Kyle Ellrott

Latest

• A compendium of next-generation patient-derived models for diverse cancers
• Eleven quick tips for Biomedical Federated Learning
• Towards a decentralized future for open-science databases
• Pooling multimodal cancer data across unaligned embedding spaces maintains tumor of origin signal
• A decentralized future for the open-science databases
• Robust software development practices improve citations of RNA-seq tools
• Protocol for assessing distances in pathway space for classifier feature sets from machine learning methods
• Protocol for obtaining cancer type and subtype predictions using subSCOPE
• Aggregating multimodal cancer data across unaligned embedding spaces maintains tumor of origin signal
• Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction
• Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets
• Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets
• SyntheVAEiser: augmenting traditional machine learning methods with VAE-based gene expression sample generation for improved cancer subtype predictions
• The GA4GH Task Execution Application Programming Interface: Enabling Easy Multicloud Task Execution
• The GA4GH Task Execution Application Programming Interface: Enabling Easy Multicloud Task Execution
• recountmethylation enables flexible analysis of public blood DNA methylation array data
• Bridge2AI
• Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space
• A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery
• Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
• Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
• A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer
• Exploring Integrative Analysis Using the BioMedical Evidence Graph
• neoepiscope improves neoepitope prediction with multivariant phasing
• A community effort to create standards for evaluating tumor subclonal reconstruction
• Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges
• Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection
• Valection: design optimization for validation and verification studies
• Population-level distribution and putative immunogenicity of cancer neoepitopes
• Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines
• Germline contamination and leakage in whole genome somatic single nucleotide variant detection
• A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines
• TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal
• G2P Whitepaper
• Prophetic Granger Causality to infer gene regulatory networks
• Reproducible Science: Cancer Researchers Embrace Containers in the Cloud
• Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection
• Global optimization of somatic variant identification in cancer genomes with a global community challenge
• Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas
• The Cancer Genome Atlas Pan-Cancer analysis project
• The UCSC Cancer Genomics Browser: update 2013
• TOPSAN: a dynamic web database for structural genomics
• The crystal structure of a bacterial Sufu-like protein defines a novel group of bacterial proteins that are similar to the N-terminal domain of human Sufu
• A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) from Bacteroides thetaiotaomicron at 2.2 Å resolution
• Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron
• Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Å resolution: the first structural representative of a new protein family that may play a role in carbohydrate metabolism
• Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules
• Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases
• Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism
• Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary C-terminal treble-clef zinc finger
• The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function
• The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold
• The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation
• Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families
• Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain
• Structural and functional characterizations of SsgB, a conserved activator of developmental cell division in morphologically complex actinomycetes
• Improving the performance of protein threading using insertion/deletion frequency arrays
• A historical perspective of template-based protein structure prediction
• Improvement in protein sequence-structure alignment using insertion/deletion frequency arrays
• A generalized threading model using integer programming that allows for secondary structure element deletion
• PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction
• A computational pipeline for protein structure prediction and analysis at genome scale
• PROSPECT II: protein structure prediction program for genome-scale applications
• Identifying transcription factor binding sites through Markov chain optimization