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ORCIDBriefings in Bioinformatics, Volume 17
Volume 17, Number 1, January 2016
- Russ B. Altman:
Current Progress in Bioinformatics 2016. 1
- Jiao Li
, Si Zheng, Bin Chen, Atul J. Butte, S. Joshua Swamidass, Zhiyong Lu:
A survey of current trends in computational drug repositioning. 2-12 - Anna L. Tyler, Dana C. Crawford, Sarah A. Pendergrass:
The detection and characterization of pleiotropy: discovery, progress, and promise. 13-22 - Ritu Khare, Benjamin M. Good, Robert Leaman, Andrew I. Su, Zhiyong Lu:
Crowdsourcing in biomedicine: challenges and opportunities. 23-32 - Graciela 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. 33-42 - Anna C. Greene, Kristine A. Giffin, Casey S. Greene, Jason H. Moore:
Adapting bioinformatics curricula for big data. 43-50
- Christoph Bartenhagen, Martin Dugas:
Robust and exact structural variation detection with paired-end and soft-clipped alignments: SoftSV compared with eight algorithms. 51-62 - Youhuang Bai, Xiaozhuan Dai, Andrew P. Harrison, Caroline E. Johnston, Ming Chen:
Toward a next-generation atlas of RNA secondary structure. 63-77 - Hongwei 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. 78-87 - Jing Yan, Stefanie Friedrich, Lukasz A. Kurgan:
A comprehensive comparative review of sequence-based predictors of DNA- and RNA-binding residues. 88-105 - Fabrizio Ferrè, Alessio Colantoni, Manuela Helmer-Citterich:
Revealing protein-lncRNA interaction. 106-116 - Reyhaneh Esmaielbeiki, Konrad Krawczyk, Bernhard Knapp, Jean-Christophe Nebel, Charlotte M. Deane:
Progress and challenges in predicting protein interfaces. 117-131 - Chung-Chi Huang, Zhiyong Lu:
Community challenges in biomedical text mining over 10 years: success, failure and the future. 132-144 - Andrea Sboner, Olivier Elemento:
A primer on precision medicine informatics. 145-153
- David Laehnemann, Arndt Borkhardt, Alice Carolyn McHardy:
Denoising DNA deep sequencing data - high-throughput sequencing errors and their correction. 154-179
- Georgina Stegmayer, Milton Pividori, Diego H. Milone:
A very simple and fast way to access and validate algorithms in reproducible research. 180-183
Volume 17, Number 2, March 2016
- Jae-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. 185-192 - Xiangxiang Zeng, Xuan Zhang, Quan Zou:
Integrative approaches for predicting microRNA function and prioritizing disease-related microRNA using biological interaction networks. 193-203 - Francesco 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. 204-212
- Alicia Poplawski, Federico Marini, Moritz Hess, Tanja Zeller, Johanna Mazur, Harald Binder:
Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective. 213-223
- Pan 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. 224-232 - Lishuang 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. 233-242 - Xun Gu:
Statistical detection of differentially expressed genes based on RNA-seq: from biological to phylogenetic replicates. 243-248 - Xun Gu:
Understanding tissue expression evolution: from expression phylogeny to phylogenetic network. 249-254 - Monica Chagoyen, Juan A. García-Martín, Florencio Pazos:
Practical analysis of specificity-determining residues in protein families. 255-261 - Sinjini Sikdar, Ryan Gill, Susmita Datta:
Improving protein identification from tandem mass spectrometry data by one-step methods and integrating data from other platforms. 262-269 - Chen Li, Catherine Ching Han Chang, Jeremy Nagel, Benjamin T. Porebski, Morihiro Hayashida, Tatsuya Akutsu, Jiangning Song, Ashley M. Buckle:
Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins. 270-282 - Wynand Alkema, Jos Boekhorst, Michiel Wels, Sacha A. F. T. van Hijum:
Microbial bioinformatics for food safety and production. 283-292 - Damian Gola, Jestinah M. Mahachie John, Kristel Van Steen, Inke R. König:
A roadmap to multifactor dimensionality reduction methods. 293-308 - Ahmed Mohamed, Canh Hao Nguyen, Hiroshi Mamitsuka:
Current status and prospects of computational resources for natural product dereplication: a review. 309-321 - John C. Siavelis, Marilena M. Bourdakou, Emmanouil I. Athanasiadis, George M. Spyrou, Konstantina S. Nikita:
Bioinformatics methods in drug repurposing for Alzheimer's disease. 322-335 - Maria K. Jaakkola, Laura L. Elo:
Empirical comparison of structure-based pathway methods. 336-345 - Steven 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. 346-351 - Enrico Glaab:
Building a virtual ligand screening pipeline using free software: a survey. 352-366
Volume 17, Number 3, May 2016
- Werner Dubitzky:
Computational Systems Biomedicine. 367
- Alex Upton, Oswaldo Trelles, José Antonio Cornejo-García, James Richard Perkins:
Review: High-performance computing to detect epistasis in genome scale data sets. 368-379 - Ulf 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. 380-392 - Yasir Rahmatallah, Frank Emmert-Streib, Galina V. Glazko:
Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline. 393-407
- Antonio Cappuccio, Paolo Tieri, Filippo Castiglione:
Multiscale modelling in immunology: a review. 408-418
- Jun Hyuk Kang, Hosung Lee, Yun-Won Kang, Kwang-Hyun Cho:
Systems biological approaches to the cardiac signaling network. 419-428 - Alexey M. Shibeko, Mikhail A. Panteleev:
Untangling the complexity of blood coagulation network: use of computational modelling in pharmacology and diagnostics. 429-439 - Enrico Glaab:
Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification. 440-452 - Shailendra K. Gupta, Tanushree Jaitly, Ulf Schmitz, Gerold Schuler, Olaf Wolkenhauer, Julio Vera:
Personalized cancer immunotherapy using Systems Medicine approaches. 453-467 - Jung Hun Oh, Joseph O. Deasy:
A literature mining-based approach for identification of cellular pathways associated with chemoresistance in cancer. 468-478 - Lan K. Nguyen:
Dynamics of ubiquitin-mediated signalling: insights from mathematical modelling and experimental studies. 479-493 - David J. Duffy:
Problems, challenges and promises: perspectives on precision medicine. 494-504 - Mufassra Naz, Alpha Tom Kodamullil, Martin Hofmann-Apitius:
Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases. 505-516 - Archana Pan, Chandrajit Lahiri, Anjana Rajendiran, Buvaneswari Shanmugham:
Computational analysis of protein interaction networks for infectious diseases. 517-526 - Gastone 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. 527-540 - Leonor 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. 541-552
Volume 17, Number 4, July 2016
- Pietro 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. 553-561 - Andrew Parton, Victoria McGilligan, Maurice O'Kane, Francina R. Baldrick, Steven Watterson:
Computational modelling of atherosclerosis. 562-575 - Tao 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. 576-592 - Goar 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. 593-602 - Lavanya 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. 603-615 - Dagmar Iber, Zahra Karimaddini, Erkan Ünal:
Image-based modelling of organogenesis. 616-627 - Chen 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. 628-641
- Feixiong Cheng, Junfei Zhao, Zhongming Zhao:
Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. 642-656 - Ananda S. Datta, Swati Biswas:
Comparison of haplotype-based statistical tests for disease association with rare and common variants. 657-671 - Steven 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. 672-677 - Tyler Weirick, Giuseppe Militello, Raphael Rene Müller, David John, Stefanie Dimmeler, Shizuka Uchida:
The identification and characterization of novel transcripts from RNA-seq data. 678-685 - Fan Zhu, Bharat Panwar, Yuanfang Guan:
Algorithms for modeling global and context-specific functional relationship networks. 686-695 - Xing Chen, Chenggang Clarence Yan, Xiaotian Zhang, Xu Zhang, Feng Dai, Jian Yin, Yongdong Zhang:
Drug-target interaction prediction: databases, web servers and computational models. 696-712 - Sungmin Lee, Hyeyoung Min, Sungroh Yoon:
Will solid-state drives accelerate your bioinformatics? In-depth profiling, performance analysis and beyond. 713-727
- Vasileios Lapatas, Michalis Stefanidakis:
BATMat: Bioinformatics Autodiscovery of Training Materials. 728-730
- Andrei Lihu, Stefan Holban:
A review of ensemble methods for de novo motif discovery in ChIP-Seq data. 731
Volume 17, Number 5, September 2016
- Yoli Shavit, Ivan Merelli, Luciano Milanesi, Pietro Liò:
How computer science can help in understanding the 3D genome architecture. 733-744 - Vladimir B. Teif:
Nucleosome positioning: resources and tools online. 745-757 - Cristian Andrés Gallo, Rocío L. Cecchini, Jessica Andrea Carballido, Sandra Micheletto, Ignacio Ponzoni:
Discretization of gene expression data revised. 758-770 - Haleh Yasrebi:
Comparative study of joint analysis of microarray gene expression data in survival prediction and risk assessment of breast cancer patients. 771-785 - Ashley Cacho, Ekaterina Smirnova, Snehalata V. Huzurbazar, Xinping Cui:
A Comparison of Base-calling Algorithms for Illumina Sequencing Technology. 786-795 - Hans-Ulrich Klein, Katja Hebestreit:
An evaluation of methods to test predefined genomic regions for differential methylation in bisulfite sequencing data. 796-807 - Rosa J. Meijer, Jelle J. Goeman:
Multiple Testing of Gene Sets from Gene Ontology: Possibilities and Pitfalls. 808-818 - Anika 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. 819-830 - Ian Walsh, Gianluca Pollastri, Silvio C. E. Tosatto:
Correct machine learning on protein sequences: a peer-reviewing perspective. 831-840 - Khader 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. 841-862 - Denise 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. 863-876 - Peter 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. 877-890 - Rachel Cavill, Danyel Jennen, Jos Kleinjans, Jacob J. Briedé:
Transcriptomic and metabolomic data integration. 891-901
Volume 17, Number 6, November 2016
- Jónathan Heras, César Domínguez, Eloy J. Mata, Vico Pascual, Carmen Lozano, Carmen Torres, Myriam Zarazaga:
A survey of tools for analysing DNA fingerprints. 903-911 - Jónathan Heras, César Domínguez, Eloy J. Mata, Vico Pascual:
Surveying and benchmarking techniques to analyse DNA gel fingerprint images. 912-925 - Deepak 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. 926-937 - Junko Tsuji, Zhiping Weng:
Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data. 938-952
- Sebastian Steinhauser, Nils Kurzawa, Roland Eils, Carl Herrmann:
A comprehensive comparison of tools for differential ChIP-seq analysis. 953-966
- Dimitrios Kleftogiannis, Panos Kalnis, Vladimir B. Bajic:
Progress and challenges in bioinformatics approaches for enhancer identification. 967-979
- Antonio Mora, Geir Kjetil Sandve, Odd Stokke Gabrielsen, Ragnhild Eskeland:
In the loop: promoter-enhancer interactions and bioinformatics. 980-995
- Wei 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. 996-1008
- Maria Chatzou, Cedrik Magis, Jia-Ming Chang, Carsten Kemena, Giovanni Bussotti, Ionas Erb, Cédric Notredame:
Multiple sequence alignment modeling: methods and applications. 1009-1023
- Hongdong Li, Gilbert S. Omenn, Yuanfang Guan:
A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling. 1024-1031 - Xihao 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. 1032-1043 - Fan 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. 1044-1059 - Thomas Pfau, Maria Pires Pacheco, Thomas Sauter:
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. 1060-1069 - Farnaz Barneh, Mohieddin Jafari, Mehdi Mirzaie:
Updates on drug-target network; facilitating polypharmacology and data integration by growth of DrugBank database. 1070-1080
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