| MUMmer4: A fast and versatile genome alignment system |
112 |
| BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis |
111 |
| MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction |
67 |
| A computational approach to distinguish somatic vs. germline origin of genomic alterations from deep sequencing of cancer specimens without a matched normal |
42 |
| OpenSim: Simulating musculoskeletal dynamics and neuromuscular control to study human and animal movement |
41 |
| New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx |
37 |
| Sequence determinants of protein phase behavior from a coarse-grained model |
33 |
| The AmP project: Comparing species on the basis of dynamic energy budget parameters |
31 |
| LASSI: A lattice model for simulating phase transitions of multivalent proteins |
30 |
| SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions |
29 |
| Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database |
27 |
| Ensemble of decision tree reveals potential miRNA-disease associations |
26 |
| PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems |
26 |
| Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks |
26 |
| Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening |
25 |
| Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data |
25 |
| Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes |
25 |
| Ten quick tips for effective dimensionality reduction |
23 |
| Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data |
23 |
| Deep convolutional networks do not classify based on global object shape |
23 |
| Automated plant species identification-Trends and future directions |
22 |
| Reactome graph database: Efficient access to complex pathway data |
22 |
| Apollo: Democratizing genome annotation |
21 |
| Integrating Hi-C links with assembly graphs for chromosome-scale assembly |
21 |
| Machine and deep learning meet genome-scale metabolic modeling |
21 |
| Propagating annotations of molecular networks using in silico fragmentation |
21 |
| RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor |
20 |
| A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination |
19 |
| G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide |
18 |
| Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers |
17 |
| COBRAme: A computational framework for genome-scale models of metabolism and gene expression |
17 |
| A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts |
17 |
| riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data |
16 |
| Agent-based modeling of morphogenetic systems: Advantages and challenges |
16 |
| How epigenome drives chromatin folding and dynamics, insights from efficient coarse grained models of chromosomes |
15 |
| LMTRDA: Using logistic model tree to predict MiRNA-disease associations by fusing multi-source information of sequences and similarities |
15 |
| miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts |
15 |
| DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences |
15 |
| Rich-club connectivity, diverse population coupling, and dynamical activity patterns emerging from local cortical circuits |
15 |
| Deep convolutional models improve predictions of macaque V1 responses to natural images |
15 |
| The self-organization of plant microtubules inside the cell volume yields their cortical localization, stable alignment, and sensitivity to external cues |
15 |
| Clustering gene expression time series data using an infinite Gaussian process mixture model |
15 |
| RosettaAntibodyDesign (RAbD): A general framework for computational antibody design |
14 |
| The development and application of bioinformatics core competencies to improve bioinformatics training and education |
14 |
| A spectrum of routing strategies for brain networks |
14 |
| Classification of red blood cell shapes in flow using outlier tolerant machine learning |
13 |
| Visual physiology of the layer 4 cortical circuit in silico |
13 |
| ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization |
13 |
| Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities |
13 |
| Atlases of cognition with large-scale human brain mapping |
13 |
