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List of works by Quaid D Morris

A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B).

scientific article published on 6 September 2018

A compendium of RNA-binding motifs for decoding gene regulation.

scientific article

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

scientific article

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

scientific article published on 05 February 2020

A genome-wide assessment of adrenocorticotropin action in the Y1 mouse adrenal tumor cell line

scientific article published on 5 January 2007

A pair of RNA-binding proteins controls networks of splicing events contributing to specialization of neural cell types

scientific article published on 5 June 2014

A panoramic view of yeast noncoding RNA processing

scientific article

A unified model for yeast transcript definition

scientific article published on 29 October 2013

Alternative splicing of conserved exons is frequently species-specific in human and mouse

scientific article published on 01 February 2005

An RRM-ZnF RNA recognition module targets RBM10 to exonic sequences to promote exon exclusion

scientific article

An efficient algorithm to integrate network and attribute data for gene function prediction

scientific article

Application of an integrated physical and functional screening approach to identify inhibitors of the Wnt pathway

scientific article

BayMiR: inferring evidence for endogenous miRNA-induced gene repression from mRNA expression profiles

scientific article

Bayesian inference of MicroRNA targets from sequence and expression data

scientific article

Brain tumor is a sequence-specific RNA-binding protein that directs maternal mRNA clearance during the Drosophila maternal-to-zygotic transition

scientific article published on 12 May 2015

Combining many interaction networks to predict gene function and analyze gene lists ⬇️

scientific article published on May 1, 2012

Comparing nonparametric Bayesian tree priors for clonal reconstruction of tumors.

scientific article published in January 2015

Computational prediction of intronic microRNA targets using host gene expression reveals novel regulatory mechanisms

scientific article

Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction

scientific article published on 28 March 2013

Computational purification of tumor gene expression data

scientific article published on 21 November 2011

Conservation of core gene expression in vertebrate tissues

scientific article published on 16 April 2009

Contributions of steroidogenic factor 1 to the transcription landscape of Y1 mouse adrenocortical tumor cells

scientific article

Cytoscape Web: an interactive web-based network browser

scientific article

Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study

scientific article

Detection and discovery of RNA modifications using microarrays

scientific article

Diversity and complexity in DNA recognition by transcription factors

scientific article (publication date: 26 June 2009)

Dynamic modularity in protein interaction networks predicts breast cancer outcome

scientific article

Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features ⬇️

scientific article published on April 26, 2012

Evaluation of methods for modeling transcription factor sequence specificity

scientific article published on 27 January 2013

Exploration of essential gene functions via titratable promoter alleles

scientific article

Fast integration of heterogeneous data sources for predicting gene function with limited annotation

scientific article

Finding the target sites of RNA-binding proteins

scientific article

GenRate: a generative model that reveals novel transcripts in genome-tiling microarray data

scientific article

GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data

scientific article

Gene Expression Deconvolution for Uncovering Molecular Signatures in Response to Therapy in Juvenile Idiopathic Arthritis

scientific article published on 31 May 2016

GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop

scientific article

GeneMANIA prediction server 2013 update

scientific article published on July 2013

GeneMANIA update 2018.

scientific article published in July 2018

GeneMANIA: Fast gene network construction and function prediction for Cytoscape

scientific article published on July 2014

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

scientific article

Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity

scientific article published on 13 August 2013

Genome-wide analysis of alternative splicing in Caenorhabditis elegans

scientific article

Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs

scientific article published on 28 August 2005

Genome-wide analysis of the maternal-to-zygotic transition in Drosophila primordial germ cells

scientific article published on 20 February 2012

Global profiles of gene expression induced by adrenocorticotropin in Y1 mouse adrenal cells

scientific article published on 16 February 2006

Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein

scientific article

Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling

scientific journal article

High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies.

scientific article published on 25 January 2018

High-throughput characterization of protein-RNA interactions

scientific article

ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing

scientific article published on 19 June 2009

ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles.

