NDLI: Building Applications for Interactive Data Exploration in Systems Biology

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Beyond Perfect Phylogeny: Multisample Phylogeny Reconstruction via ILP

Mapping Free Text into MedDRA by Natural Language Processing: A Modular Approach in Designing and Evaluating Software Extensions

GOstruct 2.0: Automated Protein Function Prediction for Annotated Proteins

CERENKOV: Computational Elucidation of the Regulatory Noncoding Variome

Learning Deep Representations from Heterogeneous Patient Data for Predictive Diagnosis

SparkGA: A Spark Framework for Cost Effective, Fast and Accurate DNA Analysis at Scale

Rich Chromatin Structure Prediction from Hi-C Data

A Multi-view Deep Learning Method for Epileptic Seizure Detection using Short-time Fourier Transform

Predicting the Effect of Point Mutations on Protein Structural Stability

Synthesizing Species Trees from Unrooted Gene Trees: A Parameterized Approach

Seq2seq Fingerprint: An Unsupervised Deep Molecular Embedding for Drug Discovery

Bayesian Collective Markov Random Fields for Subcellular Localization Prediction of Human Proteins

Determining Optimal Features for Predicting Type IV Secretion System Effector Proteins for Coxiella burnetii

HEMnet: Integration of Electronic Medical Records with Molecular Interaction Networks and Domain Knowledge for Survival Analysis

Understanding Sequence Conservation With Deep Learning

Co-MEAL: Cost-Optimal Multi-Expert Active Learning Architecture for Mobile Health Monitoring

Circadian Rhythms in Neurospora Exhibit Biologically Relevant Driven and Damped Harmonic Oscillations

Reverse Engineering Gene Networks: A Comparative Study at Genome-scale

Tensor-Factorization-Based Phenotyping using Group Information: Case Study on the Efficacy of Statins

An Out-of-Core GPU based Dimensionality Reduction Algorithm for Big Mass Spectrometry Data and Its Application in Bottom-up Proteomics

Study of Antidepressant Molecular Structure Leading to Safer Dosing

ACM-BCB '17 Tutorial: Robotics-inspired Algorithms for Modeling Protein Structures and Motions

Instrumenting the Health Care Enterprise for Discovery in the Course of Clinical Care

Highlights Talks at ACM BCB 2017

The 2017 Computational Structural Bioinformatics Workshop: CSBW 2017

ParBio'17: 6th Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine

CNB-MAC'17: The Fourth International Workshop on Computational Network Biology: Modeling, Analysis, and Control

CAME 2017: 6th Workshop on Computational Advances in Molecular Epidemiology

A Workshop on Microbiomics, Metagenomics, and Metabolomics

A Compatibility Approach to Identify Recombination Breakpoints in Bacterial and Viral Genomes

Dependency and AMR Embeddings for Drug-Drug Interaction Extraction from Biomedical Literature

Identification and Prediction of Intrinsically Disordered Regions in Proteins Using n-grams

Exploring Frequented Regions in Pan-Genomic Graphs

Winnow: Interactive Visualization of Temporal Changes in Multidimensional Clinical Data

Fast and Highly Scalable Bayesian MDP on a GPU Platform

Cophenetic Median Trees Under the Manhattan Distance

TUCUXI: An Intelligent System for Personalized Medicine from Individualization of Treatments to Research Databases and Back

Fleximer: Accurate Quantification of RNA-Seq via Variable-Length k-mers

Detection of Differential Abundance Intervals in Longitudinal Metagenomic Data Using Negative Binomial Smoothing Spline ANOVA

Differential Community Detection in Paired Biological Networks

Knowledge Rich Natural Language Queries over Structured Biological Databases

A Novel Approach for Classifying Gene Expression Data using Topic Modeling

SeqyClean: A Pipeline for High-throughput Sequence Data Preprocessing

Antidote Application: An Educational System for Treatment of Common Toxin Overdose

Hybrid ODE/SSA Model of the Budding Yeast Cell Cycle Control Mechanism with Mutant Case Study

Unsupervised Multi-View Feature Selection for Tumor Subtype Identification

Infer Cause of Death for Population Health Using Convolutional Neural Network

Building Applications for Interactive Data Exploration in Systems Biology

Supervised Machine Learning Approaches Predict and Characterize Nanomaterial Exposures: MWCNT Markers in Lung Lavage Fluid.

Computational Modeling of Protein-RNA Interactions

Challenges of Drug Design

Model-based Transcriptome Engineering

Computational Modeling of pH-dependent gp120-CD4 Interactions in Founder and Chronic HIV Strains

GPU-PCC: A GPU Based Technique to Compute Pairwise Pearson's Correlation Coefficients for Big fMRI Data

Bayesian Graphical Models for Computational Network Biology

Phylogenetic Tree based Method for Uncovering Co-mutational Site-pairs in Influenza Viruses

Leveraging Sentiment Analysis for Classifying Patient Complaints

Deep Recurrent Conditional Random Field Network for Protein Secondary Prediction

Bayesian Hyperparameter Optimization for Machine Learning Based eQTL Analysis

Associating Genomics and Clinical Information by Means of Semantic Based Ranking

Inferring Microbial Interactions from Metagenomic Time-series Using Prior Biological Knowledge

DeepCCI: End-to-end Deep Learning for Chemical-Chemical Interaction Prediction

Interpretable Predictions of Clinical Outcomes with An Attention-based Recurrent Neural Network

A Sparse Latent Regression Approach for Integrative Analysis of Glycomic and Glycotranscriptomic Data

Cell Neighbor Determination in the Metazoan Embryo System

TINTIN: Exploiting Target Features for Signaling Network Similarity Computation and Ranking

Discovering Inconsistencies in PubMed Abstracts through Ontology-Based Information Extraction

Differential Compound Prioritization via Bi-Directional Selectivity Push with Power

Distributed Memory Partitioning of High-Throughput Sequencing Datasets for Enabling Parallel Genomics Analyses

Automated Off-label Drug Use Detection from User Generated Content

RBFNN-based Modelling and Analysis for the Signal Reconstruction of Peripheral Nerve Tissue

Computational Intractability Generates the Topology of Biological Networks

Automated Breast Cancer Diagnosis Using Deep Learning and Region of Interest Detection (BC-DROID)

Mining Faces from Biomedical Literature using Deep Learning

Prokaryotic Autolysin Database Construction

Stochastic Process Model and Its Applications to Analysis of Longitudinal Data

Genome-scale Estimation of the Tree of Life

Analysis of Single Cells on a Pseudotime Scale along Postnatal Pancreatic Beta Cell Development

Analysis of ß-strand Twist from the 3-dimensional Image of a Protein

Ensemble Convolution Neural Network with a Simple Voting Method for Lung Tumor Detection

Detangling PPI Networks to Uncover Functionally Meaningful Clusters

Identifying Harm Events in Clinical Care through Medical Narratives

Coal-Miner: A Statistical Method for GWA Studies of Quantitative Traits with Complex Evolutionary Origins

Tailoring Training for Obese Individuals with Case-Based Reasoning

Secure Cloud Computing for Pairwise Sequence Alignment

Confused or not Confused?: Disentangling Brain Activity from EEG Data Using Bidirectional LSTM Recurrent Neural Networks

Use of Structural Properties of Underlying Graphs in Pathway Enrichment Analysis of Genomic Data

Predictive and Comparative Network Analysis of the Gut Microbiota in Type 2 Diabetes

TRuML: A Translator for Rule-Based Modeling Languages

Scalable Genomic Assembly through Parallel de Bruijn Graph Construction for Multiple K-mers

A Flexible and Robust Multi-Source Learning Algorithm for Drug Repositioning

A Physiological Thermal Regulation Model with Application to the Diagnosis of Diabetic Peripheral Neuropathy

A Correlation Network Model Utilizing Gait Parameters for Evaluating Health Levels

