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ORCIDBriefings in Bioinformatics, Volume 20
Volume 20, Number 1, January 2019
- Chia-Wei Chen, Hsin-Chou Yang
:
OPATs: Omnibus P-value association tests. 1-14 - Gennady G. Fedonin, Yury S. Fantin, Alexander V. Favorov, German A. Shipulin, Alexey D. Neverov:
VirGenA: a reference-based assembler for variable viral genomes. 15-25 - Shan-Shan Dong, Yan Guo, Shi Yao, Yi-Xiao Chen, Mo-Nan He, Yu-Jie Zhang, Xiao-Feng Chen, Jia-Bin Chen, Tie-Lin Yang:
Integrating regulatory features data for prediction of functional disease-associated SNPs. 26-32 - Ik-Soo Huh, Xin Wu, Taesung Park, Soojin V. Yi:
Detecting differential DNA methylation from sequencing of bisulfite converted DNA of diverse species. 33-46 - Ya Wang, Andrew E. Teschendorff, Martin Widschwendter, Shuang Wang:
Accounting for differential variability in detecting differentially methylated regions. 47-57 - Jiazhen Ye, Lin Wang, Shuzhang Li, Qinran Zhang, Qinglei Zhang, Wenhao Tang, Kai Wang, Kun Song, Gaurav Sablok, Xiaoyong Sun, Hongwei Zhao:
AtCircDB: a tissue-specific database for Arabidopsis circular RNAs. 58-65 - Yongsheng Li, Caiqin Huo, Tao Pan, Lili Li, Xiyun Jin, Xiaoyu Lin, Juan Chen, Jinwen Zhang, Zheng Guo, Juan Xu, Xia Li:
Systematic review regulatory principles of non-coding RNAs in cardiovascular diseases. 66-76 - Adrian Baez-Ortega, Kevin Gori:
Computational approaches for discovery of mutational signatures in cancer. 77-88 - Duanchen Sun, Xian-Wen Ren, Eszter Ari, Tamás Korcsmáros, Peter Csermely, Ling-Yun Wu:
Discovering cooperative biomarkers for heterogeneous complex disease diagnoses. 89-101 - Li Yao, Heming Wang, Yuanyuan Song, Zhen Dai, Hao Yu, Ming Yin, Dongxu Wang, Xin Yang, Jinlin Wang, Tiedong Wang, Nan Cao, Jimin Zhu, Xizhong Shen, Guangqi Song, Yicheng Zhao:
Large-scale prediction of ADAR-mediated effective human A-to-I RNA editing. 102-109 - Cong Zeng, Lingyun Zou:
An account of in silico identification tools of secreted effector proteins in bacteria and future challenges. 110-129 - Ajanthah Sangaralingam, Abu Z. Dayem Ullah, Jacek Marzec, Emanuela Gadaleta, Ai Nagano, Helen Ross-Adams, Jun Wang, Nicholas R. Lemoine, Claude Chelala:
'Multi-omic' data analysis using O-miner. 130-143 - Hongwei Wang, Yan Wang, Zhi Xie:
Computational resources for ribosome profiling: from database to Web server and software. 144-155 - Xiaoming Wang, Carolyn Williams, Zhen Hua Liu, Joe Croghan:
Big data management challenges in health research - a literature review. 156-167 - Qian Yang, Shuyuan Wang, Enyu Dai, Shunheng Zhou, Dianming Liu, Haizhou Liu, Qianqian Meng, Bin Jiang, Wei Jiang:
Pathway enrichment analysis approach based on topological structure and updated annotation of pathway. 168-177 - Xue Li, Xinlei Wang, Guanghua Xiao:
A comparative study of rank aggregation methods for partial and top ranked lists in genomic applications. 178-189 - Emir Muñoz, Vít Novácek, Pierre-Yves Vandenbussche:
Facilitating prediction of adverse drug reactions by using knowledge graphs and multi-label learning models. 190-202 - Liang Cheng, Haixiu Yang, Hengqiang Zhao, Xiaoya Pei, Hongbo Shi, Jie Sun, Yunpeng Zhang, Zhenzhen Wang, Meng Zhou:
MetSigDis: a manually curated resource for the metabolic signatures of diseases. 203-209 - Stijn Hawinkel, Federico Mattiello, Luc Bijnens, Olivier Thas:
A broken promise: microbiome differential abundance methods do not control the false discovery rate. 210-221 - Saira Afzal, Irene Gil-Farina, Richard Gabriel, Shahzad Ahmad, Christof von Kalle, Manfred Schmidt, Raffaele Fronza:
Systematic comparative study of computational methods for T-cell receptor sequencing data analysis. 222-234 - Somali Chaterji, Jinkyu Koo, Ninghui Li, Folker Meyer, Ananth Grama, Saurabh Bagchi:
Federation in genomics pipelines: techniques and challenges. 235-244 - Mohamad Saad, Ellen M. Wijsman:
Association score testing for rare variants and binary traits in family data with shared controls. 245-253 - Yulan Deng, Shangyi Luo, Chunyu Deng, Tao Luo, Wenkang Yin, Hongyi Zhang, Yong Zhang, Xinxin Zhang, Yujia Lan, Yanyan Ping, Yun Xiao, Xia Li:
Identifying mutual exclusivity across cancer genomes: computational approaches to discover genetic interaction and reveal tumor vulnerability. 254-266 - Reuben J. Pengelly, Alejandra Vergara-Lope, Dareen Alyousfi, M. Reza Jabalameli, Andrew Collins:
