Journal: Bioinformatics

Volume 39, Issue 11

0 -- 0Emad Alamoudi, Yannik Schälte, Robert Müller, Jörn Starruß, Nils Bundgaard, Frederik Graw, Lutz Brusch, Jan Hasenauer. FitMultiCell: simulating and parameterizing computational models of multi-scale and multi-cellular processes
0 -- 0Trisevgeni Rapakoulia, Sara Lopez Ruiz De Vargas, Persia Akbari Omgba, Verena Laupert, Igor Ulitsky, Martin Vingron. CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction
0 -- 0Peihong Hu, Qi Ye, Weiyan Zhang, JingPing Liu, Tong Ruan. Integration of multiple terminology bases: a multi-view alignment method using the hierarchical structure
0 -- 0Hyukpyo Hong, Mark Jayson Cortez, Yu-Yu Cheng, Hang Joon Kim, Boseung Choi, Kresimir Josic, Jae Kyoung Kim. Inferring delays in partially observed gene regulation processes
0 -- 0Xuehua Bi, Weiyang Liang, Qichang Zhao, Jianxin Wang. SSLpheno: a self-supervised learning approach for gene-phenotype association prediction using protein-protein interactions and gene ontology data
0 -- 0Yannik Schälte, Fabian Fröhlich, Paul J. Jost, Jakob Vanhoefer, Dilan Pathirana, Paul Stapor, Polina A. Lakrisenko, Dantong Wang, Elba Raimúndez-Álvarez, Simon Merkt, Leonard Schmiester, Philipp Städter, Stephan Grein, Erika Dudkin, Domagoj Doresic, Daniel Weindl, Jan Hasenauer. pyPESTO: a modular and scalable tool for parameter estimation for dynamic models
0 -- 0Qian Wang, Zhiqiang Wei, Xiaotong Hu, Zhuoya Wang, Yujie Dong, Hao Liu. Molecular generation strategy and optimization based on A2C reinforcement learning in de novo drug design
0 -- 0Dmitry Konanov, Vladislav V. Babenko, Aleksandra M. Belova, Arina G. Madan, Daria I Boldyreva, Oksana E. Glushenko, Ivan Butenko, Dmitry E. Fedorov, Alexander I Manolov, Danil V. Krivonos, Vassili N. Lazarev, Vadim M. Govorun, Elena N. Ilina. Snapper: high-sensitive detection of methylation motifs based on Oxford Nanopore reads
0 -- 0. Correction to: HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition
0 -- 0Leon Weber, Fabio Barth, Leonie Lorenz, Fabian Konrath, Kirsten Huska, Jana Wolf, Ulf Leser. PEDL+: protein-centered relation extraction from PubMed at your fingertip
0 -- 0Xiaoqing Ru, Quan Zou 0001, Chen Lin. Optimization of drug-target affinity prediction methods through feature processing schemes
0 -- 0Divya Sharma, Wei Xu. ReGeNNe: genetic pathway-based deep neural network using canonical correlation regularizer for disease prediction
0 -- 0Pingping Sun, Shijie Fan, Shaochuan Li, Yingwei Zhao, Chang Lu, Ka Chun Wong, Xiangtao Li. Automated exploitation of deep learning for cancer patient stratification across multiple types
0 -- 0Michail Chatzianastasis, Michalis Vazirgiannis, Zijun Zhang. Explainable Multilayer Graph Neural Network for cancer gene prediction
0 -- 0Jun Wu, Jian Ouyang, Haipeng Qing, Jiajia Zhou, Ruth Roberts, Rania Siam, Lan Wang, Weida Tong, Zhichao Liu, Tieliu Shi. PLM-ARG: antibiotic resistance gene identification using a pretrained protein language model
0 -- 0Jeffrey Cifello, Pavel P. Kuksa, Naveensri Saravanan, Otto Valladares, Li-San Wang, Yuk Yee Leung. hipFG: high-throughput harmonization and integration pipeline for functional genomics data
0 -- 0Javier D. Gomez, Martha L. Wall, Mohsin Rahim, Shrikaar Kambhampati, Bradley S. Evans, Doug K. Allen, Maciek R. Antoniewicz, Jamey D. Young. Program for Integration and Rapid Analysis of Mass Isotopomer Distributions (PIRAMID)
0 -- 0Yuliia Varenyk, Thomas Spicher, Ivo L. Hofacker, Ronny Lorenz. Modified RNAs and predictions with the ViennaRNA Package
0 -- 0. Correction to: CITEdb: a manually curated database of cell-cell interactions in human
0 -- 0Elena S. Dimitrova, Adam C. Knapp, Brandilyn Stigler, Michael Eugene Stillman. Cyclone: open-source package for simulation and analysis of finite dynamical systems
0 -- 0Abdul Rehman Khan, Marcel J. T. Reinders, Indu Khatri. Determining epitope specificity of T-cell receptors with transformers
0 -- 0Dat Thanh Nguyen. An integrative pipeline for circular RNA quantitative trait locus discovery with application in human T cells