Journal: Bioinformatics

Volume 35, Issue 11

1805 -- 1812Beibei Ru, Jianlong Sun, Qingzheng Kang, Yin Tong, Jiangwen Zhang. A framework for identifying dysregulated chromatin regulators as master regulators in human cancer
1813 -- 1819Anton Pirogov, Peter Pfaffelhuber, Angelika Börsch-Haubold, Bernhard Haubold. High-complexity regions in mammalian genomes are enriched for developmental genes
1820 -- 1828Wei Zheng, Le Yang, Robert J. Genco, Jean Wactawski-Wende, Michael Buck, Yijun Sun. SENSE: Siamese neural network for sequence embedding and alignment-free comparison
1829 -- 1836Baraa Orabi, Emre Erhan, Brian McConeghy, Stanislav V. Volik, Stephane Le Bihan, Robert Bell, Colin C. Collins, Cédric Chauve, Faraz Hach. Alignment-free clustering of UMI tagged DNA molecules
1837 -- 1843Zhen Cao, Shihua Zhang. Simple tricks of convolutional neural network architectures improve DNA-protein binding prediction
1844 -- 1851Loris Nanni, Sheryl Brahnam. Set of approaches based on 3D structure and position specific-scoring matrix for predicting DNA-binding proteins
1852 -- 1861Niema Moshiri, Manon Ragonnet-Cronin, Joel O. Wertheim, Siavash Mirarab. FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences
1862 -- 1869Rui Borges, João Paulo Machado, Cidália Gomes, Ana Paula Rocha 0002, Agostinho Antunes. Measuring phylogenetic signal between categorical traits and phylogenies
1870 -- 1876Sebastian Daberdaku, Carlo Ferrari. Antibody interface prediction with 3D Zernike descriptors and SVM
1877 -- 1884Yumi Kawamura, Shinsuke Koyama, Ryo Yoshida. Statistical inference of the rate of RNA polymerase II elongation by total RNA sequencing
1885 -- 1892Anna Papiez, Michal Marczyk, Joanna Polanska, Andrzej Polanski. BatchI: Batch effect Identification in high-throughput screening data using a dynamic programming algorithm
1893 -- 1900Ruiqing Zheng, Min Li, Xiang Chen, Fang-Xiang Wu, Yi Pan 0001, Jianxin Wang. BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks
1901 -- 1906Mary D. Fortune, Chris Wallace. simGWAS: a fast method for simulation of large scale case-control GWAS summary statistics
1907 -- 1915Tzipi Braun, Antonio V. Bordería, Cyril Barbezange, Marco Vignuzzi, Yoram Louzoun. Long-term context-dependent genetic adaptation of the viral genetic cloud
1916 -- 1922Andrea Rodriguez-Martinez, Rafael Ayala, Joram M. Posma, Nikita Harvey, Beatriz Jiménez, Kazuhiro Sonomura, Taka-Aki Sato, Fumihiko Matsuda, Pierre A. Zalloua, Dominique Gauguier, Jeremy K. Nicholson, Marc-Emmanuel Dumas. pJRES Binning Algorithm (JBA): a new method to facilitate the recovery of metabolic information from pJRES 1H NMR spectra
1923 -- 1930Yonghyun Nam, Jong Ho Jhee, Junhee Cho, Ji-Hyun Lee, Hyunjung Shin. Disease gene identification based on generic and disease-specific genome networks
1931 -- 1939Milton Pividori, Andres Cernadas, Luis A. de Haro, Fernando Carrari, Georgina Stegmayer, Diego H. Milone. Clustermatch: discovering hidden relations in highly diverse kinds of qualitative and quantitative data without standardization
1940 -- 1947Johannes Leuschner, Maximilian Schmidt, Pascal Fernsel, Delf Lachmund, Tobias Boskamp, Peter Maass. Supervised non-negative matrix factorization methods for MALDI imaging applications
1948 -- 1957Meiling Wang, Xiaoke Hao, Jiashuang Huang, Wei Shao 0005, Daoqiang Zhang. Discovering network phenotype between genetic risk factors and disease status via diagnosis-aligned multi-modality regression method in Alzheimer's disease
1958 -- 1959Xu Ren, Pei Fen Kuan. methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing
1960 -- 1962Roberto Vera Alvarez, Sándor Pongor, Leonardo Mariño-Ramírez, David Landsman. TPMCalculator: one-step software to quantify mRNA abundance of genomic features
1963 -- 1965Rebecca Rose, Olga Golosova, Dmitrii Sukhomlinov, Aleksey Tiunov, Mattia C. F. Prosperi. Flexible design of multiple metagenomics classification pipelines with UGENE
1966 -- 1967Ashish Jain, Geetu Tuteja. TissueEnrich: Tissue-specific gene enrichment analysis
1968 -- 1970Abbas A. Rizvi, Ezgi Karaesmen, Martin Morgan, Leah Preus, Junke Wang, Michael Sovic, Theresa Hahn, Lara E. Sucheston-Campbell. gwasurvivr: an R package for genome-wide survival analysis
1971 -- 1973Milton Pividori, Hae Kyung Im. ukbREST: efficient and streamlined data access for reproducible research in large biobanks
1974 -- 1977Tiago C. Silva, Simon G. Coetzee, Nicole Gull, Lijing Yao, Dennis J. Hazelett, Houtan Noushmehr, De-Chen Lin, Benjamin P. Berman. ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles
1978 -- 1980Christos Kopanos, Vasilis Tsiolkas, Alexandros Kouris, Charles E. Chapple, Monica Albarca Aguilera, Richard Meyer, Andreas Massouras. VarSome: the human genomic variant search engine
1981 -- 1984Matthew C. Canver, Daniel E. Bauer, Takahiro Maeda, Luca Pinello. DrugThatGene: integrative analysis to streamline the identification of druggable genes, pathways and protein complexes from CRISPR screens
1985 -- 0Yuk Yee Leung, Otto Valladares, Yi-Fan Chou, Han-Jen Lin, Amanda Kuzma, Laura Cantwell, Liming Qu, Prabhakaran Gangadharan, William J. Salerno, Gerard D. Schellenberg, Li-San Wang. VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project