New Articles From BMC Bioinformatics
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Apr 27, 2020, 5:31:21 AM4/27/20
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May 4, 2020, 5:26:33 AM5/4/20
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SOFTWARE |
wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data |
| Marius Wöste, Elsa Leitão, Sandra Laurentino, Bernhard Horsthemke, Sven Rahmann and Christopher Schröder |
| BMC Bioinformatics 2020, 21:169 | Published on: 1 May 2020 |
Negative binomial additive model for RNA-Seq data analysis |
| Xu Ren and Pei-Fen Kuan |
| BMC Bioinformatics 2020, 21:171 | Published on: 1 May 2020 |
Enhancing fragment-based protein structure prediction by customising fragment cardinality according to local secondary structure |
| Jad Abbass and Jean-Christophe Nebel |
| BMC Bioinformatics 2020, 21:170 | Published on: 1 May 2020 |
SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation |
| Joseph Bergenstråhle, Ludvig Bergenstråhle and Joakim Lundeberg |
| BMC Bioinformatics 2020, 21:161 | Published on: 29 April 2020 |
YSMR: a video tracking and analysis program for bacterial motility |
| Julian Schwanbeck, Ines Oehmig, Jerôme Dretzke, Andreas E. Zautner, Uwe Groß and Wolfgang Bohne |
| BMC Bioinformatics 2020, 21:166 | Published on: 29 April 2020 |
CYPminer: an automated cytochrome P450 identification, classification, and data analysis tool for genome data sets across kingdoms |
| Ohgew Kweon, Seong-Jae Kim, Jae Hyun Kim, Seong Won Nho, Dongryeoul Bae, Jungwhan Chon, Mark Hart, Dong-Heon Baek, Young-Chang Kim, Wenjun Wang, Sung-Kwan Kim, John B. Sutherland and Carl E. Cerniglia |
| BMC Bioinformatics 2020, 21:160 | Published on: 29 April 2020 |
vivaGen – a survival data set generator for software testing |
| Matthias Gietzelt, Christian Karmen, Petra Knaup-Gregori and Matthias Ganzinger |
| BMC Bioinformatics 2020, 21:167 | Published on: 29 April 2020 |
circRNAprofiler: an R-based computational framework for the downstream analysis of circular RNAs |
| Simona Aufiero, Yolan J. Reckman, Anke J. Tijsen, Yigal M. Pinto and Esther E. Creemers |
| BMC Bioinformatics 2020, 21:164 | Published on: 29 April 2020 |
Predicting potential adverse events using safety data from marketed drugs |
| Chathuri Daluwatte, Peter Schotland, David G. Strauss, Keith K. Burkhart and Rebecca Racz |
| BMC Bioinformatics 2020, 21:163 | Published on: 29 April 2020 |
2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome |
| Rui Kong, Xinnan Xu, Xiaoqing Liu, Pingan He, Michael Q. Zhang and Qi Dai |
| BMC Bioinformatics 2020, 21:159 | Published on: 29 April 2020 |
GrAPFI: predicting enzymatic function of proteins from domain similarity graphs |
| Bishnu Sarker, David W. Ritchie and Sabeur Aridhi |
| BMC Bioinformatics 2020, 21:168 | Published on: 29 April 2020 |
Intrinsic limitations in mainstream methods of identifying network motifs in biology |
| James Fodor, Michael Brand, Rebecca J. Stones and Ashley M. Buckle |
| BMC Bioinformatics 2020, 21:165 | Published on: 29 April 2020 |
Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes |
| Nathan Mih, Jonathan M. Monk, Xin Fang, Edward Catoiu, David Heckmann, Laurence Yang and Bernhard O. Palsson |
| BMC Bioinformatics 2020, 21:162 | Published on: 29 April 2020 |
| Full Text | PDF |
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May 11, 2020, 5:33:53 AM5/11/20
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May 18, 2020, 10:29:37 AM5/18/20
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SOFTWARE |
CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments |
| H. Atakan Ekiz, Christopher J. Conley, W. Zac Stephens and Ryan M. O’Connell |
| BMC Bioinformatics 2020, 21:191 | Published on: 15 May 2020 |
