Asa Ben‐Hur
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View article: CaDAVEr: a metagenome-assembled genome catalog of microbial decomposers across vertebrate environments
CaDAVEr: a metagenome-assembled genome catalog of microbial decomposers across vertebrate environments Open
Microbial degradation of organic matter is a fundamental Earth process, yet a mechanistic understanding of microbial metabolisms and successional ecology involved in decomposition remains poorly understood. Here, we announce the recovery o…
View article: The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models
The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models Open
Complex deep learning models trained on very large datasets have become key enabling tools for current research in natural language processing and computer vision. By providing pre-trained models that can be fine-tuned for specific applica…
View article: A Comprehensive Evaluation of Self Attention for Detecting Regulatory Feature Interactions
A Comprehensive Evaluation of Self Attention for Detecting Regulatory Feature Interactions Open
The successful use of deep learning in computational biology depends on the ability to extract meaningful biological information from the trained models. Recent work has demonstrated that the attention maps generated by self-attention laye…
View article: Predicting small-molecule inhibition of protein complexes
Predicting small-molecule inhibition of protein complexes Open
Motivation Protein-Protein Interactions (PPIs) are crucial in biological processes and disease mechanisms, underscoring the importance of discovering PPI inhibitors in drug development. Machine learning can expedite this discovery process.…
View article: The spectrum of <scp>pre‐mRNA</scp> splicing in autism
The spectrum of <span>pre‐mRNA</span> splicing in autism Open
Disruptions in spatiotemporal gene expression can result in atypical brain function. Specifically, autism spectrum disorder (ASD) is characterized by abnormalities in pre‐mRNA splicing. Abnormal splicing patterns have been identified in th…
View article: A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables
A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables Open
Microbial breakdown of organic matter is one of the most important processes on Earth, yet the controls of decomposition are poorly understood. Here we track 36 terrestrial human cadavers in three locations and show that a phylogenetically…
View article: The role of chromatin state in intron retention: a case study in leveraging large scale deep learning models
The role of chromatin state in intron retention: a case study in leveraging large scale deep learning models Open
Complex deep learning models trained on very large datasets have become key enabling tools for current research in natural language processing and computer vision. By providing pre-trained models that can be fine-tuned for specific applica…
View article: Cross-linking breast tumor transcriptomic states and tissue histology
Cross-linking breast tumor transcriptomic states and tissue histology Open
Identification of the gene expression state of a cancer patient from routine pathology imaging and characterization of its phenotypic effects have significant clinical and therapeutic implications. However, prediction of expression of indi…
View article: Phenotyping and predicting wheat spike characteristics using image analysis and machine learning
Phenotyping and predicting wheat spike characteristics using image analysis and machine learning Open
Improvements in trait phenotyping are needed to increase the quantity and quality of data available for genetic improvement of crops. In this study, we used moderate throughput image analysis and machine learning as a pipeline for phenotyp…
View article: Protein quality assessment with a loss function designed for high-quality decoys
Protein quality assessment with a loss function designed for high-quality decoys Open
Motivation: The prediction of a protein 3D structure is essential for understanding protein function, drug discovery, and disease mechanisms; with the advent of methods like AlphaFold that are capable of producing very high-quality decoys,…
View article: Alphafold decoys on CASP15 target Fasta Files
Alphafold decoys on CASP15 target Fasta Files Open
This contains the decoys along with the results produced by alphafold2 when run on a subset of CASP15 Fasta Files
View article: Alphafold decoys on CASP15 target Fasta Files
Alphafold decoys on CASP15 target Fasta Files Open
This contains the decoys along with the results produced by alphafold2 when run on a subset of CASP15 Fasta Files
View article: CASP15
CASP15 Open
This folder contains the unprocessed and processed decoys, targets along with their true lDDT scores.
View article: CASP15
CASP15 Open
This folder contains the unprocessed and processed decoys, targets along with their true lDDT scores.
