Journal: Briefings in Bioinformatics

Volume 17, Issue 6

903 -- 911Jónathan Heras, César Domínguez, Eloy Mata, Vico Pascual, Carmen Lozano, Carmen Torres, Myriam Zarazaga. A survey of tools for analysing DNA fingerprints
912 -- 925Jónathan Heras, César Domínguez, Eloy Mata, Vico Pascual. Surveying and benchmarking techniques to analyse DNA gel fingerprint images
926 -- 937Deepak Nag Ayyala, David E. Frankhouser, Javkhlan-Ochir Ganbat, Guido Marcucci, Ralf Bundschuh, Pearlly Yan, Shili Lin. Statistical methods for detecting differentially methylated regions based on MethylCap-seq data
938 -- 952Junko Tsuji, Zhiping Weng. Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data
953 -- 966Sebastian Steinhauser, Nils Kurzawa, Roland Eils, Carl Herrmann. A comprehensive comparison of tools for differential ChIP-seq analysis
967 -- 979Dimitrios Kleftogiannis, Panos Kalnis, Vladimir B. Bajic. Progress and challenges in bioinformatics approaches for enhancer identification
980 -- 995Antonio Mora, Geir Kjetil Sandve, Odd Stokke Gabrielsen, Ragnhild Eskeland. In the loop: promoter-enhancer interactions and bioinformatics
996 -- 1008Wei Jiang, Ramkrishna Mitra, Chen-Ching Lin, Quan Wang, Feixiong Cheng, Zhongming Zhao. Systematic dissection of dysregulated transcription factor-miRNA feed-forward loops across tumor types
1009 -- 1023Maria Chatzou, Cedrik Magis, Jia-Ming Chang, Carsten Kemena, Giovanni Bussotti, Ionas Erb, Cédric Notredame. Multiple sequence alignment modeling: methods and applications
1024 -- 1031Hongdong Li, Gilbert S. Omenn, Yuanfang Guan. A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling
1032 -- 1043Xihao Hu, Yang Wu, Zhi John Lu, Kevin Y. Yip. Analysis of sequencing data for probing RNA secondary structures and protein-RNA binding in studying posttranscriptional regulations
1044 -- 1059Fan Zhang, Chunyan Ren, Kwun Kit Lau, Zihan Zheng, Geming Lu, Zhengzi Yi, Yongzhong Zhao, Fei Su, Shaojun Zhang, Bin Zhang, Eric A. Sobie, Weijia Zhang, Martin J. Walsh. A network medicine approach to build a comprehensive atlas for the prognosis of human cancer
1060 -- 1069Thomas Pfau, Maria Pires Pacheco, Thomas Sauter. Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond
1070 -- 1080Farnaz Barneh, Mohieddin Jafari, Mehdi Mirzaie. Updates on drug-target network; facilitating polypharmacology and data integration by growth of DrugBank database

Volume 17, Issue 5

733 -- 744Yoli Shavit, Ivan Merelli, Luciano Milanesi, Pietro Liò. How computer science can help in understanding the 3D genome architecture
745 -- 757Vladimir B. Teif. Nucleosome positioning: resources and tools online
758 -- 770Cristian Andrés Gallo, Rocío L. Cecchini, Jessica Andrea Carballido, Sandra Micheletto, Ignacio Ponzoni. Discretization of gene expression data revised
771 -- 785Haleh Yasrebi. Comparative study of joint analysis of microarray gene expression data in survival prediction and risk assessment of breast cancer patients
786 -- 795Ashley Cacho, Ekaterina Smirnova, Snehalata Huzurbazar, Xinping Cui. A Comparison of Base-calling Algorithms for Illumina Sequencing Technology
796 -- 807Hans-Ulrich Klein, Katja Hebestreit. An evaluation of methods to test predefined genomic regions for differential methylation in bisulfite sequencing data
808 -- 818Rosa J. Meijer, Jelle J. Goeman. Multiple Testing of Gene Sets from Gene Ontology: Possibilities and Pitfalls
819 -- 830Anika Oellrich, Nigel Collier, Tudor Groza, Dietrich Rebholz-Schuhmann, Nigam Shah, Olivier Bodenreider, Mary Regina Boland, Ivo I. Georgiev, Hongfang Liu, Kevin M. Livingston, Augustin Luna, Ann-Marie Mallon, Prashanti Manda, Peter N. Robinson, Gabriella Rustici, Michelle Simon, Liqin Wang, Rainer Winnenburg, Michel Dumontier. The digital revolution in phenotyping
831 -- 840Ian Walsh, Gianluca Pollastri, Silvio C. E. Tosatto. Correct machine learning on protein sequences: a peer-reviewing perspective
841 -- 862Khader Shameer, Lokesh P. Tripathi, Krishna R. Kalari, Joel T. Dudley, Ramanathan Sowdhamini. Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment
863 -- 876Denise Gameiro, Martín Pérez-Pérez, Gael Pérez Rodríguez, Gonçalo Monteiro, Nuno F. Azevedo, Anália Lourenço. Computational resources and strategies to construct single-molecule metabolic models of microbial cells
877 -- 890Peter D. Karp, Mario Latendresse, Suzanne M. Paley, Markus Krummenacker, Quang Ong, Richard Billington, Anamika Kothari, Daniel S. Weaver, Thomas J. Lee, Pallavi Subhraveti, Aaron Spaulding, Carol A. Fulcher, Ingrid M. Keseler, Ron Caspi. Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology
891 -- 901Rachel Cavill, Danyel Jennen, Jos Kleinjans, Jacob J. Briedé. Transcriptomic and metabolomic data integration