CSN: unsupervised approach for inferring biological networks based on the genome alone |
| Maya Galili and Tamir Tuller |
| BMC Bioinformatics 2020, 21:190 | Published on: 15 May 2020 |
ICEKAT: an interactive online tool for calculating initial rates from continuous enzyme kinetic traces |
| Michael D. Olp, Kelsey S. Kalous and Brian C. Smith |
| BMC Bioinformatics 2020, 21:186 | Published on: 14 May 2020 |
Broad-coverage biomedical relation extraction with SemRep |
| Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman and Dongwook Shin |
| BMC Bioinformatics 2020, 21:188 | Published on: 14 May 2020 |
Automated image analysis system for studying cardiotoxicity in human pluripotent stem cell-Derived cardiomyocytes |
| Lu Cao, Andries D. van der Meer, Fons J. Verbeek and Robert Passier |
| BMC Bioinformatics 2020, 21:187 | Published on: 14 May 2020 |
TAMA: improved metagenomic sequence classification through meta-analysis |
| Mikang Sim, Jongin Lee, Daehwan Lee, Daehong Kwon and Jaebum Kim |
| BMC Bioinformatics 2020, 21:185 | Published on: 12 May 2020 |
methCancer-gen: a DNA methylome dataset generator for user-specified cancer type based on conditional variational autoencoder |
| Joungmin Choi and Heejoon Chae |
| BMC Bioinformatics 2020, 21:181 | Published on: 11 May 2020 |
MEPHAS: an interactive graphical user interface for medical and pharmaceutical statistical analysis with R and Shiny |
| Yi Zhou, Siu-wai Leung, Shosuke Mizutani, Tatsuya Takagi and Yu-Shi Tian |
| BMC Bioinformatics 2020, 21:183 | Published on: 11 May 2020 |
SCeQTL: an R package for identifying eQTL from single-cell parallel sequencing data |
| Yue Hu, Xi Xi, Qian Yang and Xuegong Zhang |
| BMC Bioinformatics 2020, 21:184 | Published on: 11 May 2020 |
Cluster correlation based method for lncRNA-disease association prediction |
| Qianqian Yuan, Xingli Guo, Yang Ren, Xiao Wen and Lin Gao |
| BMC Bioinformatics 2020, 21:180 | Published on: 11 May 2020 |
Multi-task learning sparse group lasso: a method for quantifying antigenicity of influenza A(H1N1) virus using mutations and variations in glycosylation of Hemagglutinin |
| Lei Li, Deborah Chang, Lei Han, Xiaojian Zhang, Joseph Zaia and Xiu-Feng Wan |
| BMC Bioinformatics 2020, 21:182 | Published on: 11 May 2020 |
| Full Text | PDF |
Virtual Post Bioclues
May 25, 2020, 7:31:25 AM5/25/20
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| The following new articles have just been published in BMC Bioinformatics |
SOFTWARE |
Substitution matrix based color schemes for sequence alignment visualization |
| Patrick Kunzmann, Benjamin E. Mayer and Kay Hamacher |
| BMC Bioinformatics 2020, 21:209 | Published on: 24 May 2020 |
A novel investigation of the effect of iterations in sliding semi-landmarks for 3D human facial images |
| Azree Nazri, Olalekan Agbolade, Razali Yaakob, Abdul Azim Ghani and Yoke Kqueen Cheah |
| BMC Bioinformatics 2020, 21:208 | Published on: 24 May 2020 |
RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp |
| Hiroki Takizawa, Junichi Iwakiri and Kiyoshi Asai |
| BMC Bioinformatics 2020, 21:210 | Published on: 24 May 2020 |
Data-based RNA-seq simulations by binomial thinning |
| David Gerard |
| BMC Bioinformatics 2020, 21:206 | Published on: 24 May 2020 |
Bio-semantic relation extraction with attention-based external knowledge reinforcement |
| Zhijing Li, Yuchen Lian, Xiaoyong Ma, Xiangrong Zhang and Chen Li |
| BMC Bioinformatics 2020, 21:213 | Published on: 24 May 2020 |
PACVr: plastome assembly coverage visualization in R |
| Michael Gruenstaeudl and Nils Jenke |
| BMC Bioinformatics 2020, 21:207 | Published on: 24 May 2020 |
Subcellular location prediction of apoptosis proteins using two novel feature extraction methods based on evolutionary information and LDA |