The Fate of Retrotransposed Processed Genes in Arabidopsis Thaliana

Analyzing the eICU Collaborative Research Database

Drug Response Prediction as a Link Prediction Problem

ProMuteHT: A High Throughput Compute Pipeline for Generating Protein Mutants in silico

Fuzzy Prediction of Incipient Alzheimer's Disease cases from Mild Cognitive Impaired cases

SMILE: A Novel Procedure for Subcellular Module Identification with Localization Expansion

Super-enhancer Dynamics Throughout Myogenesis

Fast, Clash-Free RNA Conformational Morphing using Molecular Junctions

String-Based Models for Predicting RNA-Protein Interaction

Using GenotypeAnalytics to Analyze Pharmacogenomic Datasets

Overlapping Functional Modules Detection in PPI Network with Pairwise Constrained Nonnegative Matrix Tri-Factorization

Varsimlab: A Docker-based Pipeline to Automatically Synthesize Short Reads with Genomic Aberrations

Network-based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

Ranking Protein-Protein Binding Using Evolutionary Information and Machine Learning

Discovery of Regular Domains in Large DNA Data Sets

Heuristic Algorithms for Feature Selection under Bayesian Models with Block-diagonal Covariance Structure

An Advanced Workflow for Metabolite Annotation

3D Genome Structure Modeling by Lorentzian Objective Function

Evolving Conformation Paths to Model Protein Structural Transitions

Feature Selection with Interactions in Logistic Regression Models using Multivariate Synergies for a GWAS Application

Development of a Polymer-Theoretic Approach to Describing Constraints on Reactions Between Antipeptide Antibodies and Intrinsically Disordered Peptide Antigens: Implications for B-Cell Epitope Prediction

Folding Large Proteins by Ultra-Deep Learning

Statistical Analysis of Computed Energy Landscapes to Understand Dysfunction in Pathogenic Protein Variants

Simulating Variance Heterogeneity in Quantitative Genome Wide Association Studies

Development of Nicotinic Acetylcholine Receptor nAChR α7 Binding Activity Prediction Model: Coupling Machine Learning with Competitive Molecular Docking

Automated Protein Chain Isolation from 3D Cryo-EM Data and Volume Comparison Tool

Sparse Tensor Decomposition for Haplotype Assembly of Diploids and Polyploids

Automated Next Generation Sequencing Bioinformatics Pipelines for Pathogen Discovery and Surveillance

A Graph Based Method for the Prediction of Backbone Trace from Cryo-EM Density Maps

Intrinsically Bayesian Robust Classifier for Single-Cell Gene Expression Time Series in Gene Regulatory Networks

Protein Classification using Modified N-Gram and Skip-Gram Models: Extended Abstract

Investigating Rigidity Properties of Protein Cavities

Constraints On Signaling Networks Logic Reveal Functional Subgraphs On Multiple Myeloma OMIC Data

Self-Tuning Spectral Clustering for Full-length Viral Quasispecies Reconstruction with PacBio Long Reads

Geometric Sampling Framework for Exploring Molecular Walker Energetics and Dynamics

Protein-Protein Interaction Extraction Using Attention-Based Convolution Neural Networks

Best Setting of Model Parameters in Applying Topic Modeling on Textual Documents.

Gaussian Mixture Models with Constrained Flexibility for Fitting Tomographic Tilt Series

Investigation of Model Stacking for Drug Sensitivity Prediction

Neopepsee: Accurate Genome-level Prediction of Neoantigens by Harnessing Sequence and Amino Acid Immunogenicity Information

Geometry Analysis for Protein Secondary Structures Matching Problem

A Bayesian Approach to Determine the Composition of Heterogeneous Cancer Tissue

Novel Unsupervised Named Entity Recognition Used in Text Annotation Tool (OntoMate) At Rat Genome Database

Bias and Noise Cancellation for Robust Copy Number Variation Detection

Applying Bayesian Changepoint Model and Hierarchical Divisive Model for Detecting Anomalies in Clinical Decision Support Alert Firing

Preconditioned Random Forest Regression: Application to Genome-Wide Study for Radiotherapy Toxicity Prediction