View article: RITUXIMAB‐CONTAINING COMBINED MODALITY THERAPY IN LIMITED STAGE FOLLICULAR LYMPHOMA: MATURE FOLLOW UP AND DERIVATION OF A NOVEL PROGNOSTIC SCORE FROM THE TROG99.03 TRIAL
RITUXIMAB‐CONTAINING COMBINED MODALITY THERAPY IN LIMITED STAGE FOLLICULAR LYMPHOMA: MATURE FOLLOW UP AND DERIVATION OF A NOVEL PROGNOSTIC SCORE FROM THE TROG99.03 TRIAL Open
Introduction: The TROG99.03 represents the only randomised phase III trial of combined modality therapy (CMT) in limited-stage follicular lymphoma 'LSFL', reporting a prolonged progression-free survival (PFS) in the CMT arm (MacManus, JCO,…
View article: Data-Driven Modelling of Gene Expression States in Breast Cancer and their Prediction from Routine Whole Slide Images
Data-Driven Modelling of Gene Expression States in Breast Cancer and their Prediction from Routine Whole Slide Images Open
Summary Identification of gene expression state of a cancer patient from routine pathology imaging and characterization of its phenotypic effects have significant clinical and therapeutic implications. However, prediction of expression of …
View article: LDDT
LDDT Open
This repo consist of the LDDT scores of all the decoys
View article: Evidence for the role of transcription factors in the co-transcriptional regulation of intron retention
Evidence for the role of transcription factors in the co-transcriptional regulation of intron retention Open
Background Alternative splicing is a widespread regulatory phenomenon that enables a single gene to produce multiple transcripts. Among the different types of alternative splicing, intron retention is one of the least explored despite its …
View article: qepsilon LDDT model
qepsilon LDDT model Open
This repo contains the best model with respect to LDDT scores for qepsilon
View article: qepsilon LDDT model
qepsilon LDDT model Open
This repo contains the best model with respect to LDDT scores for qepsilon
View article: LDDT
LDDT Open
This repo consist of the LDDT scores of all the decoys
View article: LDDT
LDDT Open
This repo consist of the LDDT scores of all the decoys
View article: Data for the manuscript "Protein quality assessment with graph convolution guided by a loss function designed for high quality decoys"
Data for the manuscript "Protein quality assessment with graph convolution guided by a loss function designed for high quality decoys" Open
Supporting material
View article: Supporting data for the manuscript "Protein quality assessment with graph convolution guided by a loss function designed for high quality decoys"
Supporting data for the manuscript "Protein quality assessment with graph convolution guided by a loss function designed for high quality decoys" Open
This dataset provides the predictions of the protein quality assessment method Q_epsilon with respect to CASP13 and CASP14, as well as a snapshot of the github repository providing the code for the method. The format of the file is as foll…
View article: Supporting data for the manuscript "Protein quality assessment with graph convolution guided by a loss function designed for high quality decoys"
Supporting data for the manuscript "Protein quality assessment with graph convolution guided by a loss function designed for high quality decoys" Open
This dataset provides the predictions of the protein quality assessment method Q_epsilon with respect to CASP13 and CASP14, as well as a snapshot of the github repository providing the code for the method. The format of the file is as foll…
View article: Residue Neighbours
Residue Neighbours Open
It contains the residue neighbours of the decoys
View article: Residue Neighbours
Residue Neighbours Open
It contains the residue neighbours of the decoys
View article: Decoy Features of CASP 9,10,11,12,13,14
Decoy Features of CASP 9,10,11,12,13,14 Open
This repository contains the zip files that has the information regarding atom features,same and different residue neighbours of atoms, gdtts and the number of atoms in a residue associated with the decoy files of CASP 9,10,11,12,13, 14 an…
View article: Decoy Features of CASP 9,10,11,12,13,14
Decoy Features of CASP 9,10,11,12,13,14 Open
This repository contains the zip files that has the information regarding atom features,same and different residue neighbours of atoms, gdtts and the number of atoms in a residue associated with the decoy files of CASP 9,10,11,12,13, 14 an…
View article: Decoy Features of CASP 9,10,11,12,13,14
Decoy Features of CASP 9,10,11,12,13,14 Open
This repository contains the zip files that has the information regarding atom features,same and different residue neighbours of atoms, gdtts and the number of atoms in a residue associated with the decoy files of CASP 9,10,11,12,13 and 14.