| Lei Du, Qingfang Meng, Yuehui Chen and Peng Wu |
| BMC Bioinformatics 2020, 21:212 | Published on: 24 May 2020 |
VADR: validation and annotation of virus sequence submissions to GenBank |
| Alejandro A. Schäffer, Eneida L. Hatcher, Linda Yankie, Lara Shonkwiler, J. Rodney Brister, Ilene Karsch-Mizrachi and Eric P. Nawrocki |
| BMC Bioinformatics 2020, 21:211 | Published on: 24 May 2020 |
fcScan: a versatile tool to cluster combinations of sites using genomic coordinates |
| Abdullah El-Kurdi, Ghiwa Ali Khalil, Georges Khazen and Pierre Khoueiry |
| BMC Bioinformatics 2020, 21:194 | Published on: 19 May 2020 |
Power analysis for RNA-Seq differential expression studies using generalized linear mixed effects models |
| Lianbo Yu, Soledad Fernandez and Guy Brock |
| BMC Bioinformatics 2020, 21:198 | Published on: 19 May 2020 |
Direct comparison shows that mRNA-based diagnostics incorporate information which cannot be learned directly from genomic mutations |
| Hersh D. Ravkin, Ofer Givton, David B. Geffen and Eitan Rubin |
| BMC Bioinformatics 2020, 21:196 | Published on: 19 May 2020 |
Enhancing SVM for survival data using local invariances and weighting |
| Hector Sanz, Ferran Reverter and Clarissa Valim |
| BMC Bioinformatics 2020, 21:193 | Published on: 19 May 2020 |
Uncovering the prognostic gene signatures for the improvement of risk stratification in cancers by using deep learning algorithm coupled with wavelet transform |
| Yiru Zhao, Yifan Zhou, Yuan Liu, Yinyi Hao, Menglong Li, Xuemei Pu, Chuan Li and Zhining Wen |
| BMC Bioinformatics 2020, 21:195 | Published on: 19 May 2020 |
Repetitive DNA profile of the amphibian mitogenome |
| Noel Cabañas, Arturo Becerra, David Romero, Tzipe Govezensky, Jesús Javier Espinosa-Aguirre and Rafael Camacho-Carranza |
| BMC Bioinformatics 2020, 21:197 | Published on: 19 May 2020 |
| Full Text | PDF |
Virtual Post Bioclues
Jun 1, 2020, 7:51:24 AM6/1/20
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| The following new articles have just been published in BMC Bioinformatics |
Research article |
Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads |
| William S. Pearman, Nikki E. Freed and Olin K. Silander |
| BMC Bioinformatics 2020, 21:220 | Published on: 29 May 2020 |
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Methodology article |
A Bayesian data fusion based approach for learning genome-wide transcriptional regulatory networks |
| Elisabetta Sauta, Andrea Demartini, Francesca Vitali, Alberto Riva and Riccardo Bellazzi |
| BMC Bioinformatics 2020, 21:219 | Published on: 29 May 2020 |
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Software |
BEAVR: a browser-based tool for the exploration and visualization of RNA-seq data |
| Pirunthan Perampalam and Frederick A. Dick |
| BMC Bioinformatics 2020, 21:221 | Published on: 29 May 2020 |
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Research article |
The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data |
| Cheng Ye, Alberto Paccanaro, Mark Gerstein and Koon-Kiu Yan |
| BMC Bioinformatics 2020, 21:222 | Published on: 29 May 2020 |
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Research article |
Extracting chemical reactions from text using Snorkel |
| Emily K. Mallory, Matthieu de Rochemonteix, Alex Ratner, Ambika Acharya, Chris Re, Roselie A. Bright and Russ B. Altman |
| BMC Bioinformatics 2020, 21:217 | Published on: 27 May 2020 |
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Software |
SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data |
| Collin Giguere, Harsh Vardhan Dubey, Vishal Kumar Sarsani, Hachem Saddiki, Shai He and Patrick Flaherty |
