List of works - Jesse Gillis

A Caenorhabditis elegans Model for Integrating the Functions of Neuropsychiatric Risk Genes Identifies Components Required for Normal Dendritic Morphology

scientific article published on 06 April 2020

A genome-wide RNAi screen draws a genetic framework for transposon control and primary piRNA biogenesis in Drosophila

scientific article (publication date: 6 June 2013)

A limited set of transcriptional programs define major cell types

scientific article published on 29 July 2020

A methodology for the analysis of differential coexpression across the human lifespan

scientific article

A multimodal cell census and atlas of the mammalian primary motor cortex

scientific article

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

scientific article

Acquired dependence of acute myeloid leukemia on the DEAD-box RNA helicase DDX5.

scientific article

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

scientific article

An in vitro model of hippocampal sharp waves: regional initiation and intracellular correlates

scientific article

Analytical guidelines for co-fractionation mass spectrometry obtained through global profiling of gold standard Saccharomyces cerevisiae protein complexes

scientific article published on 18 August 2020

Assessing identity, redundancy and confounds in Gene Ontology annotations over time

scientific article published on 06 January 2013

Assessing the replicability of spatial gene expression using atlas data from the adult mouse brain

scientific article

AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression

scientific article

Bias tradeoffs in the creation and analysis of protein-protein interaction networks

scientific article published on 27 January 2014

Cellular anatomy of the mouse primary motor cortex

scientific article

Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor.

scientific article published on 28 February 2018

Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA)

scientific article (publication date: 2013)

Co-expression in Single-Cell Analysis: Saving Grace or Original Sin?

scientific article published on 23 August 2018

CoCoCoNet: conserved and comparative co-expression across a diverse set of species

scientific article published on 11 May 2020

Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms

scientific article published on 22 April 2022

Comparative cellular analysis of motor cortex in human, marmoset and mouse

scientific article published on 06 October 2021

Comparative transcriptomics reveals human-specific cortical features

scientific article published on 12 October 2023

Controlling for spatial variability in single site recordings in an in vitro hippocampal preparation with a spontaneous rhythm.

scientific article published on 6 July 2007

Copolymerization of single-cell nucleic acids into balls of acrylamide gel

scientific article published on 14 November 2019

De novo mutations in schizophrenia implicate chromatin remodeling and support a genetic overlap with autism and intellectual disability

scientific article

Diverse epigenetic strategies interact to control epidermal differentiation

scientific article

EGAD: Ultra-fast functional analysis of gene networks

article

EGAD: ultra-fast functional analysis of gene networks

scientific article published on 19 December 2016

Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

scientific article published in April 2020

Exploiting single-cell expression to characterize co-expression replicability

scientific article published on 06 May 2016

FTO, obesity and the adolescent brain

scientific article published on 30 November 2012

Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data

scientific article

Gene function analysis in complex data sets using ErmineJ.

scientific article

Gene-specific patterns of expression variation across organs and species

scientific article published on 08 July 2016

Genome-wide expression profiling of schizophrenia using a large combined cohort

scientific article published on 3 January 2012

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

scientific article published on 24 February 2015

High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing

scientific article published on 01 October 2019

How many markers are needed to robustly determine a cell's type?

scientific article published in November 2021

Intraductal transplantation models of human pancreatic ductal adenocarcinoma reveal progressive transition of molecular subtypes

scientific article published on 23 July 2020

Is it time to change the reference genome?

scientific article published on 09 August 2019

KCTD8 gene and brain growth in adverse intrauterine environment: a genome-wide association study.

scientific article

Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction

scientific article

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

scientific article published on 08 June 2020

Measuring the wisdom of the crowds in network-based gene function inference.

scientific article published on 29 October 2014

Meta-analysis of gene coexpression networks in the post-mortem prefrontal cortex of patients with schizophrenia and unaffected controls

scientific article

Meta-analytic markers reveal a generalizable description of cortical cell types

scientific article

Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses

scientific article published on 07 March 2022

Positive and negative forms of replicability in gene network analysis

scientific article published on 14 December 2015

Predictability of human differential gene expression

article

Progress and challenges in the computational prediction of gene function using networks

scientific article published on 7 September 2012

Progress and challenges in the computational prediction of gene function using networks

article

Progress and challenges in the computational prediction of gene function using networks: 2012-2013 update

scientific article published on 31 October 2013

Repeated hypoxic episodes induce seizures and alter hippocampal network activities in mice

scientific article published on 24 March 2009

Scaling up reproducible research for single-cell transcriptomics using MetaNeighbor

scientific article published in 2021

Single cell RNA-sequencing: replicability of cell types

scientific article published on 09 January 2019

Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery

scientific article published on 30 December 2020

Single-cell transcriptomics of the developing lateral geniculate nucleus reveals insights into circuit assembly and refinement.

scientific article published on 17 January 2018

Size does matter: generation of intrinsic network rhythms in thick mouse hippocampal slices

scientific article published on 10 November 2004

Spatial coherence and stationarity of local field potentials in an isolated whole hippocampal preparation in vitro

scientific article published on 16 January 2010

Spontaneous rhythmic field potentials of isolated mouse hippocampal-subicular-entorhinal cortices in vitro.

