List of works - Timothy Ravasi

A chromosome-scale genome assembly of the false clownfish, Amphiprion ocellaris

scientific article published on 01 May 2022

A promoter-level mammalian expression atlas

scientific article

A systems approach to delineate functions of paralogous transcription factors: role of the Yap family in the DNA damage response.

scientific article

Actinomycetes from Red Sea sponges: sources for chemical and phylogenetic diversity

scientific article (publication date: 12 May 2014)

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

An Inflammatory Role for the Mammalian Carboxypeptidase Inhibitor Latexin: Relationship to Cystatins and the Tumor Suppressor TIG1

scientific article

An atlas of combinatorial transcriptional regulation in mouse and man

scientific article

An integrated systems analysis implicates EGR1 downregulation in simian immunodeficiency virus encephalitis-induced neural dysfunction

scientific article published on October 2009

An interplay between plasticity and parental phenotype determines impacts of ocean acidification on a reef fish

scientific article published on 18 December 2017

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

scientific article (publication date: 5 December 2002)

Anti-cancer agents in Saudi Arabian herbals revealed by automated high-content imaging

scientific article

Astrocyte-specific overexpressed gene signatures in response to methamphetamine exposure in vitro

scientific article published on 09 March 2017

Bacterial community profiles in low microbial abundance sponges

scientific article

Beyond buying time: the role of plasticity in phenotypic adaptation to rapid environmental change

scientific article published on 01 March 2019

Characterization of piRNAs across postnatal development in mouse brain.

scientific article published on 26 April 2016

Co-transcriptomic Analysis by RNA Sequencing to Simultaneously Measure Regulated Gene Expression in Host and Bacterial Pathogen

scientific article

Coevolution within a transcriptional network by compensatory trans and cis mutations.

scientific article

Concordant epigenetic silencing of transforming growth factor-beta signaling pathway genes occurs early in breast carcinogenesis.

scientific article published on December 2007

Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage

scientific article published in June 2003

Correction: miRNA Repertoires of Demosponges Stylissa carteri and Xestospongia testudinaria

scientific article published on 11 April 2016

Corrigendum: Genome-wide analysis of mammalian promoter architecture and evolution

scholarly article published in Nature Genetics

Cytotoxic effects of nickel nanowires in human fibroblasts

scientific article published on 9 March 2016

Cytotoxicity and intracellular dissolution of nickel nanowires.

scientific article published on 22 December 2015

Defining the protein interaction network of human malaria parasite Plasmodium falciparum ⬇️

scientific article published on 08 December 2011

Dependency on de novo protein synthesis and proteomic changes during metamorphosis of the marine bryozoan Bugula neritina

scientific article

Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49

scientific article published on 6 March 2014

Dynamic epigenetic control of highly conserved noncoding elements

scientific article

Erratum: From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks

scientific article published on 21 July 2015

Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering

scientific article

Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome

scientific article

Exploitation of genetic interaction network topology for the prediction of epistatic behavior

scientific article published on 25 July 2013

Exploring seascape genetics and kinship in the reef sponge Stylissa carteri in the Red Sea.

scientific article published in June 2015

Finding Nemo's Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula

article

Finding Nemo’s Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula

article

First proteome of the egg perivitelline fluid of a freshwater gastropod with aerial oviposition

scientific article published on 13 July 2012

From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks

scientific article published on January 2013

Functionalized magnetic nanowires for chemical and magneto-mechanical induction of cancer cell death

scientific article (publication date: 24 October 2016)

Generation of diversity in the innate immune system: macrophage heterogeneity arises from gene-autonomous transcriptional probability of individual inducible genes

scientific article

Genetic control of the innate immune response

scientific article

Genome-wide analysis of mammalian promoter architecture and evolution

scientific article (publication date: June 2006)

Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle

scientific article published on 22 December 2016

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater

scientific article

Highlighting nonlinear patterns in population genetics datasets

scientific article

Histone deacetylase inhibitors decrease Toll-like receptor-mediated activation of proinflammatory gene expression by impairing transcription factor recruitment

article

Hologenome analysis of two marine sponges with different microbiomes

scientific article

Identification and analysis of chromodomain-containing proteins encoded in the mouse transcriptome

scientific article (publication date: June 2003)

Identification and predictive value of interleukin-6+ interleukin-10+ and interleukin-6- interleukin-10+ cytokine patterns in ST-elevation acute myocardial infarction

scientific article published on 29 August 2012

Inductively actuated micro needles for on-demand intracellular delivery.