Understanding the disease genome: gene essentiality and the interplay of selection, recombination and mutation. 267-273 - Shiping Yang, Hong Li, Huaqin He, Yuan Zhou, Ziding Zhang:
Critical assessment and performance improvement of plant-pathogen protein-protein interaction prediction methods. 274-287 - Daniel Spies, Peter F. Renz, Tobias A. Beyer, Constance Ciaudo:
Comparative analysis of differential gene expression tools for RNA sequencing time course data. 288-298 - Elizabeth Sam, Prashanth Athri:
Web-based drug repurposing tools: a survey. 299-316 - Yipeng Song, Johan A. Westerhuis, Nanne Aben, Magali Michaut, Lodewyk F. A. Wessels, Age K. Smilde:
Principal component analysis of binary genomics data. 317-329 - Yumeng Liu, Xiaolong Wang, Bin Liu:
A comprehensive review and comparison of existing computational methods for intrinsically disordered protein and region prediction. 330-346 - Wilson Wen Bin Goh, Limsoon Wong:
Advanced bioinformatics methods for practical applications in proteomics. 347-355
- Cristina Marino Buslje, Alexander Miguel Monzon, Diego Javier Zea, María Silvina Fornasari, Gustavo D. Parisi:
On the dynamical incompleteness of the Protein Data Bank. 356-359
Volume 20, Number 2, March 2019
- Vivienne Baillie Gerritsen, Patricia M. Palagi, Christine Durinx:
Bioinformatics on a national scale: an example from Switzerland. 361-369 - Andreas Tauch, Arwa Al-Dilaimi:
Bioinformatics in Germany: toward a national-level infrastructure. 370-374 - Celia W. G. van Gelder, Rob W. W. Hooft, Merlijn N. van Rijswijk, Linda van den Berg, Ruben G. Kok, Marcel J. T. Reinders, Barend Mons, Jaap Heringa:
Bioinformatics in the Netherlands: the value of a nationwide community. 540-550 - Maria Victoria Schneider, Philippa C. Griffin, Sonika Tyagi, Madison Flannery, Saravanan Dayalan, Simon Gladman, Nathan S. Watson-Haigh, Philipp E. Bayer, Michael A. Charleston, Ira Cooke, Rob Cook, Richard J. Edwards, David Edwards, Dominique Gorse, Malcolm J. McConville, David Powell, Marc R. Wilkins, Andrew Lonie:
Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. 384-389 - Javier De Las Rivas, César Bonavides-Martínez, Francisco Jose Campos-Laborie:
Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures. 390-397 - Teresa K. Attwood, Sarah Blackford, Michelle D. Brazas, Angela C. Davies, Maria Victoria Schneider:
A global perspective on evolving bioinformatics and data science training needs. 398-404 - Allegra Via, Teresa K. Attwood, Pedro L. Fernandes, Sarah L. Morgan, Maria Victoria Schneider, Patricia M. Palagi, Gabriella Rustici, Rochelle E. Tractenberg:
A new pan-European Train-the-Trainer programme for bioinformatics: pilot results on feasibility, utility and sustainability of learning. 405-415 - Rochelle E. Tractenberg:
Degrees of freedom analysis in educational research and decision-making: leveraging qualitative data to promote excellence in bioinformatics training and education. 416-425 - Guillaume Bernard, Cheong Xin Chan, Yao-ban Chan, Xin-Yi Chua, Yingnan Cong, James M. Hogan, Stefan R. Maetschke, Mark A. Ragan:
Alignment-free inference of hierarchical and reticulate phylogenomic relationships. 426-435 - Maria Angela Diroma, Loredana Ciaccia, Graziano Pesole, Ernesto Picardi:
Elucidating the editome: bioinformatics approaches for RNA editing detection. 436-447 - Shiwei Ma, Qi Song, Huan Tao, Andrew P. Harrison, Shaobo Wang, Wei Liu, Shoukai Lin, Ziding Zhang, Yufang Ai, Huaqin He:
Prediction of protein-protein interactions between fungus (Magnaporthe grisea) and rice (Oryza sativa L.). 448-456 - Nicholas P. Tatonetti:
Translational medicine in the Age of Big Data. 457-462 - Pablo Mier, Miguel A. Andrade-Navarro:
Toward completion of the Earth's proteome: an update a decade later. 463-470 - Gabriela Alejandra Merino, Ana Conesa, Elmer Andrés Fernández:
A benchmarking of workflows for detecting differential splicing and differential expression at isoform level in human RNA-seq studies. 471-481 - Xiangyu Li, Hao Cai, Xianlong Wang, Lu Ao, You Guo, Jun He, Yunyan Gu, Lishuang Qi, Qingzhou Guan, Xu Lin, Zheng Guo:
A rank-based algorithm of differential expression analysis for small cell line data with statistical control. 482-491 - Frauke Degenhardt, Stephan Seifert, Silke Szymczak:
Evaluation of variable selection methods for random forests and omics data sets. 492-503 - Emmanuel S. Adabor, George K. Acquaah-Mensah:
Machine learning approaches to decipher hormone and HER2 receptor status phenotypes in breast cancer. 504-514 - Xing Chen, Di Xie, Qi Zhao, Zhu-Hong You:
MicroRNAs and complex diseases: from experimental results to computational models. 515-539
- Maxwell Lewis Neal, Matthias König, David P. Nickerson, Goksel Misirli, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T. Cooling, Daniel L. Cook, Sharon M. Crook, Miguel de Alba, Samuel H. Friedman, Alan Garny, John H. Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick S. Juty, Chris J. Myers, Brett G. Olivier, Herbert M. Sauro, Martin Scharm, Jacky L. Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath:
Harmonizing semantic annotations for computational models in biology. 540-550 - Ivan V. Antonov, Evgeny Mazurov, Mark Borodovsky, Yulia A. Medvedeva:
Prediction of lncRNAs and their interactions with nucleic acids: benchmarking bioinformatics tools. 551-564 - Armin Scheben, Chon-Kit Kenneth Chan, Locedie Mansueto, Ramil Mauleon, Pierre Larmande, Nickolai Alexandrov, Rod A. Wing, Kenneth L. McNally, Hadi Quesneville, David Edwards:
Progress in single-access information systems for wheat and rice crop improvement. 565-571 - Lan Zhao, Victor H. F. Lee, Michael K. Ng, Hong Yan, Maarten F. Bijlsma:
Molecular subtyping of cancer: current status and moving toward clinical applications. 572-584 - Hao Feng, Peng Jin, Hao Wu:
Disease prediction by cell-free DNA methylation. 585-597 - Meng Zhou, Hengqiang Zhao, Xinyu Wang, Jie Sun, Jianzhong Su:
Analysis of long noncoding RNAs highlights region-specific altered expression patterns and diagnostic roles in Alzheimer's disease. 598-608 - Mansoor A. S. Saqi, Artem Lysenko, Yike Guo, Tatsuhiko Tsunoda, Charles Auffray:
Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. 609-623 - Mengyun Wu, Shuangge Ma:
Robust genetic interaction analysis. 624-637 - Jiangning Song, Yanan Wang, Fuyi Li, Tatsuya Akutsu, Neil D. Rawlings, Geoffrey I. Webb, Kuo-Chen Chou:
iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites. 638-658 - Marek Ostaszewski, Stephan Gebel, Inna Kuperstein, Alexander Mazein, Andrei Yu. Zinovyev, Ugur Dogrusoz, Jan Hasenauer, Ronan M. T. Fleming, Nicolas Le Novère, Piotr Gawron, Thomas S. Ligon, Anna Niarakis, David P. Nickerson, Daniel Weindl, Rudi Balling, Emmanuel Barillot, Charles Auffray, Reinhard Schneider:
Community-driven roadmap for integrated disease maps. 659-670 - Bettina M. Pucher, Oana A. Zeleznik, Gerhard G. Thallinger:
Comparison and evaluation of integrative methods for the analysis of multilevel omics data: a study based on simulated and experimental cancer data. 671-681 - Tatianne da Costa Negri, Wonder Alexandre Luz Alves, Pedro Henrique Bugatti, Priscila Tiemi Maeda Saito, Douglas Silva Domingues, Alexandre Rossi Paschoal:
Pattern recognition analysis on long noncoding RNAs: a tool for prediction in plants. 682-689 - Emile R. Chimusa, Shareefa Dalvie, Collet Dandara, Ambroise Wonkam, Gaston K. Mazandu:
Post genome-wide association analysis: dissecting computational pathway/network-based approaches. 690-700 - L. Cristobal Monraz Gomez, Maria Kondratova, Jean-Marie Ravel, Emmanuel Barillot, Andrei Yu. Zinovyev, Inna Kuperstein:
Application of Atlas of Cancer Signalling Network in preclinical studies. 701-716
- Farnaz Barneh, Mehdi Mirzaie, Payman Nickchi, Tuan Zea Tan, Jean-Paul Thiery, Mehran Piran, Mona Salimi, Fatemeh Goshadrou, Amir R. Aref, Mohieddin Jafari:
Integrated use of bioinformatic resources reveals that co-targeting of histone deacetylases, IKBK and SRC inhibits epithelial-mesenchymal transition in cancer. 717-731
- Feng Gao:
Recent developments of software and database in microbial genomics and functional genomics. 732-734 - Maria Victoria Schneider:
Bioinformatics: scalability, capabilities and training in the data-driven era. 735-736
Volume 20, Number 3, May 2019
- Jing Feng, Yu Xiang, Siyu Xia, Huan Liu, Jun Wang, Fatma Muge Ozguc, Lijun Lei, Ruoshan Kong, Lixia Diao, Chunjiang He, Leng Han:
CircView: a visualization and exploration tool for circular RNAs. 745-751 - Gonzalo Gómez-López, Joaquín Dopazo, Juan C. Cigudosa, Alfonso Valencia, Fátima Al-Shahrour:
Precision medicine needs pioneering clinical bioinformaticians. 752-766 - Girolamo Giudice, Evangelia Petsalaki:
Proteomics and phosphoproteomics in precision medicine: applications and challenges. 767-777 - Jochen Singer, Anja Irmisch, Hans-Joachim Ruscheweyh, Franziska Singer, Nora C. Toussaint, Mitchell P. Levesque, Daniel J. Stekhoven, Niko Beerenwinkel:
Bioinformatics for precision oncology. 778-788 - Francesca Vitali, Qike Li, A. Grant Schissler, Joanne Berghout, Colleen Kenost, Yves A. Lussier:
Developing a 'personalome' for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes. 789-805 - Anastasis Oulas, George Minadakis, Margarita Zachariou, Kleitos Sokratous, Marilena M. Bourdakou, George M. Spyrou:
Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches. 806-824 - Nikolas Dovrolis, George Kolios, George M. Spyrou, Ioanna Maroulakou:
Computational profiling of the gut-brain axis: microflora dysbiosis insights to neurological disorders. 825-841 - Jessica D. Tenenbaum, Krithika Bhuvaneshwar, Jane P. Gagliardi, Kate Fultz Hollis, Peilin Jia, Liang Ma, Radhakrishnan Nagarajan, Gopalkumar Rakesh, Vignesh Subbian, Shyam Visweswaran, Zhongming Zhao, Leon Rozenblit:
Translational bioinformatics in mental health: open access data sources and computational biomarker discovery. 842-856 - Cedric Christian Laczny, Valentina Galata, Achim Plum, Andreas E. Posch, Andreas Keller:
Assessing the heterogeneity of in silico plasmid predictions based on whole-genome-sequenced clinical isolates. 857-865 - Vasanthan Jayakumar, Yasubumi Sakakibara:
Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data. 866-876 - Fei Liu, Monika Heiner, David R. Gilbert:
Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems. 877-886 - Md Momin Al Aziz, Md. Nazmus Sadat, Dima Alhadidi, Shuang Wang, Xiaoqian Jiang, Cheryl L. Brown, Noman Mohammed:
Privacy-preserving techniques of genomic data - a survey. 887-895 - Xing Chen, Ya-Zhou Sun, Hui Liu, Lin Zhang, Jian-Qiang Li, Jia Meng:
RNA methylation and diseases: experimental results, databases, Web servers and computational models. 896-917 - Michele Bortolomeazzi, Enrico Gaffo, Stefania Bortoluzzi:
A survey of software tools for microRNA discovery and characterization using RNA-seq. 918-930 - Jiawei Wang, Bingjiao Yang, Yi An, Tatiana T. Marquez-Lago, André Leier, Jonathan Wilksch, Qingyang Hong, Yang Zhang, Morihiro Hayashida, Tatsuya Akutsu, Geoffrey I. Webb, Richard A. Strugnell, Jiangning Song, Trevor Lithgow:
Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches. 931-951 - Yuxin Lin, Fuliang Qian, Li Shen, Feifei Chen, Jiajia Chen, Bairong Shen:
Computer-aided biomarker discovery for precision medicine: data resources, models and applications. 952-975 - Yun-Ru Chen, Hsuan-Cheng Huang, Chen-Ching Lin:
Regulatory feedback loops bridge the human gene regulatory network and regulate carcinogenesis. 976-984 - Leili Shahriyari:
Effect of normalization methods on the performance of supervised learning algorithms applied to HTSeq-FPKM-UQ data sets: 7SK RNA expression as a predictor of survival in patients with colon adenocarcinoma. 985-994 - Boyang Li, Qiongshi Lu, Hongyu Zhao:
An evaluation of noncoding genome annotation tools through enrichment analysis of 15 genome-wide association studies. 995-1003 - Ágnes Osz, Lorinc Sándor Pongor, Danuta Szirmai, Balazs Györffy:
A snapshot of 3649 Web-based services published between 1994 and 2017 shows a decrease in availability after 2 years. 1004-1010 - Tobias Fehlmann, Shashwat Sahay, Andreas Keller, Christina Backes:
A review of databases predicting the effects of SNPs in miRNA genes or miRNA-binding sites. 1011-1020 - Hairong Wei:
Construction of a hierarchical gene regulatory network centered around a transcription factor. 1021-1031 - Aitor Blanco-Míguez, Florentino Fdez-Riverola, Borja Sánchez, Anália Lourenço:
Resources and tools for the high-throughput, multi-omic study of intestinal microbiota. 1032-1056 - Massimiliano Zanin, Ivan Chorbev, Blaz Stres, Egils Stalidzans, Julio Vera, Paolo Tieri, Filippo Castiglione, Derek Groen, Huiru Zheng, Jan Baumbach, Johannes A. Schmid, José Basilio, Peter Klimek, Natasa Debeljak, Damjana Rozman, Harald H. H. W. Schmidt:
Community effort endorsing multiscale modelling, multiscale data science and multiscale computing for systems medicine. 1057-1062
Volume 20, Number 4, July 2019
- Michael Y. Galperin, David M. Kristensen, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin:
