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List of works by Nathan Salomonis

A mouse mammary gland involution mRNA signature identifies biological pathways potentially associated with breast cancer metastasis

scientific article published on 30 April 2009

A robust method to derive functional neural crest cells from human pluripotent stem cells

scientific article published on 30 June 2013

AKAP13 Rho-GEF and PKD-binding domain deficient mice develop normally but have an abnormal response to β-adrenergic-induced cardiac hypertrophy

scientific article

ANOSVA: a statistical method for detecting splice variation from expression data

scientific article

Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia

scientific article published on 13 May 2019

AltAnalyze and DomainGraph: analyzing and visualizing exon expression data

scientific article

Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors

scientific article

Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cells

scientific article

Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation

scientific article

An Introduction to Pathway Analysis with GenMAPP

Analyzing alternative splicing data of splice junction arrays from Parkinson patients' leukocytes before and after deep brain stimulation as compared with control donors

scientific article

Asymmetrically Segregated Mitochondria Provide Cellular Memory of Hematopoietic Stem Cell Replicative History and Drive HSC Attrition

scientific article published on 13 February 2020

Author Correction: Single-cell analysis of mixed-lineage states leading to a binary cell fate choice

scientific article published on 01 May 2019

Combinatorial Single-Cell Analyses of Granulocyte-Monocyte Progenitor Heterogeneity Reveals an Early Uni-potent Neutrophil Progenitor

scientific article published on 22 June 2020

Cross-platform single cell analysis of kidney development shows stromal cells express Gdnf

scientific article

Cxcr3-expressing leukocytes are necessary for neurofibroma formation in mice

scientific article published on 07 February 2019

DNMT3A Haploinsufficiency Transforms FLT3ITD Myeloproliferative Disease into a Rapid, Spontaneous, and Fully Penetrant Acute Myeloid Leukemia

scientific article

DR-06REACTIVE OXYGEN SPECIES MEDIATE THERAPEUTIC RESPONSE AND RESISTANCE IN GLIOBLASTOMA

scientific article published in November 2014

DeepImmuno: Deep learning-empowered prediction and generation of immunogenic peptides for T cell immunity

scientific article published on 24 December 2020

Defective transcription elongation in a subset of cancers confers immunotherapy resistance

scientific article published in Nature Communications

Deficiency of the lipid synthesis enzyme, DGAT1, extends longevity in mice ⬇️

scientific article published on January 1, 2012

Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis

scientific article published in Nature Communications

Differential transcriptome response to proton versus X-ray radiation reveals novel candidate targets for combinatorial PT therapy in lymphoma

scientific article published on 20 October 2020

DoubletDecon: Cell-State Aware Removal of Single-Cell RNA-Seq Doublets

scholarly article published 8 July 2018

DoubletDecon: Deconvoluting Doublets from Single-Cell RNA-Sequencing Data

scientific article published on 01 November 2019

FOXO activity adaptation safeguards the hematopoietic stem cell compartment in hyperglycemia

scientific article published on 01 November 2020

G(i)-coupled GPCR signaling controls the formation and organization of human pluripotent colonies

scientific article (publication date: 2009)

GO-Elite: a flexible solution for pathway and ontology over-representation

scientific article

Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies

scientific article published on 03 November 2021

GenMAPP 2: new features and resources for pathway analysis

scientific article

Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A.

scientific article

Granulocyte-Monocyte Progenitors and Monocyte-Dendritic Cell Progenitors Independently Produce Functionally Distinct Monocytes.

scientific article published in November 2017

IL-1 signaling mediates intrauterine inflammation and chorio-decidua neutrophil recruitment and activation.

scientific article published on 22 March 2018

Identification of Spt5 target genes in zebrafish development reveals its dual activity in vivo

scientific article

Identifying genetic networks underlying myometrial transition to labor

scientific article

In situ mapping identifies distinct vascular niches for myelopoiesis

scientific article

Integrated Genomic Analysis of Diverse Induced Pluripotent Stem Cells from the Progenitor Cell Biology Consortium

scientific article

Integrative Analysis of Proteomics Data to Obtain Clinically Relevant Markers

scientific article published on 18 November 2017

Intragraft Antiviral-Specific Gene Expression as a Distinctive Transcriptional Signature for Studies in Polyomavirus-Associated Nephropathy.

scientific article published on 2 May 2016

Intrinsic Age-Dependent Changes and Cell-Cell Contacts Regulate Nephron Progenitor Lifespan

scientific article published in October 2015

Investigating Cell Fate Decisions with ICGS Analysis of Single Cells

scientific article published on 01 January 2019

KIF3A genetic variation is associated with pediatric asthma in the presence of eczema independent of allergic rhinitis

scientific article published on 23 February 2017

Lentiviral vectors and protocols for creation of stable hESC lines for fluorescent tracking and drug resistance selection of cardiomyocytes

scientific article

Loaded, locked, drawn: kSORT validated for patient samples

scientific article published on 14 November 2016

Long non-coding RNA and alternative splicing modulations in Parkinson's leukocytes identified by RNA sequencing