scientific article published on 2 July 2018

Inflammation suppressor genes: please switch out all the lights

scientific article

Integrated approaches to uncovering transcription regulatory networks in mammalian cells

scientific article published on 08 January 2008

Interferon-γ: an overview of signals, mechanisms and functions ⬇️

scientific article (publication date: February 2004)

Intramacrophage survival of uropathogenic Escherichia coli: differences between diverse clinical isolates and between mouse and human macrophages

scientific article published on 24 May 2011

Involvement of Wnt signaling pathways in the metamorphosis of the bryozoan Bugula neritina

scientific article published on 20 March 2012

Iron-Based Core-Shell Nanowires for Combinatorial Drug Delivery and Photothermal and Magnetic Therapy

scientific article published on 18 November 2019

LPS regulates a set of genes in primary murine macrophages by antagonising CSF-1 action

scientific article

LPS regulates proinflammatory gene expression in macrophages by altering histone deacetylase expression

scientific article published on July 2006

Magnetic core-shell nanowires as MRI contrast agents for cell tracking

scientific article published on 12 March 2020

Mesenchymal stem cells cultured on magnetic nanowire substrates

scientific article published on 28 December 2016

Methamphetamine abuse affects gene expression in brain-derived microglia of SIV-infected macaques to enhance inflammation and promote virus targets

scientific article

Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding

scientific article published on July 2013

Molecular basis of parental contributions to the behavioural tolerance of elevated pCO<sub>2</sub> in a coral reef fish

scientific article published on 08 December 2021

Molecular processes of transgenerational acclimation to a warming ocean

article

Molecular signatures of transgenerational response to ocean acidification in a species of reef fish

article

Morphological characterization of virus-like particles in coral reef sponges

scientific article published in 2018

Mouse neutrophilic granulocytes express mRNA encoding the macrophage colony-stimulating factor receptor (CSF-1R) as well as many other macrophage-specific transcripts and can transdifferentiate into macrophages in vitro in response to CSF-1.

scientific article published on 16 April 2007

Non-chemotoxic induction of cancer cell death using magnetic nanowires

scientific article published on 17 March 2015

Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes

scientific article

Novel polymorphic microsatellite markers developed for a common reef sponge, Stylissa carteri

scholarly article by Emily C. Giles published in April 2013

Novel systems biology insights using antifibrotic approaches for diabetic kidney disease

scientific article published on 01 January 2010

Nuclear AGO1 Regulates Gene Expression by Affecting Chromatin Architecture in Human Cells

scientific article published on 16 October 2019

PU.1 and ICSBP control constitutive and IFN-gamma-regulated Tlr9 gene expression in mouse macrophages

scientific article

Parents exposed to warming produce offspring lower in weight and condition

scientific article published in 2022

Phenotypic and molecular consequences of stepwise temperature increase across generations in a coral reef fish

scientific article published on 24 October 2018

Phosphoregulators: protein kinases and protein phosphatases of mouse.

scientific article

Pilot studies on the parallel production of soluble mouse proteins in a bacterial expression system.

scientific article

Pirfenidone is renoprotective in diabetic kidney disease

scientific article published on 02 July 2009

Pivotal role of the muscle-contraction pathway in cryptorchidism and evidence for genomic connections with cardiomyopathy pathways in RASopathies

scientific article

Probing SWATH-MS as a tool for proteome level quantification in a non-model fish

scientific article published on 20 July 2020

Probing the S100 protein family through genomic and functional analysis

scientific article published in July 2004

Proteomic Changes Associated with Successive Reproductive Periods in Male Polychaetous Neanthes arenaceodentata

scientific article

Proteomic and metabolomic profiles of marine Vibrio sp. 010 in response to an antifoulant challenge

scientific article

Proteomic changes between male and female worms of the polychaetous annelid Neanthes arenaceodentata before and after spawning

scientific article

Proteomic profiling during the pre-competent to competent transition of the biofouling polychaete Hydroides elegans

scientific article published on September 2014

Proteomics insights: proteins related to larval attachment and metamorphosis of marine invertebrates

Quantitative analysis of oyster larval proteome provides new insights into the effects of multiple climate change stressors

scientific article

Quantitative proteomics identify molecular targets that are crucial in larval settlement and metamorphosis of Bugula neritina

scientific article published on 16 December 2010

Quantitative proteomics study of larval settlement in the Barnacle Balanus amphitrite

scientific article (publication date: 2014)

Questing for circadian dependence in ST-segment-elevation acute myocardial infarction: a multicentric and multiethnic study.