Volume 17, Issue 4

553 -- 561Pietro Hiram Guzzi, Giuseppe Agapito, Marianna Milano, Mario Cannataro. Methodologies and experimental platforms for generating and analysing microarray and mass spectrometry-based omics data to support P4 medicine
562 -- 575Andrew Parton, Victoria McGilligan, Maurice O'Kane, Francina R. Baldrick, Steven Watterson. Computational modelling of atherosclerosis
576 -- 592Tao Zeng, Wanwei Zhang, Xiangtian Yu, Xiaoping Liu, Meiyi Li, Luonan Chen. Big-data-based edge biomarkers: study on dynamical drug sensitivity and resistance in individuals
593 -- 602Goar Sánchez-Sanz, David Matallanas, Lan K. Nguyen, Boris N. Kholodenko, Edina Rosta, Walter Kolch, Nicolae-Viorel Buchete. MST2-RASSF protein-protein interactions through SARAH domains
603 -- 615Lavanya Kannan, Marcel Ramos, Angela Re, Nehme Hachem, Zhaleh Safikhani, Deena M. A. Gendoo, Sean Davis, David Gomez-Cabrero, Robert Castelo, Kasper D. Hansen, Vincent J. Carey, Martin Morgan, Aedín C. Culhane, Benjamin Haibe-Kains, Levi Waldron. Public data and open source tools for multi-assay genomic investigation of disease
616 -- 627Dagmar Iber, Zahra Karimaddini, Erkan Ünal. Image-based modelling of organogenesis
628 -- 641Chen Meng, Oana A. Zeleznik, Gerhard G. Thallinger, Bernhard Küster, Amin Moghaddas Gholami, Aedín C. Culhane. Dimension reduction techniques for the integrative analysis of multi-omics data
642 -- 656Feixiong Cheng, Junfei Zhao, Zhongming Zhao. Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes
657 -- 671Ananda S. Datta, Swati Biswas. Comparison of haplotype-based statistical tests for disease association with rare and common variants
672 -- 677Steven N. Hart, Kara N. Maxwell, Tinu Thomas, Vignesh Ravichandran, Bradley Wubberhorst, Robert J. Klein, Kasmintan Schrader, Csilla Szabo, Jeffrey N. Weitzel, Susan L. Neuhausen, Katherine Nathanson, Kenneth Offit, Fergus J. Couch, Joseph Vijai. Collaborative science in the next-generation sequencing era: a viewpoint on how to combine exome sequencing data across sites to identify novel disease susceptibility genes
678 -- 685Tyler Weirick, Giuseppe Militello, Raphael Mueller, David John, Stefanie Dimmeler, Shizuka Uchida. The identification and characterization of novel transcripts from RNA-seq data
686 -- 695Fan Zhu, Bharat Panwar, Yuanfang Guan. Algorithms for modeling global and context-specific functional relationship networks
696 -- 712Xing Chen, Chenggang Clarence Yan, Xiaotian Zhang, Xu Zhang, Feng Dai, Jian Yin, Yongdong Zhang. Drug-target interaction prediction: databases, web servers and computational models
713 -- 727Sungmin Lee, Hyeyoung Min, Sungroh Yoon. Will solid-state drives accelerate your bioinformatics? In-depth profiling, performance analysis and beyond
728 -- 730Vasileios Lapatas, Michalis Stefanidakis. BATMat: Bioinformatics Autodiscovery of Training Materials
731 -- 0Andrei Lihu, Stefan Holban. de novo motif discovery in ChIP-Seq data