scientific article

Strength of functional signature correlates with effect size in autism

scientific article

The Impact of Multifunctional Genes on "Guilt by Association" Analysis ⬇️

scientific article published on February 18, 2011

The fractured landscape of RNA-seq alignment: The default in our STARs

scholarly article published 16 November 2017

The fractured landscape of RNA-seq alignment: the default in our STARs

scientific article published in May 2018

The role of indirect connections in gene networks in predicting function ⬇️

scientific article published on May 6, 2011

Transcriptional Architecture of Synaptic Communication Delineates GABAergic Neuron Identity

scientific article

Using predictive specificity to determine when gene set analysis is biologically meaningful

scientific article published in February 2017

Using predictive specificity to determine when gene set analysis is biologically meaningful

article

“Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks ⬇️

scientific article published on March 29, 2012

List of works by Jesse Gillis

A Caenorhabditis elegans Model for Integrating the Functions of Neuropsychiatric Risk Genes Identifies Components Required for Normal Dendritic Morphology

A genome-wide RNAi screen draws a genetic framework for transposon control and primary piRNA biogenesis in Drosophila

A limited set of transcriptional programs define major cell types

A methodology for the analysis of differential coexpression across the human lifespan

A multimodal cell census and atlas of the mammalian primary motor cortex

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

Acquired dependence of acute myeloid leukemia on the DEAD-box RNA helicase DDX5.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

An in vitro model of hippocampal sharp waves: regional initiation and intracellular correlates

Analytical guidelines for co-fractionation mass spectrometry obtained through global profiling of gold standard Saccharomyces cerevisiae protein complexes

Assessing identity, redundancy and confounds in Gene Ontology annotations over time

Assessing the replicability of spatial gene expression using atlas data from the adult mouse brain

AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression

Bias tradeoffs in the creation and analysis of protein-protein interaction networks

Cellular anatomy of the mouse primary motor cortex

Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor.

Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA)

Co-expression in Single-Cell Analysis: Saving Grace or Original Sin?

CoCoCoNet: conserved and comparative co-expression across a diverse set of species

Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms

Comparative cellular analysis of motor cortex in human, marmoset and mouse

Comparative transcriptomics reveals human-specific cortical features

Controlling for spatial variability in single site recordings in an in vitro hippocampal preparation with a spontaneous rhythm.

Copolymerization of single-cell nucleic acids into balls of acrylamide gel

De novo mutations in schizophrenia implicate chromatin remodeling and support a genetic overlap with autism and intellectual disability

Diverse epigenetic strategies interact to control epidermal differentiation

EGAD: Ultra-fast functional analysis of gene networks

EGAD: ultra-fast functional analysis of gene networks

Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

Exploiting single-cell expression to characterize co-expression replicability

FTO, obesity and the adolescent brain

Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data

Gene function analysis in complex data sets using ErmineJ.

Gene-specific patterns of expression variation across organs and species

Genome-wide expression profiling of schizophrenia using a large combined cohort

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing

How many markers are needed to robustly determine a cell's type?

Intraductal transplantation models of human pancreatic ductal adenocarcinoma reveal progressive transition of molecular subtypes

Is it time to change the reference genome?

KCTD8 gene and brain growth in adverse intrauterine environment: a genome-wide association study.

Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

Measuring the wisdom of the crowds in network-based gene function inference.

Meta-analysis of gene coexpression networks in the post-mortem prefrontal cortex of patients with schizophrenia and unaffected controls

Meta-analytic markers reveal a generalizable description of cortical cell types

Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses

Positive and negative forms of replicability in gene network analysis

Predictability of human differential gene expression

Progress and challenges in the computational prediction of gene function using networks

Progress and challenges in the computational prediction of gene function using networks

Progress and challenges in the computational prediction of gene function using networks: 2012-2013 update

Repeated hypoxic episodes induce seizures and alter hippocampal network activities in mice

Scaling up reproducible research for single-cell transcriptomics using MetaNeighbor

Single cell RNA-sequencing: replicability of cell types

Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery

Single-cell transcriptomics of the developing lateral geniculate nucleus reveals insights into circuit assembly and refinement.

Size does matter: generation of intrinsic network rhythms in thick mouse hippocampal slices

Spatial coherence and stationarity of local field potentials in an isolated whole hippocampal preparation in vitro

Spontaneous rhythmic field potentials of isolated mouse hippocampal-subicular-entorhinal cortices in vitro.

Strength of functional signature correlates with effect size in autism

The Impact of Multifunctional Genes on "Guilt by Association" Analysis ⬇️

The fractured landscape of RNA-seq alignment: The default in our STARs

The fractured landscape of RNA-seq alignment: the default in our STARs

The role of indirect connections in gene networks in predicting function ⬇️

Transcriptional Architecture of Synaptic Communication Delineates GABAergic Neuron Identity

Using predictive specificity to determine when gene set analysis is biologically meaningful

Using predictive specificity to determine when gene set analysis is biologically meaningful

“Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks ⬇️