scientific article

Rapid adaptive responses to climate change in corals

article

Rapid evolution fuels transcriptional plasticity to ocean acidification

scientific article published in 2022

Rapid transcriptome and proteome profiling of a non-model marine invertebrate, Bugula neritina

scientific article published on August 2010

Research priorities for the sustainability of coral-rich western Pacific seascapes

Revealing microbial functional activities in the Red Sea sponge Stylissa carteri by metatranscriptomics

scientific article

SECOM: a novel hash seed and community detection based-approach for genome-scale protein domain identification

scientific article

Selective phosphorylation during early macrophage differentiation

scientific article published on 26 August 2015

Semi-automated quantification of living cells with internalized nanostructures

scientific article

Sex Change in Clownfish: Molecular Insights from Transcriptome Analysis.

scientific article published on 17 October 2016

Sex- and time-specific parental effects of warming on reproduction and offspring quality in a coral reef fish

scientific article published on 13 January 2021

Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling

scientific article (publication date: 31 October 2016)

Species-specific molecular responses of wild coral reef fishes during a marine heatwave

scientific article published on 18 March 2020

Specificity and transcriptional activity of microbiota associated with low and high microbial abundance sponges from the Red Sea.

scientific article

Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome

scientific article

Systems biology of innate immunity

scientific article

Systems biology of transcription control in macrophages

scientific article published on December 2007

The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes

scientific article

The JNK are important for development and survival of macrophages

scientific article published on February 2006

The alternative splicing landscape of a coral reef fish during a marine heatwave

scientific article published on 18 March 2022

The co-transcriptome of uropathogenic Escherichia coli-infected mouse macrophages reveals new insights into host-pathogen interactions

scientific article published on 24 January 2015

The effects of climate change on the ecology of fishes

scientific article published in 2023

The epigenetic landscape of transgenerational acclimation to ocean warming

article

The evolution of ultraconserved elements with different phylogenetic origins

scientific article

The sponge microbiome project

scientific article published on October 2017

The transcriptional landscape of the mammalian genome

scientific article

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

scientific article

Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs

scientific article published in April 2006

Transcription factor Tfec contributes to the IL-4-inducible expression of a small group of genes in mouse macrophages including the granulocyte colony-stimulating factor receptor

scientific article

Transcriptional network dynamics in macrophage activation

scientific article published on 12 May 2006

Transcriptome analysis elucidates key developmental components of bryozoan lophophore development

scientific article published on 10 October 2014

Transcriptome and Proteome Studies Reveal Candidate Attachment Genes during the Development of the Barnacle Amphibalanus Amphitrite

Transcriptome and proteome dynamics in larvae of the barnacle Balanus Amphitrite from the Red Sea.

scientific article published on 15 December 2015

Transcriptome and quantitative proteome analysis reveals molecular processes associated with larval metamorphosis in the polychaete Pseudopolydora vexillosa

scientific article published on 29 January 2013

Unexpected complexity of the reef-building coral Acropora millepora transcription factor network ⬇️

scientific article

miRNA Repertoires of Demosponges Stylissa carteri and Xestospongia testudinaria

scientific article

List of works by Timothy Ravasi

A chromosome-scale genome assembly of the false clownfish, Amphiprion ocellaris

A promoter-level mammalian expression atlas

A systems approach to delineate functions of paralogous transcription factors: role of the Yap family in the DNA damage response.

Actinomycetes from Red Sea sponges: sources for chemical and phylogenetic diversity

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

An Inflammatory Role for the Mammalian Carboxypeptidase Inhibitor Latexin: Relationship to Cystatins and the Tumor Suppressor TIG1

An atlas of combinatorial transcriptional regulation in mouse and man

An integrated systems analysis implicates EGR1 downregulation in simian immunodeficiency virus encephalitis-induced neural dysfunction

An interplay between plasticity and parental phenotype determines impacts of ocean acidification on a reef fish

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

Anti-cancer agents in Saudi Arabian herbals revealed by automated high-content imaging

Astrocyte-specific overexpressed gene signatures in response to methamphetamine exposure in vitro

Bacterial community profiles in low microbial abundance sponges

Beyond buying time: the role of plasticity in phenotypic adaptation to rapid environmental change

Characterization of piRNAs across postnatal development in mouse brain.

Co-transcriptomic Analysis by RNA Sequencing to Simultaneously Measure Regulated Gene Expression in Host and Bacterial Pathogen

Coevolution within a transcriptional network by compensatory trans and cis mutations.

Concordant epigenetic silencing of transforming growth factor-beta signaling pathway genes occurs early in breast carcinogenesis.

Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage

Correction: miRNA Repertoires of Demosponges Stylissa carteri and Xestospongia testudinaria

Corrigendum: Genome-wide analysis of mammalian promoter architecture and evolution

Cytotoxic effects of nickel nanowires in human fibroblasts

Cytotoxicity and intracellular dissolution of nickel nanowires.

Defining the protein interaction network of human malaria parasite Plasmodium falciparum ⬇️

Dependency on de novo protein synthesis and proteomic changes during metamorphosis of the marine bryozoan Bugula neritina

Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49

Dynamic epigenetic control of highly conserved noncoding elements

Erratum: From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks

Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering

Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome

Exploitation of genetic interaction network topology for the prediction of epistatic behavior

Exploring seascape genetics and kinship in the reef sponge Stylissa carteri in the Red Sea.

Finding Nemo's Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula

Finding Nemo’s Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula

First proteome of the egg perivitelline fluid of a freshwater gastropod with aerial oviposition

From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks

Functionalized magnetic nanowires for chemical and magneto-mechanical induction of cancer cell death

Generation of diversity in the innate immune system: macrophage heterogeneity arises from gene-autonomous transcriptional probability of individual inducible genes

Genetic control of the innate immune response

Genome-wide analysis of mammalian promoter architecture and evolution

Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater

Highlighting nonlinear patterns in population genetics datasets

Histone deacetylase inhibitors decrease Toll-like receptor-mediated activation of proinflammatory gene expression by impairing transcription factor recruitment

Hologenome analysis of two marine sponges with different microbiomes

Identification and analysis of chromodomain-containing proteins encoded in the mouse transcriptome

Identification and predictive value of interleukin-6+ interleukin-10+ and interleukin-6- interleukin-10+ cytokine patterns in ST-elevation acute myocardial infarction

Inductively actuated micro needles for on-demand intracellular delivery.

Inflammation suppressor genes: please switch out all the lights

Integrated approaches to uncovering transcription regulatory networks in mammalian cells

Interferon-γ: an overview of signals, mechanisms and functions ⬇️

Intramacrophage survival of uropathogenic Escherichia coli: differences between diverse clinical isolates and between mouse and human macrophages

Involvement of Wnt signaling pathways in the metamorphosis of the bryozoan Bugula neritina

Iron-Based Core-Shell Nanowires for Combinatorial Drug Delivery and Photothermal and Magnetic Therapy

LPS regulates a set of genes in primary murine macrophages by antagonising CSF-1 action

LPS regulates proinflammatory gene expression in macrophages by altering histone deacetylase expression

Magnetic core-shell nanowires as MRI contrast agents for cell tracking

Mesenchymal stem cells cultured on magnetic nanowire substrates

Methamphetamine abuse affects gene expression in brain-derived microglia of SIV-infected macaques to enhance inflammation and promote virus targets

Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding

Molecular basis of parental contributions to the behavioural tolerance of elevated pCO<sub>2</sub> in a coral reef fish

Molecular processes of transgenerational acclimation to a warming ocean

Molecular signatures of transgenerational response to ocean acidification in a species of reef fish

Morphological characterization of virus-like particles in coral reef sponges

Mouse neutrophilic granulocytes express mRNA encoding the macrophage colony-stimulating factor receptor (CSF-1R) as well as many other macrophage-specific transcripts and can transdifferentiate into macrophages in vitro in response to CSF-1.

Non-chemotoxic induction of cancer cell death using magnetic nanowires

Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes

Novel polymorphic microsatellite markers developed for a common reef sponge, Stylissa carteri

Novel systems biology insights using antifibrotic approaches for diabetic kidney disease

Nuclear AGO1 Regulates Gene Expression by Affecting Chromatin Architecture in Human Cells

PU.1 and ICSBP control constitutive and IFN-gamma-regulated Tlr9 gene expression in mouse macrophages

Parents exposed to warming produce offspring lower in weight and condition

Phenotypic and molecular consequences of stepwise temperature increase across generations in a coral reef fish

Phosphoregulators: protein kinases and protein phosphatases of mouse.

Pilot studies on the parallel production of soluble mouse proteins in a bacterial expression system.

Pirfenidone is renoprotective in diabetic kidney disease

Pivotal role of the muscle-contraction pathway in cryptorchidism and evidence for genomic connections with cardiomyopathy pathways in RASopathies

Probing SWATH-MS as a tool for proteome level quantification in a non-model fish

Probing the S100 protein family through genomic and functional analysis