Outlier Genes as Biomarkers of Breast Cancer Survivability in Time-Series Data

Pisces: An Accurate and Versatile Single Sample Somatic and Germline Variant Caller

Nirvana: Clinical Grade Variant Annotator

Streptomyces Clavuligerus Constraint-Based Modeling and Gene Expression Analysis for Clavulanic Acid Production

Notch Signaling Plays an Important Role in mTEC Specification during Fetal Thymus Development

Analysis of 16S Genomic Data using Graphical Databases

High Dimensional Ensemble Neuronal Activity Pattern Analysis: Visualization and Wave Detection Focused

Tumor Neoantigens Derived from RNA Sequencing Analysis

Challenges in Prediction of different Cancer Stages using Gene Expression Profile of Cancer Patients

NGSPipes: Fostering Reproducibility and Scalability in Biosciences

Dynamic Phylogenetic Inference for Sequence-based Typing Data

Classification and Prediction of Antimicrobial Peptides Using N-gram Representation and Machine Learning

Network Analysis Identifies Regulatory Hotspots in Regions of Chromosome Interactions

Machine Learning Model for Identifying Gene Biomarkers for Breast Cancer Treatment Survival

Genome-Wide Association Study (GWAS) for the Infliximab Responsiveness in Korean Inflammatory Bowel Disease Patients

Integrating Prior Information with Bayesian Feature Selection

An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution

Assessing the Impact of Uncertain Gene Tree Rooting on Phylogenetic Reconciliation Using a Simulation Framework

Overlap Graph Reduction for Genome Assembly using Apache Spark

A Cross-Platform System Architecture for Form Design and Data Analytics for Public Health

Deep Residual Nets for Improved Alzheimer's Diagnosis

Integrative Sufficient Dimension Reduction Methods for Multi-Omics Data Analysis

Predicting Breast Cancer Outcome under Different Treatments by Feature Selection Approaches

Breaking Ties in Weighted Interactomes

Microbiome Dynamics as Predictors of Lung Transplant Rejection

Analysis of Controls in ChIP-seq

SeqAnt: Cloud-Based Whole-Genome Annotation and Search

A Tool for Predicting the Dark Side of Enzymes

Pathway Enrichment Analysis for Untargeted Metabolomics

Towards the Design of Matrix Metalloproteinases (MMP) Antibody Sequences

ProSol DB: A Protein Solubility Database

Building a Molecular Taxonomy of Disease

Network Analysis of Correlated Mutations in Influenza

Building Applications for Interactive Data Exploration in Systems Biology

Content Provider	ACM Digital Library
Author	Hallett, Michael Olsen, Karina Standahl Lund, Eiliv Bongo, Lars Ailo Fjukstad, Bjørn Dumeaux, Vanessa
Abstract	The significant increase in the rate of data generation by the systems biology community creates a need for interactive exploration tools to explore the resultant datasets. Such tools need to combine advanced statistical analyses, prior knowledge from biological databases, and interactive visualizations with intuitive user interfaces. Each specific research question potentially requires a specialized user interface and visualization methods. Although some features are application-specific, the underlying components of the data analysis tool can be shared and reused. Our approach for developing data exploration tools in systems biology builds on the microservice architecture that separates an application into smaller components which can communicate using language-agnostic protocols. We show that this design is well suited for bioinformatics applications where different tools written in different languages by different research groups is the norm. Packaging each service in a software container enables re-use and sharing of key components between applications, reducing development, deployment, and maintenance time. We demonstrate the viability of our approach through a web application, entitled MIxT blood-tumor, for exploring and comparing transcriptional profiles from blood and tumor samples in breast cancer patients. The application integrates advanced statistical software, up-to-date information from biological databases, and modern data visualization libraries.
Starting Page	556
Ending Page	561
Page Count	6
File Format	PDF
ISBN	9781450347228
DOI	10.1145/3107411.3107481
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2017-08-20
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Software containers Visualization Systems biology Breast cancer Interactive data exploration Microservices
Content Type	Text
Resource Type	Article

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