Carlos H. M. Rodrigues

Circulating microRNA profiles associated with tick bite and debilitating symptom complexes attributed to ticks (DSCATT)

Ryan J. Farr, Carlos H. M. Rodrigues, Siobhon Egan, Jenny Su et autres

Tick bites in Australia are associated with a poorly understood syndrome known as Debilitating Symptom Complexes Attributed to Ticks (DSCATT), however, the underlying biological mechanisms remain unclear. Here, we investigate host responses to tick bite and DSCATT by profiling circulating host-encoded microRNAs …

au, br, us, gb (code pays fourni par la source)

Development and validation of a serum microRNA biomarker panel for bovine Johne's disease

Carlos H. M. Rodrigues, Jenny Su, NAGENDRAKUMAR SINGANALLUR BALASUBRAMANIAN, Christina L. Rootes et autres

Johne's disease (JD) is a chronic wasting disease of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP).For decades, JD management has been hampered by the lack of a sensitive diagnostic test.Here we have developed a machine-learning (ML)driven pipeline that identifies host-encoded microRNA …

au (code pays fourni par la source)

Circulating microRNA profiles are associated with acute pain and stress in castrated and tail docked lambs

Ryan J. Farr, Christopher Cowled, Carlos H. M. Rodrigues, Christina L. Rootes et autres

• Over 1100 novel miRNAs identified from deep sequencing of serum-isolated small RNA. • Altered expression of 18 miRNAs were observed in castrated and tail-docked lambs. • Machine learning identified a five-miRNA signature classifying post-procedure lambs. Host-encoded miRNAs are potential biomarkers of …

au (code pays fourni par la source)

Proximity proteomics reveals a mechanism of fatty acid transfer at lipid droplet-mitochondria- endoplasmic reticulum contact sites

Ayenachew Bezawork‐Geleta, Camille J. Devereux, Stacey N. Keenan, Jieqiong Lou et autres

Membrane contact sites between organelles are critical for the transfer of biomolecules. Lipid droplets store fatty acids and form contacts with mitochondria, which regulate fatty acid oxidation and adenosine triphosphate production. Protein compartmentalization at lipid droplet-mitochondria contact sites and their effects on …

au (code pays fourni par la source)

Assessing the predicted impact of single amino acid substitutions in MAPK proteins for CAGI6 challenges

Paola Turina, Maria Petrosino, Carlos A. Enriquez Sandoval, Leonore Novak et autres

it, us, au, cn, be, ca (code pays fourni par la source)

Assessing the predicted impact of single amino acid substitutions in calmodulin for CAGI6 challenges

Paola Turina, Giuditta Dal Cortivo, Carlos A. Enriquez Sandoval, Emil Alexov et autres

it, us, au, be, ca (code pays fourni par la source)

piscesCSM: prediction of anticancer synergistic drug combinations

Raghad Al‐Jarf, Carlos H. M. Rodrigues, Yoochan Myung, Douglas E. V. Pires et autres

While drug combination therapies are of great importance, particularly in cancer treatment, identifying novel synergistic drug combinations has been a challenging venture. Computational methods have emerged in this context as a promising tool for prioritizing drug combinations for further evaluation, though they …

au (code pays fourni par la source)

MTR3D ‐ AF2 : Expanding the coverage of spatially derived missense tolerance scores across the human proteome using AlphaFold2

Aaron S. Kovacs, Stephanie Portelli, Michael Silk, Carlos H. M. Rodrigues et autres

The missense tolerance ratio (MTR) was developed as a novel approach to assess the deleteriousness of variants. Its three-dimensional successor, MTR3D, was demonstrated powerful at discriminating pathogenic from benign variants. However, its reliance on experimental structures and homologs limited its coverage of …

au (code pays fourni par la source)

EFG ‐ CS : Predicting chemical shifts from amino acid sequences with protein structure prediction using machine learning and deep learning models

Xiaotong Gu, Yoochan Myung, Carlos H. M. Rodrigues, David B. Ascher

Nuclear magnetic resonance (NMR) crystallography is one of the main methods in structural biology for analyzing protein stereochemistry and structure. The chemical shift of the resonance frequency reflects the effect of the protons in a molecule producing distinct NMR signals in different …

au (code pays fourni par la source)

DDMut-PPI: predicting effects of mutations on protein–protein interactions using graph-based deep learning

Yunzhuo Zhou, Yoochan Myung, Carlos H. M. Rodrigues, David B. Ascher

Protein-protein interactions (PPIs) play a vital role in cellular functions and are essential for therapeutic development and understanding diseases. However, current predictive tools often struggle to balance efficiency and precision in predicting the effects of mutations on these complex interactions. To address …

au (code pays fourni par la source)

Exploring the effects of missense mutations on protein thermodynamics through structure-based approaches: findings from the CAGI6 challenges

Carlos H. M. Rodrigues, Stephanie Portelli, David B. Ascher

Missense mutations are known contributors to diverse genetic disorders, due to their subtle, single amino acid changes imparted on the resultant protein. Because of this, understanding the impact of these mutations on protein stability and function is crucial for unravelling disease mechanisms …

au (code pays fourni par la source)

CSM‐Potential2 : A comprehensive deep learning platform for the analysis of protein interacting interfaces

Carlos H. M. Rodrigues, David B. Ascher

Proteins are molecular machinery that participate in virtually all essential biological functions within the cell, which are tightly related to their 3D structure. The importance of understanding protein structure-function relationship is highlighted by the exponential growth of experimental structures, which has been …

au (code pays fourni par la source)