scientific article

MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data

scientific article

MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data

scientific article

MBNL1 regulates essential alternative RNA splicing patterns in MLL-rearranged leukemia

scientific article published on 12 May 2020

Mammary gland involution as a multi-step process

scientific article published on March 2007

Maturation of heart valve cell populations during postnatal remodeling

scientific article published on 12 March 2019

Molecular Characterization of Pediatric Restrictive Cardiomyopathy from Integrative Genomics

scientific article published on 18 January 2017

Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives

scientific article

Monocyte and bone marrow macrophage transcriptional phenotypes in systemic juvenile idiopathic arthritis reveal TRIM8 as a mediator of IFN-γ hyper-responsiveness and risk for macrophage activation syndrome

scientific article published on 04 December 2020

Mosaic: making biological sense of complex networks

scientific article

Mouse models of neutropenia reveal progenitor-stage-specific defects

scientific article published on 22 April 2020

Obesity alters the long-term fitness of the hematopoietic stem cell compartment through modulation of Gfi1 expression.

scientific article published on 27 December 2017

PHIP as a therapeutic target for driver-negative subtypes of melanoma, breast, and lung cancer

scientific article published on 04 June 2018

PHIP drives glioblastoma motility and invasion by regulating the focal adhesion complex

scientific article published on 09 April 2020

Pathobiological Pseudohypoxia as a Putative Mechanism Underlying Myelodysplastic Syndromes

scientific article published on 23 August 2018

Pbx4 limits heart size and fosters arch artery formation by partitioning second heart field progenitors and restricting proliferation

scientific article published on 02 March 2020

Protocol for Identification and Removal of Doublets with DoubletDecon

scientific article published on 11 August 2020

Publisher Correction: MBNL1 regulates essential alternative RNA splicing patterns in MLL-rearranged leukemia

scientific article published on 07 July 2020

Rational targeting Cdc42 restrains Th2 cell differentiation and prevents allergic airway inflammation

scientific article published on 13 November 2018

Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF

scientific article published on 24 March 2020

SKI controls MDS-associated chronic TGF-β signaling, aberrant splicing, and stem cell fitness

scientific article published on 24 September 2018

Single-cell analysis of mixed-lineage states leading to a binary cell fate choice.

scientific article published on 31 August 2016

Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers

scientific article published on 11 December 2020

Small RNA sequencing-microarray analyses in Parkinson leukocytes reveal deep brain stimulation-induced splicing changes that classify brain region transcriptomes ⬇️

scientific article published on 13 May 2013

Stem cell pluripotency: Alternative modes of transcription regulation ⬇️

scientific article published on August 2, 2010

Synthetic Gene Network with Positive Feedback Loop Amplifies Cellulase Gene Expression in Neurospora crassa

scientific article published on 20 April 2018

Systems biology evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity

scientific article published on 22 October 2015

Systems-level perspective of sudden infant death syndrome

scientific article

TRAF6 Mediates Basal Activation of NF-κB Necessary for Hematopoietic Stem Cell Homeostasis

scientific article published in January 2018

The Human Cell Atlas bone marrow single-cell interactive web portal

scientific article published on 21 September 2018

The Molecular Signature of Megakaryocyte-Erythroid Progenitors Reveals a Role for the Cell Cycle in Fate Specification

scientific article published on 01 December 2018

The Molecular Signature of Megakaryocyte-Erythroid Progenitors Reveals a Role for the Cell Cycle in Fate Specification

scientific article published on 01 November 2018

The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution

scientific article published on 28 March 2019

The identification of novel potential injury mechanisms and candidate biomarkers in renal allograft rejection by quantitative proteomics

scientific article published on 12 December 2013

The kSORT assay to detect renal transplant patients at high risk for acute rejection: results of the multicenter AART study

scientific article

Time- and exercise-dependent gene regulation in human skeletal muscle ⬇️

scientific article published on September 25, 2003

Tissues Harvested Using an Automated Surgical Approach Confirm Molecular Heterogeneity of Glioblastoma and Enhance Specimen's Translational Research Value

scientific article published on 23 October 2019

Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity

scientific article published on 16 April 2018

Transcriptional Perturbations in Graft Rejection

scientific article published on 03 July 2015

Transcriptomic and epigenomic differences in human induced pluripotent stem cells generated from six reprogramming methods

scientific article published on 03 October 2017

U2AF1 mutations induce oncogenic IRAK4 isoforms and activate innate immune pathways in myeloid malignancies

scientific article published on 22 April 2019

Ubiquitination of hnRNPA1 by TRAF6 links chronic innate immune signaling with myelodysplasia.

scientific article

Unraveling bone marrow architecture

scientific article published on 01 January 2020

Whole transcriptome RNA sequencing data from blood leukocytes derived from Parkinson's disease patients prior to and following deep brain stimulation treatment

scientific article

Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data

scientific article

cellHarmony: Cell-level matching and comparison of single-cell transcriptomes

cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes

scientific article published on 01 December 2019

miR-196b target screen reveals mechanisms maintaining leukemia stemness with therapeutic potential

scientific article published on 11 July 2018

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