| BMC Bioinformatics 2020, 21:215 | Published on: 26 May 2020 |
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Methodology Article |
Discovery of significant porcine SNPs for swine breed identification by a hybrid of information gain, genetic algorithm, and frequency feature selection technique |
| Kitsuchart Pasupa, Wanthanee Rathasamuth and Sissades Tongsima |
| BMC Bioinformatics 2020, 21:216 | Published on: 26 May 2020 |
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Software |
ARTDeco: automatic readthrough transcription detection |
| Samuel J. Roth, Sven Heinz and Christopher Benner |
| BMC Bioinformatics 2020, 21:214 | Published on: 26 May 2020 |
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Virtual Post Bioclues
Jun 8, 2020, 5:04:52 AM6/8/20
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| he following new articles have just been published in BMC Bioinformatics |
Methodology article |
PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures |
| Mohammad Asif Emon, Daniel Domingo-Fernández, Charles Tapley Hoyt and Martin Hofmann-Apitius |
| BMC Bioinformatics 2020, 21:231 | Published on: 5 June 2020 |
Assistant diagnosis with Chinese electronic medical records based on CNN and BiLSTM with phrase-level and word-level attentions |
| Tong Wang, Ping Xuan, Zonglin Liu and Tiangang Zhang |
| BMC Bioinformatics 2020, 21:230 | Published on: 5 June 2020 |
Matrix factorization with neural network for predicting circRNA-RBP interactions |
| Zhengfeng Wang and Xiujuan Lei |
| BMC Bioinformatics 2020, 21:229 | Published on: 5 June 2020 |
Origins and characterization of variants shared between databases of somatic and germline human mutations |
| William Meyerson, John Leisman, Fabio C. P. Navarro and Mark Gerstein |
| BMC Bioinformatics 2020, 21:227 | Published on: 4 June 2020 |
DryMass: handling and analyzing quantitative phase microscopy images of spherical, cell-sized objects |
| Paul Müller, Gheorghe Cojoc and Jochen Guck |
| BMC Bioinformatics 2020, 21:226 | Published on: 3 June 2020 |
Exploiting geometric similarity for statistical quantification of fluorescence spatial patterns in bacterial colonies |
| David R. Espeso, Elena Algar, Esteban Martínez-García and Víctor de Lorenzo |
| BMC Bioinformatics 2020, 21:224 | Published on: 3 June 2020 |
An empirical Bayes approach to normalization and differential abundance testing for microbiome data |
| Tiantian Liu, Hongyu Zhao and Tao Wang |
| BMC Bioinformatics 2020, 21:225 | Published on: 3 June 2020 |
CRISPRpred(SEQ): a sequence-based method for sgRNA on target activity prediction using traditional machine learning |
| Ali Haisam Muhammad Rafid, Md. Toufikuzzaman, Mohammad Saifur Rahman and M. Sohel Rahman |
| BMC Bioinformatics 2020, 21:223 | Published on: 1 June 2020 |
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Virtual Post Bioclues
Jun 15, 2020, 8:53:52 AM6/15/20
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Virtual Post Bioclues
Jun 22, 2020, 5:34:46 AM6/22/20
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| The following new articles have just been published in BMC Bioinformatics |
Research article |
Implementing sequence-based antigenic distance calculation into immunological shape space model |
| Christopher S. Anderson, Mark Y. Sangster, Hongmei Yang, Thomas J. Mariani, Sidhartha Chaudhury and David J. Topham |
| BMC Bioinformatics 2020, 21:256 | Published on: 19 June 2020 |
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Software |
Deriving stratified effects from joint models investigating gene-environment interactions |
| Vincent Laville, Timothy Majarian, Paul S. de Vries, Amy R. Bentley, Mary F. Feitosa, Yun J. Sung, D. C. Rao, Alisa Manning and Hugues Aschard |
