricio Yankilevich
- Content type: Methodology Article
- Open Access
- Published: 11 December 2019
- Article: 655
This is part of 2 collections: -
Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage
Authors
- Louis Ranjard
- Thomas K. F. Wong
- Allen G. Rodrigo
- Content type: Research Article
- Open Access
- Published: 11 December 2019
- Article: 654
This is part of 1 collection: -
Time-resolved evaluation of compound repositioning predictions on a text-mined knowledge network
Authors (first, second and last of 4)
- Michael Mayers
- Tong Shu Li
- Andrew I. Su
- Content type: Research article
- Open Access
- Published: 11 December 2019
- Article: 653
This is part of 1 collection: -
Longitudinal linear combination test for gene set analysis
Authors (first, second and last of 4)
- Elham Khodayari Moez
- Morteza Hajihosseini
- Irina Dinu
- Content type: Methodology article
- Open Access
- Published: 10 December 2019
- Article: 650
This is part of 1 collection: -
Vertical and horizontal integration of multi-omics data with miodin
Authors
- Benjamin Ulfenborg
- Content type: Software
- Open Access
- Published: 10 December 2019
- Article: 649
This is part of 1 collection: -
Predicting effective drug combinations using gradient tree boosting based on features extracted from drug-protein heterogeneous network
Authors (first, second and last of 6)
- Hui Liu
- Wenhao Zhang
- Ling Zou
- Content type: Methodology Article
- Open Access
- Published: 09 December 2019
- Article: 645
This is part of 1 collection: -
flowEMMi: an automated model-based clustering tool for microbial cytometric data
Authors (first, second and last of 5)
- Joachim Ludwig
- Christian Höner zu Siederdissen
- Susann Müller
- Content type: Software
- Open Access
- Published: 09 December 2019
- Article: 643
This is part of 1 collection: -
BEST: a web server for brain expression Spatio-temporal pattern analysis
Authors (first, second and last of 5)
- Liyuan Guo
- Wei Lin
- Jing Wang
- Content type: Software
- Open Access
- Published: 05 December 2019
- Article: 632
This is part of 1 collection: -
Immune repertoire fingerprinting by principal component analysis reveals shared features in subject groups with common exposures
Authors (first, second and last of 5)
- Alexander M. Sevy
- Cinque Soto
- James E. Crowe Jr
- Content type: Methodology article
- Open Access
- Published: 04 December 2019
- Article: 629
This is part of 1 collection: -
Relation extraction between bacteria and biotopes from biomedical texts with attention mechanisms and domain-specific contextual representations
Authors
- Amarin Jettakul
- Duangdao Wichadakul
- Peerapon Vateekul
- Content type: Research Article
- Open Access
- Published: 03 December 2019
- Article: 627
This is part of 1 collection: -
A novel target convergence set based random walk with restart for prediction of potential LncRNA-disease associations
Authors (first, second and last of 6)
- Jiechen Li
- Xueyong Li
- Lei Wang
- Content type: Research article
- Open Access
- Published: 03 December 2019
- Article: 626
This is part of 2 collections: -
Identifying gene-specific subgroups: an alternative to biclustering
Authors
- Vincent Branders
- Pierre Schaus
- Pierre Dupont
- Content type: Research Article
- Open Access
- Published: 03 December 2019
- Article: 625
This is part of 1 collection: -
An improved random forest-based computational model for predicting novel miRNA-disease associations
Authors
- Dengju Yao
- Xiaojuan Zhan
- Chee-Keong Kwoh
- Content type: Research article
- Open Access
- Published: 03 December 2019
- Article: 624
This is part of 1 collection: -
deltaRpkm: an R package for a rapid detection of differential gene presence between related bacterial genomes
Authors
- Hatice Akarsu
- Lisandra Aguilar-Bultet
- Laurent Falquet
- Content type: Software
- Open Access
- Published: 02 December 2019
- Article: 621
This is part of 1 collection: -
A probabilistic method for leveraging functional annotations to enhance estimation of the temporal order of pathway mutations during carcinogenesis
Authors (first, second and last of 9)
- Menghan Wang
- Tianxin Yu
- Chi Wang
- Content type: Methodology Article
- Open Access
- Published: 02 December 2019
- Article: 620
This is part of 1 collection: -
3-Dimensional facial expression recognition in human using multi-points warping
Authors (first, second and last of 5)
- Olalekan Agbolade
- Azree Nazri
- Yoke Kqueen Cheah
- Content type: Research article
- Open Access
- Published: 02 December 2019
- Article: 619
This is part of 1 collection: -
HKPocket: human kinase pocket database for drug design
Authors (first, second and last of 6)
- Huiwen Wang
- Jiadi Qiu
- Yunjie Zhao
- Content type: Database
- Open Access
- Published: 29 November 2019
- Article: 617
This is part of 1 collection: -
Correction to: Predicting protein inter-residue contacts using composite likelihood maximization and deep learning
Authors (first, second and last of 10)
- Haicang Zhang
- Qi Zhang
- Dongbo Bu
- Content type: Correction
- Open Access
- Published: 29 November 2019
- Article: 616
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Detection of biological switches using the method of Gröebner bases
Authors
- Yaman Arkun
- Content type: Methodology article
- Open Access
- Published: 28 November 2019
- Article: 615
This is part of 1 collection: -
AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data
Authors (first, second and last of 8)
- M. Shaffer
- K. Thurimella
- C. A. Lozupone
- Content type: Methodology article
- Open Access
- Published: 28 November 2019
- Article: 614
This is part of 1 collection: -
Hierarchical clustering of maximum parsimony reconciliations
Authors
- Ross Mawhorter
- Ran Libeskind-Hadas
- Content type: Methodology Article
- Open Access
- Published: 27 November 2019
- Article: 612
This is part of 1 collection: