The Center for Computational Science


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Building on the immense resources and expanding the vision of the Center for Computational Science (CCS), the University has established the Miami Institute for Data Science and Computing (IDSC “i-disc”)

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Focus Areas

Research Highlights

"Gang Ren and Mitsunori Ogihara Presented a Paper at 2019 IEEE on Big Data in L.A.

Scaling Up Heterogeneous Waveform Clustering for Long-Duration Monitoring Signal Acquisition . . .

"Enrico Capobianco Receives Two Grants for Bioinformatics Research

Collaborators with combined expertise in molecular neurobiology and large data analysis apply their knowledge to neurodegenerative diseases.

"The Krüppel-Like Factor Gene Target Dusp14 Regulates Axon Growth and Regeneration

Results link intrinsic and extrinsic regulators of axon growth and suggest modulation of the KLF9-Dusp14 pathway as a potential approach to . . .

"17th IEEE Int’l Conference on Machine Learning and Applications

Mitsu Ogihara and Gang Ren presented a paper the IEEE International Conference on Machine Learning and Applications

"DrugCentral 2018: An Update

DrugCentral is a drug information resource open to the public since 2016 and previously described in the 2017 Nucleic Acids Research Database issue.

"Structural Interactions of Resveratrol With Its Bandwagon of Targets

An overview of the varied patterns and profiles of resveratrol target proteins and the structural aspects of resveratrol binding with its multiple targets as available in the PDB . . .

"The Effect of Jun Dimerization on Neurite Outgrowth and Motif Binding

Past CCS Fellow (2015-2016) Matt Danzi and Dr. Vance Lemon work together on Axon Regeneration and spinal cord injury recovery.

"Impact of Ocean Eddy Resolution on the Sensitivity of Precipitation to CO2 Increase

In this study, we compare precipitation changes from CO2 forcing in models with and without explicit ocean eddy simulation.

"Sustainable Data and Metadata Management at the BD2K-LINCS DCIC

Here we describe the end-to-end data processing and management at the DCIC to generate a high-quality and persistent product.

"Simulated Microgravity Impairs Cardiac Autonomic Neurogenesis from Neural Crest Cells

We hypothesized that microgravity can impair NC-derived cardiac structures . . .

"CARM1 Is Essential for Myeloid Leukemogenesis but Dispensable for Normal Hematopoiesis

Here, we investigated the role of CARM1 in normal and malignant hematopoiesis.

"The South Pacific Meridional Mode as a Thermally Drive Source of ENSO Amplitude Modulation and Uncertainty

This study seeks to identify thermally driven sources of ENSO amplitude and uncertainty, as they are relatively unexplored compared to wind-driven sources.

"An Early Behavioral Index of ASD from Automated Microanalysis of Movement Dynamics

In this study, we employed microanalytic, automated measurement to examine head movement coordination between infants and parents.

"Breaking Away: The Role of Homeostatic Drive in Perpetuating Depression

We propose that the complexity of regulatory interactions modulating brain neurochemistry and behavior is such that multiple stable responses may be supported . . .

"Unexplored Therapeutic Opportunities in the Human Genome

In this article, we discuss the systematic collection and processing of a wide array of genomic, proteomic, chemical and disease-related resource data.

"CEDAR: Semantic Web Technology to Support Open Science

CEDAR technology includes Web-based methods for creating and managing libraries of templates for representing metadata.

"Can Chromatin Accessibility be Exploited for Axon Regeneration?

In this article, we assess the direct evidence in the literature for this hypothesis and re-examine other axon regeneration-promoting manipulations to see if they provide additional support.

"Drug Repositioning in Glioblastoma: A Pathway Perspective

We review here psychiatric and non-psychiatric compounds that may be effective in GBM, as well as potential drugs targeting cell death pathways.

"Student Retention and Content Analysis papers presented at IEEE Conferences

Recent IEEE papers presented in Cancun and New Orleans

"Historic American Buildings Survey and the Integration of New Technology

Architecture Professors Ricardo Lopez and Li Yi, and Chris Mader and Amin Sarafraz of CCS Software Engineering developed documentation guidelines for the Historic American Buildings Survey (HABS) set forth by the US National Park Service.

"A Matlab-Based Signal Processing Toolbox for Musical Vibrato

This paper describes a collection of signal processing methods and a toolbox for extracting and analyzing vibrato-related parameters from solo audio recordings.

"Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data

Poster "Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data: Application to Melanoma Pseudogenes" was presented at the Big Data in Biomedicine Conference at Stanford University.

"Developing a Framework for Digital Objects in the BD2K Commons

This report reviews highlights from a two-day meeting involving the BD2K CFPWG to provide insights on trends and considerations in advancing Big Data science for biomedical research in the United States.

"Public Science Insights: Rise of Digital Biomarkers and Role in Precision Medicine

With the rise of digital biomarkers, its role in precision medicine has become an important area of interest . . .

"Smart Cities, Big Data, and Communities: Reasoning from the Viewpoint of . . .

In what sense is a city smart? There are established entities defining this rich area of cross-disciplinary studies, and they refer to social, technical, economic, and . . .

"Infants Time Their Smiles to Make Their Moms Smile

The results of our analysis show that by the time infants reach 4 months of age both mothers and infants time their smiles in a purposeful, goal-oriented manner . . .

"Non-coding RNAs profiling in head and neck cancers

Cancer: The role of 'non-coding' genes Transcriptomic profiling of head and neck tumors suggests a prominent role for non-protein-coding genes in carcinogenesis.

"Launch of Data-Driven Music-Streaming Site:

CCS Postdoctoral Researcher Mohamed Sordo has launched, a powerful web application for analyzing and streaming music. Musikipedia stands at the forefront of music analysis . . .

"Identification of BRAF 3’UTR Isoforms in Melanoma

BRAF protein kinase is a crucial player in melanoma, as it belongs to the highly oncogenic RAS/RAF/MEK/ERK signaling pathway . . .

"UM Launches ‘MAP’ Digital Tool for Affordable Housing Needs

This project focuses on improving housing opportunities for residents of low- to moderate-income Miami neighborhoods . . .

"Computational Complexity Studies of Synchronous Boolean Finite Dynamical Systems

This paper studies a subclass of finite dynamical systems the synchronous BFDS where the states are Boolean and the state update takes place in discrete time and at the same on all objects.

"A Rule-Based Approach to Extracting Relations from Music Tidbits

Extracted relations are evaluated intrinsically by assessing their linguistic quality, as well as extrinsically by assessing the extent to which they map an existing music knowledge base.

"Mining library and university data to understand library use patterns

Library data are often hard to analyze because these data come from unconnected sources, and the data sets can be very large.

"Essentiality and centrality in protein interaction networks revisited

e-MDSets may provide a new method of evaluating the core proteins of an organism.

"3D Imaging of Axons in Transparent Spinal Cords from Rodents & Primates

The histological assessment of spinal cord tissue in three dimensions has previously been very time consuming and prone to errors of interpretation. Advances in tissue clearing have significantly improved visualization of fluorescently labelled axons.

"Distinct Transcriptomic Features and B-Cell Populations in the Mouse Spleen

Splenic transitional B-cells (T1 and T2) are selected to avoid self-reactivity and to safeguard against autoimmunity . . .

"Prognostic Models in Coronary Artery Disease: Cox and Network Approaches

There may be characteristic factors involved in prognostic stratification whose complexity suggests an exploration beyond the analysis provided by the still fundamental Cox approach.

"Integrative Analysis of Cancer Imaging Readouts by Networks

Illustrating how networks can integrate imaging data to explain cancer complexity, and assess potential pre-clinical and clinical impact.

"Comorbidity Networks: Beyond Disease Correlations

A new paradigm of data-intensive biomedicine is naturally leading to novel inference tools, dealing in particular with complex diseases and comorbidities.

"Regions of Homozygosity Identified by Oligonucleotide SNP Arrays

This study demonstrates that ROHs are much more frequent than previously recognized and often reflect parental relatedness, ascertain autosomal recessive diseases or unravel UPD in many cases.

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