Volume 17, Issue 3

367 -- 0Werner Dubitzky. Computational Systems Biomedicine
368 -- 379Alex Upton, Oswaldo Trelles, José Antonio Cornejo-García, James R. Perkins. Review: High-performance computing to detect epistasis in genome scale data sets
380 -- 392Ulf Schmitz, Hojjat Naderi-Meshkin, Shailendra K. Gupta, Olaf Wolkenhauer, Julio Vera. The RNA world in the 21st century - a systems approach to finding non-coding keys to clinical questions
393 -- 407Yasir Rahmatallah, Frank Emmert-Streib, Galina V. Glazko. Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline
408 -- 418Antonio Cappuccio, Paolo Tieri, Filippo Castiglione. Multiscale modelling in immunology: a review
419 -- 428Jun Hyuk Kang, Hosung Lee, Yun-Won Kang, Kwang-Hyun Cho. Systems biological approaches to the cardiac signaling network
429 -- 439Alexey M. Shibeko, Mikhail A. Panteleev. Untangling the complexity of blood coagulation network: use of computational modelling in pharmacology and diagnostics
440 -- 452Enrico Glaab. Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification
453 -- 467Shailendra K. Gupta, Tanushree Jaitly, Ulf Schmitz, Gerold Schuler, Olaf Wolkenhauer, Julio Vera. Personalized cancer immunotherapy using Systems Medicine approaches
468 -- 478Jung Hun Oh, Joseph O. Deasy. A literature mining-based approach for identification of cellular pathways associated with chemoresistance in cancer
479 -- 493Lan K. Nguyen. Dynamics of ubiquitin-mediated signalling: insights from mathematical modelling and experimental studies
494 -- 504David J. Duffy. Problems, challenges and promises: perspectives on precision medicine
505 -- 516Mufassra Naz, Alpha Tom Kodamullil, Martin Hofmann-Apitius. Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases
517 -- 526Archana Pan, Chandrajit Lahiri, Anjana Rajendiran, Buvaneswari Shanmugham. Computational analysis of protein interaction networks for infectious diseases
527 -- 540Gastone C. Castellani, Giulia Menichetti, Paolo Garagnani, Maria Giulia Bacalini, Chiara Pirazzini, Claudio Franceschi, Sebastiano Collino, Claudia Sala, Daniel Remondini, Enrico Giampieri, Ettore Mosca, Matteo Bersanelli, Silvia Vitali, Ìtalo Faria do Valle, Pietro Liò, Luciano Milanesi. Systems medicine of inflammaging
541 -- 552Leonor Puchades-Carrasco, Martina Palomino-Schätzlein, Clara Pérez-Rambla, Antonio Pineda-Lucena. Bioinformatics tools for the analysis of NMR metabolomics studies focused on the identification of clinically relevant biomarkers

