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| 0 | -- | 0 | Tao Huang, Hong Mi, Cheng-Yuan Lin, Ling Zhao, Linda L. D. Zhong, Fengbin Liu, Ge Zhang, Aiping Lu, Zhaoxiang Bian, Shuhai Lin, Man Zhang, Yanhong Li, Dongdong Hu, Chung-Wah Cheng. MOST: most-similar ligand based approach to target prediction |
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| 0 | -- | 0 | Levi D. McClenny, Mahdi Imani, Ulisses de Mendonça Braga Neto. BoolFilter: an R package for estimation and identification of partially-observed Boolean dynamical systems |
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| 0 | -- | 0 | Vikram E. Chhatre, Kevin J. Emerson. StrAuto: automation and parallelization of STRUCTURE analysis |
| 0 | -- | 0 | Rui Henriques, Francisco L. Ferreira, Sara C. Madeira. BicPAMS: software for biological data analysis with pattern-based biclustering |
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| 0 | -- | 0 | Shupeng Gui, Andrew P. Rice, Rui Chen, Liang Wu, Ji Liu, Hongyu Miao. A scalable algorithm for structure identification of complex gene regulatory network from temporal expression data |
| 0 | -- | 0 | Katrin Tebel, Vivien Boldt, Anne Steininger, Matthias Port, Grit Ebert, Reinhard Ullmann. GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants |
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| 0 | -- | 0 | Michael T. Ganger, Geoffrey D. Dietz, Sarah J. Ewing. A common base method for analysis of qPCR data and the application of simple blocking in qPCR experiments |
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| 0 | -- | 0 | Victor A. Padilha, Ricardo J. G. B. Campello. A systematic comparative evaluation of biclustering techniques |
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| 0 | -- | 0 | Veit Wiesmann, Matthias Bergler, Ralf Palmisano, Martin Prinzen, Daniela Franz, Thomas Wittenberg. Using simulated fluorescence cell micrographs for the evaluation of cell image segmentation algorithms |
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| 0 | -- | 0 | Cristiano Lacerda Nunes Pinto, Cristiane Neri Nobre, Luis Enrique Zárate. Transductive learning as an alternative to translation initiation site identification |
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| 0 | -- | 0 | Gabriella Sferra, Federica Fratini, Marta Ponzi, Elisabetta Pizzi. Phylo_dCor: distance correlation as a novel metric for phylogenetic profiling |
| 0 | -- | 0 | Sinan Abo Alchamlat, Frédéric Farnir. KNN-MDR: a learning approach for improving interactions mapping performances in genome wide association studies |
| 0 | -- | 0 | Xiang Gao, Huaiying Lin, Kashi Vishwanath Revanna, Qunfeng Dong. A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy |
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| 0 | -- | 0 | Fanchi Meng, Chen Wang, Lukasz A. Kurgan. fDETECT webserver: fast predictor of propensity for protein production, purification, and crystallization |
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| 0 | -- | 0 | Gabriella Sferra, Federica Fratini, Marta Ponzi, Elisabetta Pizzi. Phylo_dCor: distance correlation as a novel metric for phylogenetic profiling |
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| 0 | -- | 0 | Mike Myschyshyn, Marco Farren-Dai, Tien-Jui Chuang, David Vocadlo. Software for rapid time dependent ChIP-sequencing analysis (TDCA) |
| 0 | -- | 0 | Hatem Elshazly, Yassine Souilmi, Peter J. Tonellato, Dennis P. Wall, Mohamed Abouelhoda. MC-GenomeKey: a multicloud system for the detection and annotation of genomic variants |
| 0 | -- | 0 | Prabina Kumar Meher, Tanmaya Kumar Sahu, Anjali Banchariya, Atmakuri Rao. DIRProt: a computational approach for discriminating insecticide resistant proteins from non-resistant proteins |
| 0 | -- | 0 | Boris Shabash, Kay C. Wiese. Numerical integration methods and layout improvements in the context of dynamic RNA visualization |
| 0 | -- | 0 | Mona Riemenschneider, Alexander Herbst, Ari Rasch, Sergei Gorlatch, Dominik Heider. eccCL: parallelized GPU implementation of Ensemble Classifier Chains |
| 0 | -- | 0 | Marijke Van Moerbeke, Adetayo Kasim, Willem Talloen, Joke Reumers, Hinrich W. H. Göhlmann, Ziv Shkedy. A random effects model for the identification of differential splicing (REIDS) using exon and HTA arrays |
| 0 | -- | 0 | Kristian Liland, Hilde Vinje, Lars Snipen. microclass: an R-package for 16S taxonomy classification |
| 0 | -- | 0 | Zhenqing Ye, Tao Ma, Michael Kalmbach, Surendra Dasari, Jean-Pierre A. Kocher, Liguo Wang. CircularLogo: A lightweight web application to visualize intra-motif dependencies |
| 0 | -- | 0 | Philip L. Tzou, Xiaoqiu Huang, Robert W. Shafer. NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences |
| 0 | -- | 0 | Julia Koehler Leman, Sergey Lyskov, Richard Bonneau. Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP |
| 0 | -- | 0 | Onur Erbilgin, Benjamin P. Bowen, Suzanne M. Kosina, Stefan Jenkins, Rebecca K. Lau, Trent R. Northen. Dynamic substrate preferences predict metabolic properties of a simple microbial consortium |
| 0 | -- | 0 | Chenggang Yu, Hyung-June Woo, Xueping Yu, Tatsuya Oyama, Anders Wallqvist, Jaques Reifman. A strategy for evaluating pathway analysis methods |
| 0 | -- | 0 | Bastijn Koopmans, August B. Smit, Matthijs Verhage, Maarten Loos. AHCODA-DB: a data repository with web-based mining tools for the analysis of automated high-content mouse phenomics data |
| 0 | -- | 0 | Vera Rieder, Bernhard Blank-Landeshammer, Marleen Stuhr, Tilman Schell, Karsten Biß, Laxmikanth Kollipara, Achim Meyer, Markus Pfenninger, Hildegard Westphal, Albert Sickmann, Jörg Rahnenführer. DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs |
| 0 | -- | 0 | Shirin Taghipour, Peyman Zarrineh, Mohammad Ganjtabesh, Abbas Nowzari-Dalini. Improving protein complex prediction by reconstructing a high-confidence protein-protein interaction network of Escherichia coli from different physical interaction data sources |
| 0 | -- | 0 | Cedric Simillion, Robin Liechti, Heidi E. L. Lischer, Vassilios Ioannidis, Rémy Bruggmann. Avoiding the pitfalls of gene set enrichment analysis with SetRank |
| 0 | -- | 0 | Dmitry Y. Mozzherin, Alexander A. Myltsev, David J. Patterson. "gnparser": a powerful parser for scientific names based on Parsing Expression Grammar |
| 0 | -- | 0 | Yuri Bento Marques, Alcione de Paiva Oliveira, Ana Tereza Ribeiro de Vasconcelos, Fabio Ribeiro Cerqueira. Erratum to: Mirnacle: machine learning with SMOTE and random forest for improving selectivity in pre-miRNA ab initio prediction |
| 0 | -- | 0 | Yu-Chiao Chiu, Li-Ju Wang, Tzu-Pin Lu, Tzu-Hung Hsiao, Eric Y. Chuang, Yidong Chen. Differential correlation analysis of glioblastoma reveals immune ceRNA interactions predictive of patient survival |
| 0 | -- | 0 | Wei Zheng, Hongfei Lin, Ling Luo, Zhehuan Zhao, Zhengguang Li, Yijia Zhang, Zhihao Yang, Jian Wang. An attention-based effective neural model for drug-drug interactions extraction |
| 0 | -- | 0 | Steve Lefever, Filip Pattyn, Bram De Wilde, Frauke Coppieters, Sarah De Keulenaer, Jan Hellemans, Jo Vandesompele. High-throughput PCR assay design for targeted resequencing using primerXL |
| 0 | -- | 0 | Raja Ali, Mikael Bark, Jorge Miró, Sayyed Muhammad, Joel Sjöstrand, Syed M. Zubair, Raja M. Abbas, Lars Arvestad. VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces |
| 0 | -- | 0 | Michal Jablonski, Jana Starcukova, Zenon Starcuk Jr.. Processing tracking in jMRUI software for magnetic resonance spectra quantitation reproducibility assurance |
| 0 | -- | 0 | Jose Cleydson F. Silva, Thales F. M. Carvalho, Marcos F. Basso, Michihito Deguchi, Welison A. Pereira, Roberto R. Sobrinho, Pedro M. P. Vidigal, Otávio J. B. Brustolini, Fabyano F. Silva, Maximiller Dal-Bianco, Renildes L. F. Fontes, Anésia A. Santos, Francisco Murilo Zerbini, Fabio Ribeiro Cerqueira, Elizabeth P. B. Fontes. Geminivirus data warehouse: a database enriched with machine learning approaches |
| 0 | -- | 0 | John Athey, Aikaterini Alexaki, Ekaterina Osipova, Alexandre Rostovtsev, Luis V. Santana-Quintero, Upendra Katneni, Vahan Simonyan, Chava Kimchi-Sarfaty. A new and updated resource for codon usage tables |
| 0 | -- | 0 | Mohamed-Ashick M. Saleem, Marco-Antonio Mendoza-Parra, Pierre-Etienne Cholley, Matthias Blum, Hinrich Gronemeyer. Epimetheus - a multi-profile normalizer for epigenomic sequencing data |
| 0 | -- | 0 | Pratyaydipta Rudra, W. Jenny Shi, Brian Vestal, Pamela H. Russell, Aaron Odell, Robin D. Dowell, Richard Radcliffe, Laura M. Saba, Katerina Kechris. Model based heritability scores for high-throughput sequencing data |
| 0 | -- | 0 | Jia Song, Sisi Zheng, Nhung Nguyen, Youjun Wang, Yubin Zhou, Kui Lin. Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family |
| 0 | -- | 0 | Sylvester Olubolu Orimaye, Jojo Sze-Meng Wong, Karen J. Golden, Chee Piau Wong, Ireneous N. Soyiri. Predicting probable Alzheimer's disease using linguistic deficits and biomarkers |
| 0 | -- | 0 | Georgios A. Dalkas, Marianne Rooman. SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence |
| 0 | -- | 0 | Anna Kusnezowa, Lars I. Leichert. In silico approach to designing rational metagenomic libraries for functional studies |
| 0 | -- | 0 | Rui Henriques, Francisco L. Ferreira, Sara C. Madeira. Erratum to: BicPAMS: software for biological data analysis with pattern-based biclustering |
| 0 | -- | 0 | Tran Tuan Anh, Le Thi Ly, Ngo Quoc Viet, Pham The Bao. Novel methods to optimize gene and statistic test for evaluation - an application for Escherichia coli |
| 0 | -- | 0 | Shanrong Zhao, William Gordon, Sarah Du, Chi Zhang, Wen He, Li Xi, Sachin Mathur, Michael Agostino, Theresa Paradis, David von Schack, Michael Vincent, Baohong Zhang. QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing |
| 0 | -- | 0 | Donghyeon Yu, Johan Lim, Xinlei Wang 0001, Faming Liang, Guanghua Xiao. Enhanced construction of gene regulatory networks using hub gene information |
| 0 | -- | 0 | Duo Xu, Yousef Jaber, Pavlos Pavlidis, Omer Gokcumen. VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences |
| 0 | -- | 0 | Chunwei Ma, Shaohang Xu, Geng Liu, Xin Liu, Xun Xu, Bo Wen, Siqi Liu. Improvement of peptide identification with considering the abundance of mRNA and peptide |
| 0 | -- | 0 | Johannes W. R. Martini, Ning Gao, Diercles F. Cardoso, Valentin Wimmer, Malena Erbe, Rodolfo J. C. Cantet, Henner Simianer. Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE) |
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| 0 | -- | 0 | Ji-Hye Choi, Seong-Eui Hong, Hyun Goo Woo. Pan-cancer analysis of systematic batch effects on somatic sequence variations |
| 0 | -- | 0 | Preeti Choudhary, Shailesh Kumar, Anand Kumar Bachhawat, Shashi Bhushan Pandit. CSmetaPred: a consensus method for prediction of catalytic residues |
| 0 | -- | 0 | Rashmi R. Hazarika, Barbara De Coninck, Lidia R. Yamamoto, Laura R. Martin, Bruno P. A. Cammue, Vera van Noort. ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana |
| 0 | -- | 0 | Ricardo Olanda, Mariano Pérez, Juan M. Orduña, Joaquín Tárraga, Joaquín Dopazo. A new parallel pipeline for DNA methylation analysis of long reads datasets |
| 0 | -- | 0 | Yao-Ting Huang, Yu-Wen Huang. An efficient error correction algorithm using FM-index |
| 0 | -- | 0 | Muhammad Rizwan, Anam Naz, Jamil Ahmad, Kanwal Naz, Ayesha Obaid, Tamsila Parveen, Muhammad Ahsan, Amjad Ali. VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology |
| 0 | -- | 0 | Mohamed Amine Remita, Ahmed Halioui, Abou Abdallah Malick Diouara, Bruno Daigle, Golrokh Kiani, Abdoulaye Baniré Diallo. A machine learning approach for viral genome classification |
| 0 | -- | 0 | Konstantinos Zagganas, Thanasis Vergoulis, Maria D. Paraskevopoulou, Ioannis S. Vlachos, Spiros Skiadopoulos, Theodore Dalamagas. BUFET: boosting the unbiased miRNA functional enrichment analysis using bitsets |
| 0 | -- | 0 | Dongmei Li, Zidian Xie, Martin S. Zand, Thomas Fogg, Timothy D. Dye. Bon-EV: an improved multiple testing procedure for controlling false discovery rates |
| 0 | -- | 0 | Mahdi Heydari, Giles Miclotte, Piet Demeester, Yves Van de Peer, Jan Fostier. Evaluation of the impact of Illumina error correction tools on de novo genome assembly |
| 0 | -- | 0 | Antonio Martín-Navarro, Andrés Gaudioso-Simón, Jorge Álvarez-Jarreta, Julio Montoya, Elvira Mayordomo, Eduardo Ruiz-Pesini. Machine learning classifier for identification of damaging missense mutations exclusive to human mitochondrial DNA-encoded polypeptides |
| 0 | -- | 0 | Gaurang Mahajan, Shekhar C. Mande. Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis |
| 0 | -- | 0 | Yanhui Fan, You-Qiang Song. PyHLA: tests for the association between HLA alleles and diseases |
| 0 | -- | 0 | Nikhil Cheerla, Olivier Gevaert. MicroRNA based Pan-Cancer Diagnosis and Treatment Recommendation |
| 0 | -- | 0 | Reedik Mägi, Yury V. Suleimanov, Geraldine M. Clarke, Marika Kaakinen, Krista Fischer, Inga Prokopenko, Andrew P. Morris. SCOPA and META-SCOPA: software for the analysis and aggregation of genome-wide association studies of multiple correlated phenotypes |
| 0 | -- | 0 | David R. Penas, Patricia González, Jose A. Egea, Ramón Doallo, Julio R. Banga. Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy |
| 0 | -- | 0 | Xue Jiang, Han Zhang, Feng Duan, Xiongwen Quan. Identify Huntington's disease associated genes based on restricted Boltzmann machine with RNA-seq data |
| 0 | -- | 0 | Wael Karain. Detecting transitions in protein dynamics using a recurrence quantification analysis based bootstrap method |
| 0 | -- | 0 | Paolo Cifani, Mojdeh Shakiba, Sagar Chhangawala, Alex Kentsis. ProteoModlR for functional proteomic analysis |
| 0 | -- | 0 | Seirana Hashemi, Abbas Nowzari-Dalini, Adrin Jalali, Ali Mohammad Banaei-Moghaddam, Zahra Razaghi Moghadam Kashani. Cancerouspdomains: comprehensive analysis of cancer type-specific recurrent somatic mutations in proteins and domains |
| 0 | -- | 0 | Alejandro Sune-Aunon, Alvaro Jorge-Penas, Rocío Aguilar-Cuenca, Miguel Vicente-Manzanares, Hans Van Oosterwyck, Arrate Muñoz-Barrutia. Full L1-regularized Traction Force Microscopy over whole cells |
| 0 | -- | 0 | Suyeon Kang, Jongwoo Song. Robust gene selection methods using weighting schemes for microarray data analysis |
| 0 | -- | 0 | Loris Bertoldi, Claudio Forcato, Nicola Vitulo, Giovanni Birolo, Fabio De Pascale, Erika Feltrin, Riccardo Schiavon, Franca Anglani, Susanna Negrisolo, Alessandra Zanetti, Francesca D'Avanzo, Rosella Tomanin, Georgine Faulkner, Alessandro Vezzi, Giorgio Valle. QueryOR: a comprehensive web platform for genetic variant analysis and prioritization |
| 0 | -- | 0 | Seung Hoan Choi, Adam Labadorf, Richard H. Myers, Kathryn L. Lunetta, Josée Dupuis, Anita L. DeStefano. Evaluation of logistic regression models and effect of covariates for case-control study in RNA-Seq analysis |
| 0 | -- | 0 | Quan Zhang, Yuzhen Ye. Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements |
| 0 | -- | 0 | Akhilesh Kaushal, Hongmei Zhang, Wilfried Karmaus, Meredith Ray, Mylin A. Torres, Alicia K. Smith, Shu-Li Wang. Comparison of different cell type correction methods for genome-scale epigenetics studies |
| 0 | -- | 0 | Antonio Fabregat, Konstantinos Sidiropoulos, Guilherme Viteri, Oscar Forner-Martinez, Pablo Marín-García, Vicente Arnau, Peter D'Eustachio, Lincoln Stein, Henning Hermjakob. Reactome pathway analysis: a high-performance in-memory approach |
| 0 | -- | 0 | Hirokazu Chiba, Ikuo Uchiyama. SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases |
| 0 | -- | 0 | Knut D. Rand, Ivar Grytten, Alexander J. Nederbragt, Geir Storvik, Ingrid K. Glad, Geir Kjetil Sandve. Coordinates and intervals in graph-based reference genomes |
| 0 | -- | 0 | Mari van Reenen, Johan A. Westerhuis, Carolus J. Reinecke, J. Hendrik Venter. Metabolomics variable selection and classification in the presence of observations below the detection limit using an extension of ERp |
| 0 | -- | 0 | Zhi-an Huang, Zhenkun Wen, Qingjin Deng, Ying Chu, Yiwen Sun, Zexuan Zhu. LW-FQZip 2: a parallelized reference-based compression of FASTQ files |
| 0 | -- | 0 | Ergude Bao, Lingxiao Lan. HALC: High throughput algorithm for long read error correction |
| 0 | -- | 0 | Xin-Ping Xie, Yu-Feng Xie, Hong-Qiang Wang. A regulation probability model-based meta-analysis of multiple transcriptomics data sets for cancer biomarker identification |
| 0 | -- | 0 | Yanglan Gan, Han Tao, Jihong Guan, Shuigeng Zhou. iHMS: a database integrating human histone modification data across developmental stages and tissues |
| 0 | -- | 0 | Sophie Molnos, Clemens Baumbach, Simone Wahl, Martina Müller-Nurasyid, Konstantin Strauch, Rui Wang-Sattler, Melanie Waldenberger, Thomas Meitinger, Jerzy Adamski, Gabi Kastenmüller, Karsten Suhre, Annette Peters, Harald Grallert, Fabian J. Theis, Christian Gieger. pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms |
| 0 | -- | 0 | ZhenZhou Wang, Haixing Li. Generalizing cell segmentation and quantification |
| 0 | -- | 0 | Giulia Paciello, Elisa Ficarra. FuGePrior: A novel gene fusion prioritization algorithm based on accurate fusion structure analysis in cancer RNA-seq samples |
| 0 | -- | 0 | Alan Beccati, Jan Gerken, Christian Quast, Pelin Yilmaz, Frank Oliver Glöckner. SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees |
| 0 | -- | 0 | Christian Schäfer, Alexander H. Schmidt, Jürgen Sauter. Hapl-o-Mat: open-source software for HLA haplotype frequency estimation from ambiguous and heterogeneous data |
| 0 | -- | 0 | Marco Albrecht, Damian Stichel, Benedikt Müller, Ruth Merkle, Carsten Sticht, Norbert Gretz, Ursula Klingmüller, Kai Breuhahn, Franziska Matthäus. TTCA: an R package for the identification of differentially expressed genes in time course microarray data |
| 0 | -- | 0 | Pathima Nusrath Hameed, Karin Verspoor, Snezana Kusljic, Saman Halgamuge. Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes |
| 0 | -- | 0 | Valeria Montano, T. Jombart. An Eigenvalue test for spatial principal component analysis |
| 0 | -- | 0 | Fereshteh Chitsazian, Mehdi Sadeghi, Elahe Elahi. Confident gene activity prediction based on single histone modification H2BK5ac in human cell lines |
| 0 | -- | 0 | Damoon Nashta-ali, Ali Aliyari, Ahmad Ahmadian Moghadam, Mohammad Amin Edrisi, Abolfazl Seyed Motahari, Babak Hossein Khalaj. Meta-aligner: long-read alignment based on genome statistics |
| 0 | -- | 0 | Sarvesh Nikumbh, Nico Pfeifer. Genetic sequence-based prediction of long-range chromatin interactions suggests a potential role of short tandem repeat sequences in genome organization |
| 0 | -- | 0 | Yiwei Li, Lucian Ilie. SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome |
| 0 | -- | 0 | Weiwei Ouyang, Qiang An, Jinying Zhao, Huaizhen Qin. Erratum to: Integrating mean and variance heterogeneities to identify differentially expressed genes |
| 0 | -- | 0 | Soren H. Hough, Kris Kancleris, Leigh Brody, Neil Humphryes-Kirilov, Joseph Wolanski, Keith Dunaway, Ayokunmi Ajetunmobi, Victor Dillard. Erratum to: Guide Picker is a comprehensive design tool for visualizing and selecting guides for CRISPR experiments |
| 0 | -- | 0 | Joseph Guhlin, Kevin A. T. Silverstein, Peng Zhou, Peter Tiffin, Nevin D. Young. ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding |
| 0 | -- | 0 | Marco Tompitak, Gerard T. Barkema, Helmut Schiessel. Benchmarking and refining probability-based models for nucleosome-DNA interaction |
| 0 | -- | 0 | Bence Bolgár, Peter Antal. VB-MK-LMF: fusion of drugs, targets and interactions using variational Bayesian multiple kernel logistic matrix factorization |
| 0 | -- | 0 | Grace Yoon, Yinan Zheng, Zhou Zhang, Haixiang Zhang, Tao Gao, Brian Joyce, Wei Zhang, Weihua Guan, Andrea A. Baccarelli, Wenxin Jiang, Joel Schwartz, Pantel Vokonas, Lifang Hou, Lei Liu. Ultra-high dimensional variable selection with application to normative aging study: DNA methylation and metabolic syndrome |
| 0 | -- | 0 | Jinyu Li, Jörg Vervoorts, Paolo Carloni, Giulia Rossetti, Bernhard Lüscher. Structural prediction of the interaction of the tumor suppressor p27KIP1 with cyclin A/CDK2 identifies a novel catalytically relevant determinant |
| 0 | -- | 0 | Jiyun Zhou, Qin Lu, Ruifeng Xu, Yulan He, Hongpeng Wang. EL_PSSM-RT: DNA-binding residue prediction by integrating ensemble learning with PSSM Relation Transformation |
| 0 | -- | 0 | Kosuke Yoshida, Junichiro Yoshimoto, Kenji Doya. Sparse kernel canonical correlation analysis for discovery of nonlinear interactions in high-dimensional data |
| 0 | -- | 0 | Alencar Xavier, Shizhong Xu, William M. Muir, Katy Martin Rainey. Genomic prediction using subsampling |
| 0 | -- | 0 | Badri Adhikari, Jianlin Cheng. Improved protein structure reconstruction using secondary structures, contacts at higher distance thresholds, and non-contacts |
| 0 | -- | 0 | Manuel Rueda, Ali Torkamani. SG-ADVISER mtDNA: a web server for mitochondrial DNA annotation with data from 200 samples of a healthy aging cohort |
| 0 | -- | 0 | Rob Eisinga, Tom Heskes, Ben Pelzer, Manfred Te Grotenhuis. Exact p-values for pairwise comparison of Friedman rank sums, with application to comparing classifiers |
| 0 | -- | 0 | Garrett W. Birkel, Amit Ghosh, Vinay Satish Kumar, Daniel Weaver, David Ando, Tyler W. H. Backman, Adam P. Arkin, Jay D. Keasling, Héctor García Martín. Erratum to: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism |
| 0 | -- | 0 | Nicolas Bosc, Christophe Meyer, Pascal Bonnet. The use of novel selectivity metrics in kinase research |
| 0 | -- | 0 | Daniel Fischer, Mervi Honkatukia, Maria Tuiskula-Haavisto, Klaus Nordhausen, David Cavero, Rudolf Preisinger, Johanna Vilkki. Subgroup detection in genotype data using invariant coordinate selection |
| 0 | -- | 0 | Zhijiang Wan, Yishan He, Ming Hao, Jian Yang, Ning Zhong 0001. M-AMST: an automatic 3D neuron tracing method based on mean shift and adapted minimum spanning tree |
| 0 | -- | 0 | Diego Pasqualin, Marcos Barbeitos, Fabiano Silva. SFREEMAP - A simulation-free tool for stochastic mapping |
| 0 | -- | 0 | Jiapeng Zhou, Jing Xin, Yayun Niu, Shiwen Wu. DMDtoolkit: a tool for visualizing the mutated dystrophin protein and predicting the clinical severity in DMD |
| 0 | -- | 0 | You-yu Lin, Chia-Hung Hsieh, Jiun-Hong Chen, Xuemei Lu, Jia-Horng Kao, Pei-Jer Chen, Ding-Shinn Chen, Hurng-Yi Wang. De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline |
| 0 | -- | 0 | Bart Broeckx, Luc Peelman, Jimmy Saunders, Dieter Deforce, Lieven Clement. Using variant databases for variant prioritization and to detect erroneous genotype-phenotype associations |
| 0 | -- | 0 | James C. Wilgenbusch, Wen Huang, Kyle A. Gallivan. Visualizing phylogenetic tree landscapes |
| 0 | -- | 0 | Vassily A. Lyubetsky, Roman Gershgorin, Konstantin Yu. Gorbunov. Chromosome structures: reduction of certain problems with unequal gene content and gene paralogs to integer linear programming |
| 0 | -- | 0 | Matthias Beyens, Nele Boeckx, Guy Van Camp, Ken Op de Beeck, Geert Vandeweyer. pyAmpli: an amplicon-based variant filter pipeline for targeted resequencing data |
| 0 | -- | 0 | Soren H. Hough, Kris Kancleris, Leigh Brody, Neil Humphryes-Kirilov, Joseph Wolanski, Keith Dunaway, Ayokunmi Ajetunmobi, Victor Dillard. Guide Picker is a comprehensive design tool for visualizing and selecting guides for CRISPR experiments |
| 0 | -- | 0 | Wei-Sheng Wu, Meng-Jhun Jhou. MVIAeval: a web tool for comprehensively evaluating the performance of a new missing value imputation algorithm |
| 0 | -- | 0 | Annika Röhl, Alexander Bockmayr. A mixed-integer linear programming approach to the reduction of genome-scale metabolic networks |
| 0 | -- | 0 | Youngmahn Han, Dongsup Kim. Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction |
| 0 | -- | 0 | Sameh Eid, Samo Turk, Andrea Volkamer, Friedrich Rippmann, Simone Fulle. KinMap: a web-based tool for interactive navigation through human kinome data |
| 0 | -- | 0 | Xiaoyang Jing, Qiwen Dong. MQAPRank: improved global protein model quality assessment by learning-to-rank |
| 0 | -- | 0 | Saghi Nojoomi, Patrice Koehl. String kernels for protein sequence comparisons: improved fold recognition |
| 0 | -- | 0 | Massimo Narizzano, Gabriele Arnulfo, Serena Ricci, Benedetta Toselli, Martin Tisdall, Andrea Canessa, Marco Massimo Fato, Francesco Cardinale. SEEG assistant: a 3DSlicer extension to support epilepsy surgery |
| 0 | -- | 0 | Tobias Madsen, Asger Hobolth, Jens Ledet Jensen, Jakob Skou Pedersen. Significance evaluation in factor graphs |
| 0 | -- | 0 | Robin Kobus, Christian Hundt 0002, André Müller, Bertil Schmidt. Accelerating metagenomic read classification on CUDA-enabled GPUs |
| 0 | -- | 0 | Sarah Sandmann, Aniek O. de Graaf, Martin Dugas. BBCAnalyzer: a visual approach to facilitate variant calling |
| 0 | -- | 0 | J. Harry Caufield, Christopher Wimble, Shary Semarjit, Stefan Wuchty, Peter Uetz. Bacterial protein meta-interactomes predict cross-species interactions and protein function |
| 0 | -- | 0 | Benjamin Schubert, Luis de la Garza, Christopher Mohr, Mathias Walzer, Oliver Kohlbacher. ImmunoNodes - graphical development of complex immunoinformatics workflows |
| 0 | -- | 0 | Francesco Napolitano. repo: an R package for data-centered management of bioinformatic pipelines |
| 0 | -- | 0 | Mark D. Temple. An auditory display tool for DNA sequence analysis |
| 0 | -- | 0 | Kazuhiro Takemoto, Kazuki Aie. Limitations of a metabolic network-based reverse ecology method for inferring host-pathogen interactions |
| 0 | -- | 0 | Zhi-Ping Liu, Shutang Liu, Ruitang Chen, Xiaopeng Huang, Ling-Yun Wu. Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces |
| 0 | -- | 0 | Virginie Stanislas, Cyril Dalmasso, Christophe Ambroise. Eigen-Epistasis for detecting gene-gene interactions |
| 0 | -- | 0 | Olivier Sheik Amamuddy, Nigel Bishop, Özlem Tastan Bishop. Improving fold resistance prediction of HIV-1 against protease and reverse transcriptase inhibitors using artificial neural networks |
| 0 | -- | 0 | Charles C. David, Ettayapuram Ramaprasad Azhagiya Singam, Donald J. Jacobs. JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories |
| 0 | -- | 0 | Sinjini Sikdar, Susmita Datta. A novel statistical approach for identification of the master regulator transcription factor |
| 0 | -- | 0 | Thomas S. Wingo, Alex Kotlar, David J. Cutler. MPD: multiplex primer design for next-generation targeted sequencing |
| 0 | -- | 0 | Fan Zhang, Patrick Flaherty. Variational inference for rare variant detection in deep, heterogeneous next-generation sequencing data |
| 0 | -- | 0 | Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, David W. Ritchie. ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains |
| 0 | -- | 0 | Andrew E. Teschendorff, Charles E. Breeze, Shijie C. Zheng, Stephan Beck. A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies |
| 0 | -- | 0 | Vitaly A. Selivanov, Adrián Benito, Anibal Miranda, Esther Aguilar, Ibrahim Halil Polat, Josep J. Centelles, Anusha Jayaraman, Paul W.-N. Lee, Silvia Marin, Marta Cascante. MIDcor, an R-program for deciphering mass interferences in mass spectra of metabolites enriched in stable isotopes |
| 0 | -- | 0 | Sumanta Ray, Sk Md Mosaddek Hossain, Lutfunnesa Khatun, Anirban Mukhopadhyay 0001. A comprehensive analysis on preservation patterns of gene co-expression networks during Alzheimer's disease progression |
| 0 | -- | 0 | Youyi Fong, Ying Huang, Peter B. Gilbert, Sallie R. Permar. chngpt: threshold regression model estimation and inference |
| 0 | -- | 0 | Li Chen, Yuxi Lian, Yi Guo, Yuanyuan Wang, Thomas S. Hatsukami, Kristi Pimentel, Niranjan Balu, Chun Yuan. A vascular image registration method based on network structure and circuit simulation |
| 0 | -- | 0 | Sebastian Proost, Agnieszka Krawczyk, Marek Mutwil. LSTrAP: efficiently combining RNA sequencing data into co-expression networks |
| 0 | -- | 0 | Lianbo Yu, Soledad Fernandez, Guy N. Brock. Power analysis for RNA-Seq differential expression studies |
| 0 | -- | 0 | Ebrahim Afyounian, Matti Annala, Matti Nykter. Segmentum: a tool for copy number analysis of cancer genomes |
| 0 | -- | 0 | Jelena Calyseva, Mauno Vihinen. PON-SC - program for identifying steric clashes caused by amino acid substitutions |
| 0 | -- | 0 | Irene Epifanio. Intervention in prediction measure: a new approach to assessing variable importance for random forests |
| 0 | -- | 0 | Tim O. F. Conrad, Martin Genzel, Nada Cvetkovic, Niklas Wulkow, Alexander Leichtle, Jan Vybíral, Gitta Kutyniok, Christof Schütte. Sparse Proteomics Analysis - a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data |
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| 0 | -- | 0 | Maxwell T. Spadafore, Kayvan Najarian, Alan P. Boyle. A proximity-based graph clustering method for the identification and application of transcription factor clusters |
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| 0 | -- | 0 | Fei Li, Meishan Zhang, Guohong Fu, Donghong Ji. A neural joint model for entity and relation extraction from biomedical text |
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| 0 | -- | 0 | Martin Nettling, Hendrik Treutler, Jesús Cerquides, Ivo Grosse. Combining phylogenetic footprinting with motif models incorporating intra-motif dependencies |
| 0 | -- | 0 | Gayathri Thillaiyampalam, Fabio Liberante, Liam Murray, Chris Cardwell, Ken I. Mills, Shu-Dong Zhang. An integrated meta-analysis approach to identifying medications with potential to alter breast cancer risk through connectivity mapping |
| 0 | -- | 0 | Diana Domanska, Daniel Vodák, Christin Lund-Andersen, Stefania Salvatore, Eivind Hovig, Geir Kjetil Sandve. The rainfall plot: its motivation, characteristics and pitfalls |
| 0 | -- | 0 | Suyeon Kang, Jongwoo Song. Robust gene selection methods using weighting schemes for microarray data analysis |
| 0 | -- | 0 | Enfeng Qi, Dongyu Wang, Bo Gao, Yang Li, Guojun Li. Block-based characterization of protease specificity from substrate sequence profile |
| 0 | -- | 0 | Mohammed Al-Jaff, Eric Sandström, Manfred G. Grabherr. microTaboo: a general and practical solution to the k-disjoint problem |
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| 246 | -- | 0 | Andrea Tangherloni, Marco S. Nobile, Daniela Besozzi, Giancarlo Mauri, Paolo Cazzaniga. LASSIE: simulating large-scale models of biochemical systems on GPUs |
| 254 | -- | 0 | Miles Aron, Richard J. Browning, Dario Carugo, Erdinc Sezgin, Jorge Bernardino de la Serna, Christian Eggeling, Eleanor Stride. Spectral imaging toolbox: segmentation, hyperstack reconstruction, and batch processing of spectral images for the determination of cell and model membrane lipid order |
| 288 | -- | 0 | Toshiyuki Oda, Kyungtaek Lim, Kentaro Tomii. Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance |
| 289 | -- | 0 | Kazunori D. Yamada, Satoshi Omori, Hafumi Nishi, Masaru Miyagi. N-terminal acetylation through a decision tree approach |
| 290 | -- | 0 | Marek Palkowski, Wlodzimierz Bielecki. Parallel tiled Nussinov RNA folding loop nest generated using both dependence graph transitive closure and loop skewing |
| 291 | -- | 0 | Miha Stajdohar, Rafael D. Rosengarten, Janez Kokosar, Luka Jeran, Domen Blenkus, Gad Shaulsky, Blaz Zupan. Dictyostelium and beyond |
| 292 | -- | 0 | Jennifer Rogers, Andrew Fishberg, Nora Youngs, Yi-Chieh Wu. Reconciliation feasibility in the presence of gene duplication, loss, and coalescence with multiple individuals per species |
| 293 | -- | 0 | Frank Keul, Martin Hess, Michael Goesele, Kay Hamacher. PFASUM: a substitution matrix from Pfam structural alignments |
| 294 | -- | 0 | Jian Zhang, Haiting Chai, Guifu Yang, Zhiqiang Ma. Prediction of bioluminescent proteins by using sequence-derived features and lineage-specific scheme |
| 295 | -- | 0 | Atif Khan, Dejan Katanic, Juilee Thakar. Meta-analysis of cell- specific transcriptomic data using fuzzy c-means clustering discovers versatile viral responsive genes |
| 296 | -- | 0 | Alex M. Ascensión, Mikel Arrospide-Elgarresta, Ander Izeta, Marcos J. Araúzo-Bravo. NaviSE: superenhancer navigator integrating epigenomics signal algebra |
| 297 | -- | 0 | Pei Fen Kuan, Scott Powers, Shuyao He, Kaiqiao Li, Xiaoyu Zhao, Bo Huang. A systematic evaluation of nucleotide properties for CRISPR sgRNA design |
| 298 | -- | 0 | Shermin Pei, Betty L. Slinger, Michelle M. Meyer. Recognizing RNA structural motifs in HT-SELEX data for ribosomal protein S15 |
| 299 | -- | 0 | Thomas M. Poulsen, Martin C. Frith. Variable-order sequence modeling improves bacterial strain discrimination for Ion Torrent DNA reads |
| 300 | -- | 0 | Wei Wang, Lin Sun, Shiguang Zhang, Hongjun Zhang, Jinling Shi, Tianhe Xu, Keliang Li. Analysis and prediction of single-stranded and double-stranded DNA binding proteins based on protein sequences |
| 301 | -- | 0 | Stephen J. Bush, Mary E. B. McCulloch, Kim M. Summers, David A. Hume, Emily L. Clark. Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries |
| 302 | -- | 0 | Wen Torng, Russ B. Altman. 3D deep convolutional neural networks for amino acid environment similarity analysis |
| 303 | -- | 0 | Kolja Stahl, Michael Schneider, Oliver Brock. EPSILON-CP: using deep learning to combine information from multiple sources for protein contact prediction |
| 304 | -- | 0 | Reiko Nishihara, Kimberly Glass, Kosuke Mima, Tsuyoshi Hamada, Jonathan A. Nowak, Zhi Rong Qian, Peter Kraft, Edward L. Giovannucci, Charles S. Fuchs, Andrew T. Chan, John Quackenbush, Shuji Ogino, Jukka-Pekka Onnela. Biomarker correlation network in colorectal carcinoma by tumor anatomic location |
| 305 | -- | 0 | Atul Kamboj, Claus V. Hallwirth, Ian E. Alexander, Geoffrey B. McCowage, Belinda Kramer. Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data |
| 306 | -- | 0 | Ahmet Rasit Ozturk, Tolga Can. A multiplex primer design algorithm for target amplification of continuous genomic regions |
| 307 | -- | 0 | Yusuke Azuma, Shuichi Onami. C. elegans embryos |
| 308 | -- | 0 | Katsuhiro Omae, Osamu Komori, Shinto Eguchi. Quasi-linear score for capturing heterogeneous structure in biomarkers |
| 309 | -- | 0 | Xiting Yan, Anqi Liang, Jose Gomez, Lauren Cohn, Hongyu Zhao, Geoffrey L. Chupp. A novel pathway-based distance score enhances assessment of disease heterogeneity in gene expression |
| 310 | -- | 0 | Kai Battenberg, Ernest K. Lee, Joanna C. Chiu, Alison M. Berry, Daniel Potter. OrthoReD: a rapid and accurate orthology prediction tool with low computational requirement |
| 311 | -- | 0 | Andrew Bartlett, Bart Penders, Jamie Lewis. Bioinformatics: indispensable, yet hidden in plain sight? |
| 312 | -- | 0 | J. F. Mudge, Christopher J. Martyniuk, J. E. Houlahan. Optimal alpha reduces error rates in gene expression studies: a meta-analysis approach |
| 313 | -- | 0 | Sirajul Salekin, Mehrab Ghanat Bari, Itay Raphael, Thomas G. Forsthuber, Jianqiu Michelle Zhang. Early response index: a statistic to discover potential early stage disease biomarkers |
| 314 | -- | 0 | Sascha Schäuble, Anne-Kristin Stavrum, Mathias Bockwoldt, Pål Puntervoll, Ines Heiland. SBMLmod: a Python-based web application and web service for efficient data integration and model simulation |
| 315 | -- | 0 | Xi Chen, Chen Wang 0004, Shanjiang Tang, Ce Yu, Quan Zou. CMSA: a heterogeneous CPU/GPU computing system for multiple similar RNA/DNA sequence alignment |
| 316 | -- | 0 | Giorgos Minas, Hiroshi Momiji, Dafyd J. Jenkins, Maria J. Costa, David A. Rand, Bärbel Finkenstädt. ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data |
| 317 | -- | 0 | Michael I. Klein, David F. Stern, Hongyu Zhao. GRAPE: a pathway template method to characterize tissue-specific functionality from gene expression profiles |
| 318 | -- | 0 | Marcelo Rodrigo de Castro, Catherine dos Santos Tostes, Alberto M. R. Dávila, Hermes Senger, Fabrício Alves Barbosa da Silva. SparkBLAST: scalable BLAST processing using in-memory operations |
| 319 | -- | 0 | Sheng Yang Michael Loh, Yoshitaka Ogawa, Sara Kawana, Koichiro Tamura, Hwee Kuan Lee. Semi-automated quantitative Drosophila wings measurements |
| 320 | -- | 0 | Hasan Awad Aljohi, Wanfei Liu, Qiang Lin, Jun Yu, Songnian Hu. ISVASE: identification of sequence variant associated with splicing event using RNA-seq data |
| 321 | -- | 0 | Valerio Orlandini, Aldesia Provenzano, Sabrina Giglio, Alberto Magi. SLMSuite: a suite of algorithms for segmenting genomic profiles |
| 322 | -- | 0 | Nicola Lazzarini, Jaume Bacardit. RGIFE: a ranked guided iterative feature elimination heuristic for the identification of biomarkers |
| 323 | -- | 0 | Yuxuan Yuan, Philipp E. Bayer, Armin Scheben, Chon-Kit Kenneth Chan, David Edwards. BioNanoAnalyst: a visualisation tool to assess genome assembly quality using BioNano data |
| 324 | -- | 0 | Axel Wedemeyer, Lasse Kliemann, Anand Srivastav, Christian Schielke, Thorsten B. Reusch, Philip Rosenstiel. An improved filtering algorithm for big read datasets and its application to single-cell assembly |
| 325 | -- | 0 | Shailesh Tripathi, Jason Lloyd-Price, Andre S. Ribeiro, Olli Yli-Harja, Matthias Dehmer, Frank Emmert-Streib. sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters |
| 326 | -- | 0 | Lili Zhao, Mark T. Anderson, Weisheng Wu, Harry L. T. Mobley, Michael A. Bachman. TnseqDiff: identification of conditionally essential genes in transposon sequencing studies |
| 327 | -- | 0 | Hongrui Wang, Hongwei Liu, Leixin Cai, Caixia Wang, Qiang Lv. Using the multi-objective optimization replica exchange Monte Carlo enhanced sampling method for protein-small molecule docking |
| 328 | -- | 0 | Mustafa Alshawaqfeh, Ahmad Bashaireh, Erchin Serpedin, Jan Suchodolski. Reliable Biomarker discovery from Metagenomic data via RegLRSD algorithm |
| 329 | -- | 0 | Yadav Kuleesha, Feng Lin, Martin Wasser. Drosophila metamorphosis |
| 330 | -- | 0 | Dianhao Guo, Jiapeng Luo, Yuenan Zhou, Huamei Xiao, Kang He, Chuanlin Yin, Jianhua Xu, Fei Li. ACE: an efficient and sensitive tool to detect insecticide resistance-associated mutations in insect acetylcholinesterase from RNA-Seq data |
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| 332 | -- | 0 | Ziyi Li, Sandra E. Safo, Qi Long. Incorporating biological information in sparse principal component analysis with application to genomic data |
| 333 | -- | 0 | Eleni Ioanna Delatola, Emilie Lebarbier, Tristan Mary-Huard, François Radvanyi, Stéphane Robin, Jennifer Wong. SegCorr a statistical procedure for the detection of genomic regions of correlated expression |
| 334 | -- | 0 | Marc Jeanmougin, Josselin Noirel, Cédric Coulonges, Jean-François Zagury. HLA-check: evaluating HLA data from SNP information |
| 335 | -- | 0 | Sheng Zhang, Bo Wang, Lin Wan, Lei M. Li. Estimating Phred scores of Illumina base calls by logistic regression and sparse modeling |
| 336 | -- | 0 | Su Hee Chu, Yen-Tsung Huang. Integrated genomic analysis of biological gene sets with applications in lung cancer prognosis |
| 337 | -- | 0 | Sehrish Kanwal, Farah Zaib Khan, Andrew Lonie, Richard O. Sinnott. Investigating reproducibility and tracking provenance - A genomic workflow case study |
| 338 | -- | 0 | Ksenia Khelik, Karin Lagesen, Geir Kjetil Sandve, Torbjørn Rognes, Alexander J. Nederbragt. NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences |
| 339 | -- | 0 | Bogumil Konopka, Marta Marciniak, Witold Dyrka. Quantiprot - a Python package for quantitative analysis of protein sequences |
| 340 | -- | 0 | Sara González-Pérez, Florencio Pazos, Monica Chagoyen. Factors affecting interactome-based prediction of human genes associated with clinical signs |
| 341 | -- | 0 | John Alexander, Dimitris Mantzaris, Marianthi Georgitsi, Petros Drineas, Peristera Paschou. Variant Ranker: a web-tool to rank genomic data according to functional significance |
| 342 | -- | 0 | Alvin Farrel, Jun-tao Guo. An efficient algorithm for improving structure-based prediction of transcription factor binding sites |
| 343 | -- | 0 | Jie Liu, Minyi Su, Zhihai Liu, Jie Li, Yan Li, Renxiao Wang. Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints |
| 344 | -- | 0 | Sharon M. Lutz, Annie Thwing, Sarah Schmiege, Miranda Kroehl, Christopher D. Baker, Anne P. Starling, John E. Hokanson, Debashis Ghosh. Examining the role of unmeasured confounding in mediation analysis with genetic and genomic applications |
| 345 | -- | 0 | Se-Ran Jun, Intawat Nookaew, Loren J. Hauser, Andrey Gorin. Assessment of genome annotation using gene function similarity within the gene neighborhood |
| 346 | -- | 0 | Jan Schröder, Adrianto Wirawan, Bertil Schmidt, Anthony T. Papenfuss. CLOVE: classification of genomic fusions into structural variation events |
| 347 | -- | 0 | Tamás Nagy, Martin Kampmann. CRISPulator: a discrete simulation tool for pooled genetic screens |
| 348 | -- | 0 | Yanan Zhu, Qi Ouyang, Youdong Mao. A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy |
| 349 | -- | 0 | Yasser B. Ruiz-Blanco, Guillermín Agüero-Chapín, Enrique García-Hernández, Orlando Álvarez, Agostinho Antunes, James Green. the twilight zone |
| 350 | -- | 0 | Guoxian Yu, Chang Lu, Jun Wang. NoGOA: predicting noisy GO annotations using evidences and sparse representation |
| 351 | -- | 0 | Jennifer A. Tom, Jens Reeder, William F. Forrest, Robert R. Graham, Julie Hunkapiller, Timothy W. Behrens, Tushar R. Bhangale. Identifying and mitigating batch effects in whole genome sequencing data |
| 352 | -- | 0 | Antoine Basset, Patrick Bouthemy, Jérôme Boulanger, François Waharte, Jean Salamero, Charles Kervrann. An extended model of vesicle fusion at the plasma membrane to estimate protein lateral diffusion from TIRF microscopy images |
| 353 | -- | 0 | Syafiq Kamarul Azman, Muhammad Zohaib Anwar, Andreas Henschel. Visibiome: an efficient microbiome search engine based on a scalable, distributed architecture |
| 354 | -- | 0 | James E. Barrett, Andrew Feber, Javier Herrero, Miljana Tanic, Gareth A. Wilson, Charles Swanton, Stephan Beck. Quantification of tumour evolution and heterogeneity via Bayesian epiallele detection |
| 355 | -- | 0 | Sheng Liu, Cristina Zibetti, Jun Wan, Guohua Wang, Seth Blackshaw, Jiang Qian. Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility |
| 356 | -- | 0 | Zhao Li, Jin Li, Peng Yu. l1kdeconv: an R package for peak calling analysis with LINCS L1000 data |
| 357 | -- | 0 | Jeremy R. Wang, Bryan Quach, Terrence S. Furey. Correcting nucleotide-specific biases in high-throughput sequencing data |
| 358 | -- | 0 | Katrin Hainke, Sebastian Szugat, Roland Fried, Jörg Rahnenführer. Variable selection for disease progression models: methods for oncogenetic trees and application to cancer and HIV |
| 359 | -- | 0 | Daniel Amsel, Andreas Vilcinskas, André Billion. Tribolium castaneum |
| 360 | -- | 0 | Yan Xu, Yeshu Li, Zhengyang Shen, Ziwei Wu, Teng Gao, Yubo Fan, Maode Lai, Eric I-Chao Chang. Parallel multiple instance learning for extremely large histopathology image analysis |
| 361 | -- | 0 | Brian Connolly, K. Bretonnel Cohen, Daniel Santel, Ulya Bayram, John Pestian. A nonparametric Bayesian method of translating machine learning scores to probabilities in clinical decision support |
| 362 | -- | 0 | Gregory Zynda, Jawon Song, Lorenzo Concia, Emily E. Wear, Linda Hanley-Bowdoin, William F. Thompson, Matthew W. Vaughn. Repliscan: a tool for classifying replication timing regions |
| 363 | -- | 0 | Carlos Guzman, Iván D'Orso. CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction |
| 365 | -- | 0 | Alejandro Sune-Aunon, Alvaro Jorge-Penas, Rocío Aguilar-Cuenca, Miguel Vicente-Manzanares, Hans Van Oosterwyck, Arrate Muñoz-Barrutia. 1-regularized Traction Force Microscopy over whole cells |
| 375 | -- | 0 | Xin-Ping Xie, Yu-Feng Xie, Hong-Qiang Wang. A regulation probability model-based meta-analysis of multiple transcriptomics data sets for cancer biomarker identification |
| 376 | -- | 0 | James J. Yang, L. Keoki Williams, Anne Buu. Identifying pleiotropic genes in genome-wide association studies from related subjects using the linear mixed model and Fisher combination function |
| 378 | -- | 0 | Saghi Nojoomi, Patrice Koehl. A weighted string kernel for protein fold recognition |
| 379 | -- | 0 | Jiyun Zhou, Qin Lu, Ruifeng Xu, Yulan He, Hongpeng Wang. EL_PSSM-RT: DNA-binding residue prediction by integrating ensemble learning with PSSM Relation Transformation |
| 380 | -- | 0 | Badri Adhikari, Jianlin Cheng. Improved protein structure reconstruction using secondary structures, contacts at higher distance thresholds, and non-contacts |
| 387 | -- | 0 | Lian Liu, Shao-Wu Zhang, Yufei Huang, Jia Meng. QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model |
| 388 | -- | 0 | Hao Wang, Jiamao Luo, Chun Liu, Huilin Niu, Jing Wang, Qi Liu, Zhongming Zhao, Hua Xu, Yanqing Ding, Jingchun Sun, Qingling Zhang. Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer |
| 390 | -- | 0 | Xiaoyang Jing, Qiwen Dong, Ruqian Lu. RRCRank: a fusion method using rank strategy for residue-residue contact prediction |
| 406 | -- | 0 | Michael Kern, Alexander Lex, Nils Gehlenborg, Chris R. Johnson. Interactive visual exploration and refinement of cluster assignments |
| 411 | -- | 0 | Matthias Zytnicki. mmquant: how to count multi-mapping reads? |
| 412 | -- | 0 | Mengdi Zhao, Jie An, Haiwen Li, Jiazhi Zhang, Shang-Tong Li, Xue-mei Li, Meng-Qiu Dong, Heng Mao, Louis Tao. Segmentation and classification of two-channel C. elegans nucleus-labeled fluorescence images |
| 415 | -- | 0 | Wei Hu, Amrapali Zaveri, Honglei Qiu, Michel Dumontier. Cleaning by clustering: methodology for addressing data quality issues in biomedical metadata |
| 416 | -- | 0 | Thomas J. Hardcastle. Methods for discovering genomic loci exhibiting complex patterns of differential methylation |
| 417 | -- | 0 | Haiou Li, Jie Hou, Badri Adhikari, Qiang Lyu, Jianlin Cheng. Deep learning methods for protein torsion angle prediction |