Microbial genome analysis: the COG approach. 1063-1070 - Claudine Médigue, Alexandra Calteau, Stéphane Cruveiller, Mathieu Gachet, Guillaume Gautreau, Adrien Josso, Aurélie Lajus, Jordan Langlois, Hugo Pereira, Rémi Planel, David Roche, Johan Rollin, Zoé Rouy, David Vallenet:
MicroScope - an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data. 1071-1084 - Peter D. Karp, Richard Billington, Ron Caspi, Carol A. Fulcher, Mario Latendresse, Anamika Kothari, Ingrid M. Keseler, Markus Krummenacker, Peter E. Midford, Quang Ong, Wai Kit Ong, Suzanne M. Paley, Pallavi Subhraveti:
The BioCyc collection of microbial genomes and metabolic pathways. 1085-1093 - Dionysios A. Antonopoulos, Rida Assaf, Ramy Karam Aziz, Thomas S. Brettin, Christopher Bun, Neal Conrad, James J. Davis, Emily M. Dietrich, Terry Disz, Svetlana Gerdes, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Daniel E. Murphy-Olson, Eric K. Nordberg, Gary J. Olsen, Robert Olson, Ross A. Overbeek, Bruce D. Parrello, Gordon D. Pusch, John Santerre, Maulik Shukla, Rick L. Stevens, Margo VanOeffelen, Veronika Vonstein, Andrew S. Warren, Alice R. Wattam, Fangfang Xia, Hyun Seung Yoo:
PATRIC as a unique resource for studying antimicrobial resistance. 1094-1102 - Kai Blin, Hyun Uk Kim, Marnix H. Medema, Tilmann Weber:
Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters. 1103-1113 - Hao Luo, Chun-Lan Quan, Chong Peng, Feng Gao:
Recent development of Ori-Finder system and DoriC database for microbial replication origins. 1114-1124 - Florian P. Breitwieser, Jennifer Lu, Steven L. Salzberg:
A review of methods and databases for metagenomic classification and assembly. 1125-1136 - Nathan D. Olson, Todd J. Treangen, Christopher Michael Hill, Victoria Cepeda-Espinoza, Jay Ghurye, Sergey Koren, Mihai Pop:
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes. 1140-1150 - Folker Meyer, Saurabh Bagchi, Somali Chaterji, Wolfgang Gerlach, Ananth Grama, Travis Harrison, Tobias Paczian, William L. Trimble, Andreas Wilke:
MG-RAST version 4 - lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis. 1151-1159 - Kazutaka Katoh, John Rozewicki, Kazunori D. Yamada:
MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. 1160-1166 - David R. Gilbert, Monika Heiner, Yasoda Jayaweera, Christian Rohr:
Towards dynamic genome-scale models. 1167-1180 - Lionel Morgado, Frank Johannes:
Computational tools for plant small RNA detection and categorization. 1181-1192 - Yongsheng Li, Xiyun Jin, Zishan Wang, Lili Li, Hong Chen, Xiaoyu Lin, Song Yi, Yunpeng Zhang, Juan Xu:
Systematic review of computational methods for identifying miRNA-mediated RNA-RNA crosstalk. 1193-1204 - Jincheol Park, Shili Lin:
Evaluation and comparison of methods for recapitulation of 3D spatial chromatin structures. 1205-1214 - Gerhard Mayer, Christian Quast, Janine Felden, Matthias Lange, Manuel Prinz, Alfred Pühler, Chris Lawerenz, Uwe Scholz, Frank Oliver Glöckner, Wolfgang Müller, Katrin Marcus, Martin Eisenacher:
A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects. 1215-1221 - Brian B. Luczak, Benjamin T. James, Hani Z. Girgis:
A survey and evaluations of histogram-based statistics in alignment-free sequence comparison. 1222-1237 - Arnau Montagud, Pauline Traynard, Loredana Martignetti, Eric Bonnet, Emmanuel Barillot, Andrei Yu. Zinovyev, Laurence Calzone:
Conceptual and computational framework for logical modelling of biological networks deregulated in diseases. 1238-1249 - Jian Zhang, Zhiqiang Ma, Lukasz A. Kurgan:
Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chains. 1250-1268 - Giulia Tini, Luca Marchetti, Corrado Priami, Marie-Pier Scott-Boyer:
Multi-omics integration - a comparison of unsupervised clustering methodologies. 1269-1279 - Bin Liu:
BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches. 1280-1294 - Ruiping Wang, Yue Han, Zhangxiang Zhao, Fan Yang, Tingting Chen, Wenbin Zhou, Xianlong Wang, Lishuang Qi, Wenyuan Zhao, Zheng Guo, Yunyan Gu:
Link synthetic lethality to drug sensitivity of cancer cells. 1295-1307 - Yongjun Zhu, Olivier Elemento, Jyotishman Pathak, Fei Wang:
Drug knowledge bases and their applications in biomedical informatics research. 1308-1321 - Qin Tang, Qiong Zhang, Yao Lv, Ya-Ru Miao, An-Yuan Guo:
SEGreg: a database for human specifically expressed genes and their regulations in cancer and normal tissue. 1322-1328 - Florencio Pazos, Monica Chagoyen:
Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology. 1329-1336 - Ali Ezzat, Min Wu, Xiaoli Li, Chee Keong Kwoh:
Computational prediction of drug-target interactions using chemogenomic approaches: an empirical survey. 1337-1357 - Fernando Carazo, Juan P. Romero, Angel Rubio:
Upstream analysis of alternative splicing: a review of computational approaches to predict context-dependent splicing factors. 1358-1375 - Paul Medvedev:
Modeling biological problems in computer science: a case study in genome assembly. 1376-1383 - Alessandra Dal Molin, Barbara Di Camillo:
How to design a single-cell RNA-sequencing experiment: pitfalls, challenges and perspectives. 1384-1394 - Andrés Zalguizuri, Gustavo Caetano-Anollés, Viviana Claudia Lepek:
Phylogenetic profiling, an untapped resource for the prediction of secreted proteins and its complementation with sequence-based classifiers in bacterial type III, IV and VI secretion systems. 1395-1402 - Junpeng Zhang, Thuc Duy Le, Lin Liu, Jiuyong Li:
Inferring and analyzing module-specific lncRNA-mRNA causal regulatory networks in human cancer. 1403-1419 - Shasha Li, Shuaishuai Teng, Junquan Xu, Guannan Su, Yu Zhang, Jianqing Zhao, Suwei Zhang, Haiyan Wang, Wenyan Qin, Zhi John Lu, Yong Guo, Qianyong Zhu, Dong Wang:
Microarray is an efficient tool for circRNA profiling. 1420-1433 - Igor F. Tsigelny:
Artificial intelligence in drug combination therapy. 1434-1448 - Juan Xie, Anjun Ma, Anne Fennell, Qin Ma, Jing Zhao:
It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data. 1449-1464 - Ming Hao, Stephen H. Bryant, Yanli Wang:
Open-source chemogenomic data-driven algorithms for predicting drug-target interactions. 1465-1474
- Daniela Oliveira, Anila Sahar Butt, Armin Haller, Dietrich Rebholz-Schuhmann, Ratnesh Sahay:
Where to search top-K biomedical ontologies? 1477-1491 - Jue Yang, Hui Song, Kun Cao, Jialei Song, Jianjiang Zhou:
Comprehensive analysis of Helicobacter pylori infection-associated diseases based on miRNA-mRNA interaction network. 1492-1501 - Hua Sun, Pora Kim, Peilin Jia, Aekyung Park, Han Liang, Zhongming Zhao:
Distinct telomere length and molecular signatures in seminoma and non-seminoma of testicular germ cell tumor. 1502-1512 - António Cruz, Joel P. Arrais, Penousal Machado:
Interactive and coordinated visualization approaches for biological data analysis. 1513-1523 - Zhuo Zhang, Hao Li, Shuai Jiang, Ruijiang Li, Wanying Li, Hebing Chen, Xiaochen Bo:
A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data. 1524-1541 - Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu:
Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions. 1542-1559
- David Arndt, Ana Marcu, Yongjie Liang, David S. Wishart:
PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes. 1560-1567 - Huansheng Cao, Qin Ma, Xin Chen, Ying Xu:
DOOR: a prokaryotic operon database for genome analyses and functional inference. 1568-1577 - Paul Stothard, Jason R. Grant, Gary H. Van Domselaar:
Visualizing and comparing circular genomes using the CGView family of tools. 1576-1582 - Shun H. Yip, Pak Chung Sham, Junwen Wang:
Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data. 1583-1589
- Gaoyang Li, Huansheng Cao, Ying Xu:
Structural and functional analyses of microbial metabolic networks reveal novel insights into genome-scale metabolic fluxes. 1590-1603
Volume 20, Number 5, September 2019
- Shaoping Shi, Lina Wang, Man Cao, Guodong Chen, Jialin Yu:
Proteomic analysis and prediction of amino acid variations that influence protein posttranslational modifications. 1597-1606 - Georgina Stegmayer, Leandro E. Di Persia, Mariano Rubiolo, Matias Gerard, Milton Pividori, Cristian A. Yones, Leandro A Bugnon, Tadeo Rodriguez, Jonathan Raad, Diego H. Milone:
Predicting novel microRNA: a comprehensive comparison of machine learning approaches. 1607-1620 - Tingting Shao, Guangjuan Wang, Hong Chen, Yunjin Xie, Xiyun Jin, Jing Bai, Juan Xu, Xia Li, Jian Huang, Yan Jin, Yongsheng Li:
Survey of miRNA-miRNA cooperative regulation principles across cancer types. 1621-1638 - Elena Rojano, Pedro Seoane, Juan A. G. Ranea, James Richard Perkins:
Regulatory variants: from detection to predicting impact. 1639-1654 - Alicia Amadoz, Marta R. Hidalgo, Cankut Çubuk, José Carbonell-Caballero, Joaquín Dopazo:
A comparison of mechanistic signaling pathway activity analysis methods. 1655-1668 - Yu Bao, Simone Marini, Takeyuki Tamura, Mayumi Kamada, Shingo Maegawa, Hiroshi Hosokawa, Jiangning Song, Tatsuya Akutsu:
Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features. 1669-1684 - Claire Bertelli, Keith E. Tilley, Fiona S. L. Brinkman:
Microbial genomic island discovery, visualization and analysis. 1685-1698 - Francesco Pappalardo, Giulia Russo, Flora Musuamba Tshinanu, Marco Viceconti:
In silico clinical trials: concepts and early adoptions. 1699-1708 - Ephifania Geza, Jacquiline W. Mugo, Nicola J. Mulder, Ambroise Wonkam, Emile R. Chimusa, Gaston K. Mazandu:
A comprehensive survey of models for dissecting local ancestry deconvolution in human genome. 1709-1724 - Zhongneng Xu, Shuichi Asakawa:
Physiological RNA dynamics in RNA-Seq analysis. 1725-1733 - Raziur Rahman, Saugato Rahman Dhruba, Kevin Matlock, Carlos De Niz, Souparno Ghosh, Ranadip Pal:
Evaluating the consistency of large-scale pharmacogenomic studies. 1734-1753 - Dinanath Sulakhe, Mark D'Souza, Sheng Wang, Sandhya Balasubramanian, Prashanth Athri, Bingqing Xie, Stefan Canzar, Gady Agam, T. Conrad Gilliam, Natalia Maltsev:
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. 1754-1768 - Mikhail G. Dozmorov:
Disease classification: from phenotypic similarity to integrative genomics and beyond. 1769-1780 - Qi Chen, Xianwen Meng, Qi Liao, Ming Chen:
Versatile interactions and bioinformatics analysis of noncoding RNAs. 1781-1794 - Gaye Lightbody, Valeriia Haberland, Fiona Browne, Laura Taggart, Huiru Zheng, Eileen Parkes, Jaine K. Blayney:
Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application. 1795-1811 - Chunjie Jiang, Na Ding, Junyi Li, Xiyun Jin, Lili Li, Tao Pan, Caiqin Huo, Yongsheng Li, Juan Xu, Xia Li:
Landscape of the long non-coding RNA transcriptome in human heart. 1812-1825 - Dongyang Liu, Guangpeng Li, Yongchun Zuo:
Function determinants of TET proteins: the arrangements of sequence motifs with specific codes. 1826-1835 - Liang Chen, Liisa Heikkinen, Changliang Wang, Yang Yang, Huiyan Sun, Garry Wong:
Trends in the development of miRNA bioinformatics tools. 1836-1852 - Seowon Choi, Hyun-Woo Kim, Jin-Wu Nam:
The small peptide world in long noncoding RNAs. 1853-1864 - Yongjing Liu, Liangyu Fu, Kerstin Kaufmann, Dijun Chen, Ming Chen:
A practical guide for DNase-seq data analysis: from data management to common applications. 1865-1877 - Ahmet Süreyya Rifaioglu, Heval Atas, Maria Jesus Martin, Rengül Çetin-Atalay, Volkan Atalay, Tunca Dogan:
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases. 1878-1912
- Yang-Jun Wen, Ya-Wen Zhang, Jin Zhang, Jian-Ying Feng, Jim M. Dunwell, Yuan-Ming Zhang:
An efficient multi-locus mixed model framework for the detection of small and linked QTLs in F2. 1913-1924 - Zhenyu Yue, Le Zhao, Na Cheng, Hua Yan, Junfeng Xia:
dbCID: a manually curated resource for exploring the driver indels in human cancer. 1925-1933 - Zuqi Zuo, Yonghao Jin, Wen Zhang, Yichen Lu, Bin Li, Kun Qu:
ATAC-pipe: general analysis of genome-wide chromatin accessibility. 1934-1943
- Oliver Schmitt, Peter Eipert, Sebastian Schwanke, Felix Lessmann, Jennifer Meinhardt, Julia Beier, Kanar Kadir, Adrian Karnitzki, Linda Sellner, Ann-Christin Klünker, Frauke Ruß, Jörg Jenssen:
Connectome verification: inter-rater and connection reliability of tract-tracing-based intrinsic hypothalamic connectivity. 1944-1955
- Corrigendum to: How trees allocate carbon for optimal growth: insight from a game-theoretic model. 1956
Volume 20, Number 6, November 2019
- Rajeev K. Azad, Vladimir Shulaev:
Metabolomics technology and bioinformatics for precision medicine. 1957-1971 - Juan Wang, Maozu Guo:
A review of metrics measuring dissimilarity for rooted phylogenetic networks. 1972-1980 - Jeff Gauthier, Antony T. Vincent, Steve J. Charette, Nicolas Derome:
A brief history of bioinformatics. 1981-1996 - Clare Horscroft, Sarah Ennis, Reuben J. Pengelly, Timothy J. Sluckin, Andrew Collins:
Sequencing era methods for identifying signatures of selection in the genome. 1997-2008 - Siyu Han, Yanchun Liang, Qin Ma, Yangyi Xu, Yu Zhang, Wei Du, Cankun Wang, Ying Li:
LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property. 2009-2027 - Dai Hai Nguyen, Canh Hao Nguyen, Hiroshi Mamitsuka:
Recent advances and prospects of computational methods for metabolite identification: a review with emphasis on machine learning approaches. 2028-2043 - Adam McDermaid, Brandon Monier, Jing Zhao, Bingqiang Liu, Qin Ma:
Interpretation of differential gene expression results of RNA-seq data: review and integration. 2044-2054 - Johannes Brägelmann, Justo Lorenzo Bermejo:
A comparative analysis of cell-type adjustment methods for epigenome-wide association studies based on simulated and real data sets. 2055-2065 - Chen Wang, Lukasz A. Kurgan:
Review and comparative assessment of similarity-based methods for prediction of drug-protein interactions in the druggable human proteome. 2066-2087 - Xun Chen, Jason Kost, Dawei Li:
Comprehensive comparative analysis of methods and software for identifying viral integrations. 2088-2097 - Wenliang Zhang, Haiyue Zhang, Huan Yang, Miaoxin Li, Zhi Xie, Weizhong Li:
Computational resources associating diseases with genotypes, phenotypes and exposures. 2098-2115 - Kleber Padovani de Souza, João Carlos Setubal, André Carlos Ponce de Leon Ferreira de Carvalho, Guilherme Oliveira, Annie Chateau, Ronnie Alves:
Machine learning meets genome assembly. 2116-2129 - Fulong Yu, Fei Quan, Jinyuan Xu, Yan Zhang, Yi Xie, Jingyu Zhang, Yujia Lan, Huating Yuan, Hongyi Zhang, Shujun Cheng, Yun Xiao, Xia Li:
Breast cancer prognosis signature: linking risk stratification to disease subtypes. 2130-2140 - Hongyan Yin, Mengwei Li, Lin Xia, Chaozu He, Zhang Zhang:
Computational determination of gene age and characterization of evolutionary dynamics in human. 2141-2149 - Fuyi Li, Yanan Wang, Chen Li, Tatiana T. Marquez-Lago, André Leier, Neil D. Rawlings, Gholamreza Haffari, Jerico Nico De Leon Revote, Tatsuya Akutsu, Kuo-Chen Chou, Anthony W. Purcell, Robert N. Pike, Geoffrey I. Webb, Alexander Ian Smith, Trevor Lithgow, Roger J. Daly, James C. Whisstock, Jiangning Song:
Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods. 2150-2166 - Misagh Naderi, Jeffrey Mitchell Lemoine, Rajiv Gandhi Govindaraj, Omar Kana, Wei Pan Feinstein, Michal Brylinski:
Binding site matching in rational drug design: algorithms and applications. 2167-2184 - Yanju Zhang, Ruopeng Xie, Jiawei Wang, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Jiangning Song:
Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework. 2185-2199 - Fentaw Abegaz, Kridsadakorn Chaichoompu, Emmanuelle Génin, David W. Fardo, Inke R. König, Jestinah M. Mahachie John, Kristel Van Steen:
Principals about principal components in statistical genetics. 2200-2216 - Zhiyu Hao, Li Jiang, Jin Gao, Jinhua Ye, Jingli Zhao, Shuling Li, Runqing Yang:
Quick approximation of threshold values for genome-wide association studies. 2217-2223 - Saurav Mallik, Gabriel J. Odom, Zhen Gao, Lissette Gomez, Xi Chen, Lily Wang:
An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays. 2224-2235 - Wan-Yu Lin, Ching-Chieh Huang, Yu-Li Liu, Shih-Jen Tsai, Po-Hsiu Kuo:
Polygenic approaches to detect gene-environment interactions when external information is unavailable. 2236-2252 - Min Li, Hao Gao, Jianxin Wang, Fang-Xiang Wu:
Control principles for complex biological networks. 2253-2266 - Zhen Chen, Xuhan Liu, Fuyi Li, Chen Li, Tatiana T. Marquez-Lago, André Leier, Tatsuya Akutsu, Geoffrey I. Webb, Dakang Xu, Alexander Ian Smith, Lei Li, Kuo-Chen Chou, Jiangning Song:
Large-scale comparative assessment of computational predictors for lysine post-translational modification sites. 2267-2290 - Yan Zhao, Yujie Ning, Feng Zhang, Miao Ding, Yan Wen, Liang Shi, Kunpeng Wang, Mengnan Lu, Jingyan Sun, Menglu Wu, Bolun Cheng, Mei Ma, Lu Zhang, Shiqiang Cheng, Hui Shen, Qing Tian, Xiong Guo, Hong-Wen Deng:
PCA-based GRS analysis enhances the effectiveness for genetic correlation detection. 2291-2298 - Maciej Blaszczyk, Maciej Pawel Ciemny, Andrzej Kolinski, Mateusz Kurcinski, Sebastian Kmiecik:
Protein-peptide docking using CABS-dock and contact information. 2299-2305 - Meng Zou, Rui Jin, Kin Fai Au:
Revealing tumor heterogeneity of breast cancer by utilizing the linkage between somatic and germline mutations. 2306-2315 - Taiyun Kim, Irene Rui Chen, Yingxin Lin, Andy Yi-Yang Wang, Jean Yee Hwa Yang, Pengyi Yang:
Impact of similarity metrics on single-cell RNA-seq data clustering. 2316-2326 - Zhidong Tang, Xuecang Li, Jianmei Zhao, Fengcui Qian, Chenchen Feng, Yanyu Li, Jian Zhang, Yong Jiang, Yongsan Yang, Qiuyu Wang, Chunquan Li:
TRCirc: a resource for transcriptional regulation information of circRNAs. 2327-2333
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