Volume 17, Issue 2

185 -- 192Jae-Yong Nam, Nayoung K. D. Kim, Sang-Cheol Kim, Je-Gun Joung, Ruibin Xi, Semin Lee, Peter J. Park, Woong-Yang Park. Evaluation of somatic copy number estimation tools for whole-exome sequencing data
193 -- 203Xiangxiang Zeng, Xuan Zhang, Quan Zou. Integrative approaches for predicting microRNA function and prioritizing disease-related microRNA using biological interaction networks
204 -- 212Francesco Marabita, Paola de Candia, Anna Torri, Jesper Tegnér, Sergio Abrignani, Riccardo L. Rossi. Normalization of circulating microRNA expression data obtained by quantitative real-time RT-PCR
213 -- 223Alicia Poplawski, Federico Marini, Moritz Hess, Tanja Zeller, Johanna Mazur, Harald Binder. Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective
224 -- 232Pan Zhang, David C. Samuels, Brian D. Lehmann, Thomas Stricker, Jennifer A. Pietenpol, Yu Shyr, Yan Guo. Mitochondria sequence mapping strategies and practicability of mitochondria variant detection from exome and RNA sequencing data
233 -- 242Lishuang Qi, Libin Chen, Yang Li, Yuan Qin, Rufei Pan, Wenyuan Zhao, Yunyan Gu, Hongwei Wang, Ruiping Wang, Xiangqi Chen, Zheng Guo. Critical limitations of prognostic signatures based on risk scores summarized from gene expression levels: a case study for resected stage I non-small-cell lung cancer
243 -- 248Xun Gu. Statistical detection of differentially expressed genes based on RNA-seq: from biological to phylogenetic replicates
249 -- 254Xun Gu. Understanding tissue expression evolution: from expression phylogeny to phylogenetic network
255 -- 261Monica Chagoyen, Juan A. García-Martín, Florencio Pazos. Practical analysis of specificity-determining residues in protein families
262 -- 269Sinjini Sikdar, Ryan Gill, Susmita Datta. Improving protein identification from tandem mass spectrometry data by one-step methods and integrating data from other platforms
270 -- 282Chen Li, Catherine Ching Han Chang, Jeremy Nagel, Benjamin T. Porebski, Morihiro Hayashida, Tatsuya Akutsu, Jiangning Song, Ashley M. Buckle. in silico methods for prediction of coiled-coil domains in proteins
283 -- 292Wynand Alkema, Jos Boekhorst, Michiel Wels, Sacha A. F. T. van Hijum. Microbial bioinformatics for food safety and production
293 -- 308Damian Gola, Jestinah M. Mahachie John, Kristel Van Steen, Inke R. König. A roadmap to multifactor dimensionality reduction methods
309 -- 321Ahmed Mohamed, Canh Hao Nguyen, Hiroshi Mamitsuka. Current status and prospects of computational resources for natural product dereplication: a review
322 -- 335John C. Siavelis, Marilena M. Bourdakou, Emmanouil I. Athanasiadis, George M. Spyrou, Konstantina S. Nikita. Bioinformatics methods in drug repurposing for Alzheimer's disease
336 -- 345Maria K. Jaakkola, Laura L. Elo. Empirical comparison of structure-based pathway methods
346 -- 351Steven N. Hart, Patrick H. Duffy, Daniel J. Quest, Asif Hossain, Michael A. Meiners, Jean-Pierre A. Kocher. VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files
352 -- 366Enrico Glaab. Building a virtual ligand screening pipeline using free software: a survey

Volume 17, Issue 1

1 -- 0Russ B. Altman. Current Progress in Bioinformatics 2016
2 -- 12Jiao Li, Si Zheng, Bin Chen, Atul J. Butte, S. Joshua Swamidass, Zhiyong Lu. A survey of current trends in computational drug repositioning
13 -- 22Anna L. Tyler, Dana C. Crawford, Sarah A. Pendergrass. The detection and characterization of pleiotropy: discovery, progress, and promise
23 -- 32Ritu Khare, Benjamin M. Good, Robert Leaman, Andrew I. Su, Zhiyong Lu. Crowdsourcing in biomedicine: challenges and opportunities
33 -- 42Graciela Gonzalez, Tasnia Tahsin, Britton C. Goodale, Anna C. Greene, Casey S. Greene. Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery
43 -- 50Anna C. Greene, Kristine A. Giffin, Casey S. Greene, Jason H. Moore. Adapting bioinformatics curricula for big data
51 -- 62Christoph Bartenhagen, Martin Dugas. Robust and exact structural variation detection with paired-end and soft-clipped alignments: SoftSV compared with eight algorithms
63 -- 77Youhuang Bai, Xiaozhuan Dai, Andrew P. Harrison, Caroline E. Johnston, Ming Chen 0005. Toward a next-generation atlas of RNA secondary structure
78 -- 87Hongwei Wang, Hao Cai, Lu Ao, Haidan Yan, Wenyuan Zhao, Lishuang Qi, Yunyan Gu, Zheng Guo. Individualized identification of disease-associated pathways with disrupted coordination of gene expression
88 -- 105Jing Yan, Stefanie Friedrich, Lukasz A. Kurgan. A comprehensive comparative review of sequence-based predictors of DNA- and RNA-binding residues
106 -- 116Fabrizio Ferrè, Alessio Colantoni, Manuela Helmer-Citterich. Revealing protein-lncRNA interaction
117 -- 131Reyhaneh Esmaielbeiki, Konrad Krawczyk, Bernhard Knapp, Jean-Christophe Nebel, Charlotte M. Deane. Progress and challenges in predicting protein interfaces
132 -- 144Chung-Chi Huang, Zhiyong Lu. Community challenges in biomedical text mining over 10 years: success, failure and the future
145 -- 153Andrea Sboner, Olivier Elemento. A primer on precision medicine informatics
154 -- 179David Laehnemann, Arndt Borkhardt, Alice Carolyn McHardy. Denoising DNA deep sequencing data - high-throughput sequencing errors and their correction
180 -- 183Georgina Stegmayer, Milton Pividori, Diego H. Milone. A very simple and fast way to access and validate algorithms in reproducible research