Author details

Full Name

Damian Fermin

Affiliation

ORCID

Career Start Year

2006

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36627643	Single-cell transcriptomics reveals a mechanosensitive injury signaling pathway in early diabetic nephropathy.	Genome Med	2023
36208288	A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.).	DNA Res	2023
37580326	An integrated organoid omics map extends modeling potential of kidney disease.	Nat Commun	2023
37626123	MLL-AF4 cooperates with PAF1 and FACT to drive high-density enhancer interactions in leukemia.	Nat Commun	2023
36637914	SGLT2 inhibitors mitigate kidney tubular metabolic and mTORC1 perturbations in youth-onset type 2 diabetes.	J Clin Invest	2023
34732507	Discovery of Autoantibodies Targeting Nephrin in Minimal Change Disease Supports a Novel Autoimmune Etiology.	J Am Soc Nephrol	2022
35763030	Genome-wide meta-analysis and omics integration identifies novel genes associated with diabetic kidney disease.	Diabetologia	2022
36006643	Comparing Kidney Health Outcomes in Children, Adolescents, and Adults With Focal Segmental Glomerulosclerosis.	JAMA Netw Open	2022
36331122	Multi-Scalar Data Integration Links Glomerular Angiopoietin-Tie Signaling Pathway Activation With Progression of Diabetic Kidney Disease.	Diabetes	2022
36055599	Molecular programs associated with glomerular hyperfiltration in early diabetic kidney disease.	Kidney Int	2022
36550108	Epigenome-wide meta-analysis identifies DNA methylation biomarkers associated with diabetic kidney disease.	Nat Commun	2022
34929253	A glomerular transcriptomic landscape of apolipoprotein L1 in Black patients with focal segmental glomerulosclerosis.	Kidney Int	2022
33863784	A Rare Autosomal Dominant Variant in Regulator of Calcineurin Type 1 (<i>RCAN1</i>) Gene Confers Enhanced Calcineurin Activity and May Cause FSGS.	J Am Soc Nephrol	2021
33038424	SARS-CoV-2 receptor networks in diabetic and COVID-19-associated kidney disease.	Kidney Int	2020
31930623	A protein-centric approach for exome variant aggregation enables sensitive association analysis with clinical outcomes.	Hum Mutat	2020
31312515	iOmicsPASS: network-based integration of multiomics data for predictive subnetwork discovery.	NPJ Syst Biol Appl	2019
31073028	Disruption of the exocyst induces podocyte loss and dysfunction.	Journal of Biological Chemistry	2019
31015462	Sex-specific and pleiotropic effects underlying kidney function identified from GWAS meta-analysis.	Nat Commun	2019
30057032	An eQTL Landscape of Kidney Tissue in Human Nephrotic Syndrome.	Am J Hum Genet	2018
29371955	A comparative global phosphoproteomics analysis of obinutuzumab (GA101) versus rituximab (RTX) against RTX sensitive and resistant Burkitt lymphoma (BL) demonstrates differential phosphorylation of signaling pathway proteins after treatment.	Oncotarget	2017
28607076	Functional proteogenomics reveals biomarkers and therapeutic targets in lymphomas.	Proc Natl Acad Sci U S A	2017
27119218	SAINTq: Scoring protein-protein interactions in affinity purification - mass spectrometry experiments with fragment or peptide intensity data.	Proteomics	2016
26254008	QPROT: Statistical method for testing differential expression using protein-level intensity data in label-free quantitative proteomics.	J Proteomics	2015
25913743	EBprot: Statistical analysis of labeling-based quantitative proteomics data.	Proteomics	2015
25429062	LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data.	Bioinformatics	2015
25466511	Differential proteomic analysis of endemic and sporadic Epstein-Barr virus-positive and negative Burkitt lymphoma.	European Journal of Cancer	2015
26181434	Research Resource: Androgen Receptor Activity Is Regulated Through the Mobilization of Cell Surface Receptor Networks.	Mol Endocrinol	2015
24667141	Global phosphoproteomic profiling reveals distinct signatures in B-cell non-Hodgkin lymphomas.	Am J Pathol	2014
23325620	Sparsely correlated hidden Markov models with application to genome-wide location studies.	Bioinformatics	2013
23814019	Integrated phosphoproteomic and metabolomic profiling reveals NPM-ALK-mediated phosphorylation of PKM2 and metabolic reprogramming in anaplastic large cell lymphoma.	Blood	2013
24135919	Reconstructing targetable pathways in lung cancer by integrating diverse omics data.	Nat Commun	2013
23921808	The CRAPome: a contaminant repository for affinity purification-mass spectrometry data.	Nat Methods	2013
23918812	LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach.	Mol Cell Proteomics	2013
22179823	NPM-ALK signals through glycogen synthase kinase 3Î² to promote oncogenesis.	Oncogene	2012
22329341	Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data.	J Proteome Res	2012
21131968	SAINT: probabilistic scoring of affinity purification-mass spectrometry data.	Nat Methods	2011
21360675	Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis.	Proteomics	2011
21448452	Metabolites of purine nucleoside phosphorylase (NP) in serum have the potential to delineate pancreatic adenocarcinoma.	PLoS One	2011
19955085	Quantitative proteomic profiling of prostate cancer reveals a role for miR-128 in prostate cancer.	Mol Cell Proteomics	2010
20706591	SAW: a method to identify splicing events from RNA-Seq data based on splicing fingerprints.	PLoS ONE	2010
20455209	Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets.	Proteomics	2010
19118015	Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer.	Cancer Res	2009
19594485	Calorie restriction alters mitochondrial protein acetylation.	Aging Cell	2009
18644780	Significance analysis of spectral count data in label-free shotgun proteomics.	Mol Cell Proteomics	2008
17411398	Evolutionary-conserved gene expression response profiles across mammalian tissues.	OMICS	2007
16525410	Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study.	Nat Biotechnol	2006
16646984	Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.	Genome Biol	2006