| 421 | -- | 0 | José M. Juanes, Asunción Gallego, Joaquín Tárraga, Felipe J. Chaves, Pablo Marín-García, Ignacio Medina, Vicente Arnau, Joaquín Dopazo. VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy |
| 425 | -- | 0 | Ying Wang, Kun Wang, Yang Young Lu, Fengzhu Sun. Improving contig binning of metagenomic data using \( {d}_2^S \) oligonucleotide frequency dissimilarity |
| 455 | -- | 0 | Chaitanya R. Acharya, Kouros Owzar, Andrew S. Allen. Mapping eQTL by leveraging multiple tissues and DNA methylation |
| 456 | -- | 0 | Jakub Wiedemann, Tomasz Zok, Maciej Milostan, Marta Szachniuk. LCS-TA to identify similar fragments in RNA 3D structures |
| 457 | -- | 0 | R. Greg Stacey, Michael A. Skinnider, Nichollas E. Scott, Leonard J. Foster. A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE) |
| 458 | -- | 0 | Yahya Bokhari, Tomasz Arodz. QuaDMutEx: quadratic driver mutation explorer |
| 459 | -- | 0 | Jia Wen, Jue Wang, Qing Zhang, Dianjing Guo. A heuristic model for computational prediction of human branch point sequence |
| 460 | -- | 0 | Biswanath Chowdhury, Arnav Garai, Gautam Garai. An optimized approach for annotation of large eukaryotic genomic sequences using genetic algorithm |
| 461 | -- | 0 | Oana Carja, Tongji Xing, Edward W. J. Wallace, Joshua B. Plotkin, Premal Shah. riboviz: analysis and visualization of ribosome profiling datasets |
| 462 | -- | 0 | Chen Lyu, Bo Chen, Yafeng Ren, Donghong Ji. Long short-term memory RNN for biomedical named entity recognition |
| 466 | -- | 0 | Rex Shen, Lan Luo, Hui Jiang. Identification of gene pairs through penalized regression subject to constraints |
| 467 | -- | 0 | Chang Sik Kim, Martyn D. Winn, Vipin Sachdeva, Kirk E. Jordan. K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity |
| 468 | -- | 0 | Xiufeng Yang, Kazuki Yoshizoe, Akito Taneda, Koji Tsuda. RNA inverse folding using Monte Carlo tree search |
| 469 | -- | 0 | Jebediah Rosen, Kyle Handy, André Gillan, Rob Smith. JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals |
| 473 | -- | 0 | Dawit Nigatu, Patrick Sobetzko, Malik Yousef, Werner Henkel. Sequence-based information-theoretic features for gene essentiality prediction |
| 474 | -- | 0 | Heidi E. L. Lischer, Kentaro K. Shimizu. Reference-guided de novo assembly approach improves genome reconstruction for related species |
| 475 | -- | 0 | Jochen Ismer, Alexander S. Rose, Johanna K. S. Tiemann, Peter W. Hildebrand. A fragment based method for modeling of protein segments into cryo-EM density maps |
| 476 | -- | 0 | Paul M. Harrison. fLPS: Fast discovery of compositional biases for the protein universe |
| 477 | -- | 0 | Oriol Mazariegos-Canellas, Trien Do, Tim E. A. Peto, David W. Eyre, Anthony Underwood, Derrick W. Crook, David H. Wyllie. BugMat and FindNeighbour: command line and server applications for investigating bacterial relatedness |
| 479 | -- | 0 | Duc-Hau Le, Lieven P. C. Verbeke, Le Hoang Son, Dinh-Toi Chu, Van-Huy Pham 0001. Random walks on mutual microRNA-target gene interaction network improve the prediction of disease-associated microRNAs |
| 480 | -- | 0 | Oluwatosin Oluwadare, Jianlin Cheng. ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data |
| 481 | -- | 0 | Liying Yang 0001, Yunyan Shen, Xiguo Yuan, Junying Zhang, Jianhua Wei. Analysis of breast cancer subtypes by AP-ISA biclustering |
| 482 | -- | 0 | Tao Zhu, Chengzhen Liang, Zhigang Meng, Sandui Guo, Rui Zhang. GFF3sort: a novel tool to sort GFF3 files for tabix indexing |
| 486 | -- | 0 | Maria Needhamsen, Ewoud Ewing, Harald Lund, David Gomez-Cabrero, Robert Adam Harris, Lara Kular, Maja Jagodic. Usability of human Infinium MethylationEPIC BeadChip for mouse DNA methylation studies |
| 487 | -- | 0 | Richard Elias, David Hoksza. TRAVeLer: a tool for template-based RNA secondary structure visualization |
| 488 | -- | 0 | Rami Eitan, Ron Shamir. Reconstructing cancer karyotypes from short read data: the half empty and half full glass |
| 490 | -- | 0 | Eric C. Rouchka, Julia Chariker, David Tieri, Juw Won Park. Correction to: Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2017: bioinformatics |
| 493 | -- | 0 | Sérgio E. D. Dias, Ana Mafalda Martins, Quoc T. Nguyen, Abel João Padrão Gomes. GPU-based detection of protein cavities using Gaussian surfaces |
| 494 | -- | 0 | Shuyun Zhang, Libin Deng, Qiyue Jia, Shaoting Huang, Junwang Gu, Fankun Zhou, Meng Gao, Xinyi Sun, Chang Feng, Guangqin Fan. dbMDEGA: a database for meta-analysis of differentially expressed genes in autism spectrum disorder |
| 495 | -- | 0 | Yomtov Almozlino, Nir Atias, Dana Silverbush, Roded Sharan. ANAT 2.0: reconstructing functional protein subnetworks |
| 503 | -- | 0 | Khanh To Duc. bcROCsurface: an R package for correcting verification bias in estimation of the ROC surface and its volume for continuous diagnostic tests |
| 504 | -- | 0 | Nathan Sloat, Jui-Wen Liu, Susan J. Schroeder. Swellix: a computational tool to explore RNA conformational space |
| 505 | -- | 0 | Linlin Gao, Haiwei Pan, Qing Li, Xiaoqin Xie, Zhiqiang Zhang 0010, Jinming Han, Xiao Zhai. Brain medical image diagnosis based on corners with importance-values |
| 506 | -- | 0 | Daniel Castillo, Juan Manuel Galvez, Luis Javier Herrera, Belén San Román, Fernando Rojas 0001, Ignacio Rojas. Integration of RNA-Seq data with heterogeneous microarray data for breast cancer profiling |
| 507 | -- | 0 | Rhys A. Farrer. Synima: a Synteny imaging tool for annotated genome assemblies |
| 508 | -- | 0 | Hongwei Ge, Liang Sun 0003, Jinghong Yu. Fast batch searching for protein homology based on compression and clustering |
| 510 | -- | 0 | Kosai Al-Nakeeb, Thomas Nordahl Petersen, Thomas Sicheritz-Pontén. Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data |
| 512 | -- | 0 | Jie Tan, Matt Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene. ADAGE signature analysis: differential expression analysis with data-defined gene sets |
| 513 | -- | 0 | Sudipta Acharya, Sriparna Saha 0001, N. Nikhil. Unsupervised gene selection using biological knowledge : application in sample clustering |
| 515 | -- | 0 | Fen-Xiang Liu, Chunfa Tong, Shentong Tao, Jiyan Wu, Yuhua Chen, Dan Yao, Huogen Li, Jisen Shi. MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F1 population of outbred species |
| 516 | -- | 0 | Marco Beccuti, Elisa Genuardi, Greta Romano, Luigia Monitillo, Daniela Barbero, Mario Boccadoro, Marco Ladetto, Raffaele Calogero, Simone Ferrero, Francesca Cordero. HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data |