| BMC Bioinformatics 2020, 21:251 | Published on: 18 June 2020 |
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Software |
pyMeSHSim: an integrative python package for biomedical named entity recognition, normalization, and comparison of MeSH terms |
| Zhi-Hui Luo, Meng-Wei Shi, Zhuang Yang, Hong-Yu Zhang and Zhen-Xia Chen |
| BMC Bioinformatics 2020, 21:252 | Published on: 18 June 2020 |
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Methodology article |
Hap10: reconstructing accurate and long polyploid haplotypes using linked reads |
| Sina Majidian, Mohammad Hossein Kahaei and Dick de Ridder |
| BMC Bioinformatics 2020, 21:253 | Published on: 18 June 2020 |
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Software |
RWRMTN: a tool for predicting disease-associated microRNAs based on a microRNA-target gene network |
| Duc-Hau Le and Trang T. H. Tran |
| BMC Bioinformatics 2020, 21:244 | Published on: 15 June 2020 |
| Full Text | PDF |
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Jun 29, 2020, 5:04:58 AM6/29/20
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Jul 6, 2020, 6:00:55 AM7/6/20
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Virtual Post Bioclues
Jul 13, 2020, 6:05:21 AM7/13/20
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Jul 20, 2020, 5:06:25 AM7/20/20
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Jul 27, 2020, 6:59:26 AM7/27/20
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Virtual Post Bioclues
Aug 3, 2020, 9:19:44 AM8/3/20
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Virtual Post Bioclues
Aug 10, 2020, 5:09:48 AM8/10/20
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Aug 17, 2020, 5:45:43 AM8/17/20
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On Mon, Aug 17, 2020 at 2:32 PM BioMed Central <no-r...@biomedcentral.com> wrote:
BMC Bioinformatics
The following new articles have just been published in BMC Bioinformatics
Methodology article
SQMtools: automated processing and visual analysis of ’omics data with R and anvi’o
Fernando Puente-Sánchez, Natalia García-García and Javier Tamames BMC Bioinformatics 2020, 21:358 | Published on: 14 August 2020
Comparison of methods for the detection of outliers and associated biomarkers in mislabeled omics data
Hongwei Sun, Yuehua Cui, Hui Wang, Haixia Liu and Tong Wang BMC Bioinformatics 2020, 21:357 | Published on: 14 August 2020
NPF:network propagation for protein function prediction
Bihai Zhao, Zhihong Zhang, Meiping Jiang, Sai Hu, Yingchun Luo and Lei Wang BMC Bioinformatics 2020, 21:355 | Published on: 12 August 2020
Game theoretic centrality: a novel approach to prioritize disease candidate genes by combining biological networks with the Shapley value
Min Woo Sun, Stefano Moretti, Kelley M. Paskov, Nate T. Stockham, Maya Varma, Brianna S. Chrisman, Peter Y. Washington, Jae-Yoon Jung and Dennis P. Wall BMC Bioinformatics 2020, 21:356 | Published on: 12 August 2020
SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis
Stevenn Volant, Pierre Lechat, Perrine Woringer, Laurence Motreff, Pascal Campagne, Christophe Malabat, Sean Kennedy and Amine Ghozlane BMC Bioinformatics 2020, 21:345 | Published on: 10 August 2020
ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network
Michelle B. Atallah, Varun Tandon, Kamir J. Hiam, Hunter Boyce, Michelle Hori, Waleed Atallah, Matthew H. Spitzer, Edgar Engleman and Parag Mallick BMC Bioinformatics 2020, 21:346 | Published on: 10 August 2020 Full Text | PDF
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Bioclues is India's largest bioinformatics society working for bridging mentor mentee relationships. We are an affiliate of APBioNet.org and ISCB.org
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