scientific article published on 14 May 2015

Identifying cancer specific functionally relevant miRNAs from gene expression and miRNA-to-gene networks using regularized regression

scientific article

Identifying transcription factor functions and targets by phenotypic activation

scientific article

Inferring clonal evolution of tumors from single nucleotide somatic mutations

scientific article published on February 2014

Inferring global levels of alternative splicing isoforms using a generative model of microarray data

scientific article published on 10 January 2006

Interacting evolutionary pressures drive mutation dynamics and health outcomes in aging blood

scientific article published on 13 August 2021

Jury remains out on simple models of transcription factor specificity

scientific article published on 7 June 2011

LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance

scientific article

Labeling nodes using three degrees of propagation

scientific article

MECP2 Is Post-transcriptionally Regulated during Human Neurodevelopment by Combinatorial Action of RNA-Binding Proteins and miRNAs

scientific article published in October 2016

Machine learning and computer vision approaches for phenotypic profiling

scientific article published on 9 December 2016

Mixture model for sub-phenotyping in GWAS

scientific article published on January 1, 2012

Motif models for RNA-binding proteins

scientific article published on 29 August 2018

Multi-way clustering of microarray data using probabilistic sparse matrix factorization

scientific article

NIPS workshop on New Problems and Methods in Computational Biology

scientific article

Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction

scientific article

Network news: functional modules revealed during early embryogenesis in C. elegans

scientific article

Neutral tumor evolution?

scientific article

Novel cardiovascular gene functions revealed via systematic phenotype prediction in zebrafish

scientific article

Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli

scientific article

Oncogenic Activation of the RNA Binding Protein NELFE and MYC Signaling in Hepatocellular Carcinoma

scientific article published in July 2017

PERSONALIZED MEDICINE: FROM GENOTYPES AND MOLECULAR PHENOTYPES TOWARDS THERAPY.

scientific article published on January 2014

PERT: a method for expression deconvolution of human blood samples from varied microenvironmental and developmental conditions

scientific article

PLIDA: cross-platform gene expression normalization using perturbed topic models

scientific article

Patterns of joint involvement in juvenile idiopathic arthritis and prediction of disease course: A prospective study with multilayer non-negative matrix factorization

scientific article published on 26 February 2019

PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors

scientific article published on 13 February 2015

Post-transcriptional gene regulation: RNA-protein interactions, RNA processing, mRNA stability and localization.

scientific article published in January 2009

Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure

scientific article published on 23 April 2010

Predicting node characteristics from molecular networks

scientific article published in January 2011

Predicting the binding preference of transcription factors to individual DNA k-mers.

scientific article published on 16 December 2008

Predicting the target genes of intronic microRNAs using large-scale gene expression data

scientific article

Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitment

scientific article published in June 2007

Probing microRNAs with microarrays: tissue specificity and functional inference

scientific article

QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data

scientific article published on 28 March 2018

Quantifying the influence of mutation detection on tumour subclonal reconstruction

scientific article published on 07 December 2020

RBPDB: a database of RNA-binding specificities

scientific article

RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins

scientific article published on 10 June 2013

RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease

scientific article published on 18 December 2014

RNA-protein interactions: an overview

scientific article published on January 2014

RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins

scientific article published on 9 December 2016

RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection

scientific article published on 23 June 2017

RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins

scientific article

RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors

scientific article published in July 2007

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

scientific article

Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig

scientific article published on 05 February 2020

Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform

scientific article

Similarity regression predicts evolution of transcription factor sequence specificity

scientific article published on 27 May 2019

Staufen2 regulates neuronal target RNAs

scientific journal article

The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation

scientific article

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

scientific article (publication date: July 2010)

The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in . e

scientific article published on 21 December 2018

The biologic basis of clinical heterogeneity in juvenile idiopathic arthritis

scientific article

The functional landscape of mouse gene expression

scientific article

The future of genome-based medicine

scientific article published in January 2013

The genetic landscape of a cell

scientific article

Transcriptional networks: reverse-engineering gene regulation on a global scale

scientific article

Unsupervised detection of genes of influence in lung cancer using biological networks

scientific article

Using expression profiling data to identify human microRNA targets

scientific article

Using the Electronic Medical Record to Identify Patients at High Risk for Frequent Emergency Department Visits and High System Costs

scientific article published on 5 January 2017

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences

scientific article published on June 2008

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