Author details

Full Name

Raghothama Chaerkady

Affiliation

ORCID

Career Start Year

1994

Papers

107

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37228288	Multiomics links global surfactant dysregulation with airflow obstruction and emphysema in COPD.		2023
37925433	A TRIM21-based bioPROTAC highlights the therapeutic benefit of HuR degradation.		2023
35228567	Comparative systeomics to elucidate physiological differences between CHO and SP2/0 cell lines.	Scientific Reports	2022
35030984	Mitochondrial membrane potential-enriched CHO host: a novel and powerful tool for improving biomanufacturing capability.	mAbs	2022
33653945	Resistance to Pyrrolobenzodiazepine Dimers Is Associated with SLFN11 Downregulation and Can Be Reversed through Inhibition of ATR.	Molecular Cancer Therapeutics	2021
34008986	Characterization of Citrullination Sites in Neutrophils and Mast Cells Activated by Ionomycin via Integration of Mass Spectrometry and Machine Learning.	Journal of Proteome Research	2021
32966064	Development of a Parallel Reaction Monitoring Mass Spectrometry Assay for the Detection of SARS-CoV-2 Spike Glycoprotein and Nucleoprotein.	Analytical Chemistry	2020
31020842	Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements.	J Proteome Res	2019
30985291	Staphylococcus aureus drives expansion of low-density neutrophils in diabetic mice.	J Clin Invest	2019
30974046	Actomyosin contraction during cellularization is regulated in part by Src64 control of Actin 5C protein levels.	Genesis	2019
29281288	Reverse and Random Decoy Methods for False Discovery Rate Estimation in High Mass Accuracy Peptide Spectral Library Searches.	Journal of Proteome Research	2018
30479584	Correction to: Quantitative phosphoproteomic analysis reveals reciprocal activation of receptor tyrosine kinases between cancer epithelial cells and stromal fibroblasts.	Clinical Proteomics	2018
29946230	Quantitative phosphoproteomic analysis reveals reciprocal activation of receptor tyrosine kinases between cancer epithelial cells and stromal fibroblasts.	Clinical Proteomics	2018
30323221	Evidence for a direct link between PAD4-mediated citrullination and the oxidative burst in human neutrophils.	Scientific Reports	2018
29400603	A novel bicistronic gene design couples stable cell line selection with a fucose switch in a designer CHO host to produce native and afucosylated glycoform antibodies.	MAbs	2018
29228324	USP9X controls translation efficiency via deubiquitination of eukaryotic translation initiation factor 4A1.	Nucleic Acids Research	2018
27164173	Plasma Selenium Protein P Isoform 1 (SEPP1): A Predictor of Selenium Status in Nepalese Children Detected by Plasma Proteomics.	International Journal for Vitamin and Nutrition Research	2017
28993780	Spontaneous Secretion of the Citrullination Enzyme PAD2 and Cell Surface Exposure of PAD4 by Neutrophils.	Frontiers in Immunology	2017
28331001	Quantitative Tyrosine Phosphoproteomics of Epidermal Growth Factor Receptor (EGFR) Tyrosine Kinase Inhibitor-treated Lung Adenocarcinoma Cells Reveals Potential Novel Biomarkers of Therapeutic Response.	Mol Cell Proteomics	2017
28745510	Statistical Models for the Analysis of Isobaric Tags Multiplexed Quantitative Proteomics.	Journal of Proteome Research	2017
28876938	Lessons from the Hamster: Cricetulus griseus Tissue and CHO Cell Line Proteome Comparison.	Journal of Proteome Research	2017
28653853	Post-Translational Modifications (PTMs), Identified on Endogenous Huntingtin, Cluster within Proteolytic Domains between HEAT Repeats.	Journal of Proteome Research	2017
27486686	Quantitative Proteomic Analysis Reveals Similarities between Huntington's Disease (HD) and Huntington's Disease-Like 2 (HDL2) Human Brains.	Journal of Proteome Research	2016
27218149	FOXE3 contributes to Peters anomaly through transcriptional regulation of an autophagy-associated protein termed DNAJB1.	Nature Communications	2016
26418914	Elucidation of the CHO Super-Ome (CHO-SO) by Proteoinformatics.	J Proteome Res	2015
25666620	Communication between the N and C termini is required for copper-stimulated Ser/Thr phosphorylation of Cu(I)-ATPase (ATP7B).	Journal of Biological Chemistry	2015
25404012	Identifying novel targets of oncogenic EGF receptor signaling in lung cancer through global phosphoproteomics.	Proteomics	2015
25354783	Identification of miR-145 targets through an integrated omics analysis.	Mol Biosyst	2015
25263469	Quantitative phosphoproteomics reveals crosstalk between phosphorylation and O-GlcNAc in the DNA damage response pathway.	Proteomics	2015
25807139	Proteomic Signature of Endothelial Dysfunction Identified in the Serum of Acute Ischemic Stroke Patients by the iTRAQ-Based LC-MS Approach.	Journal of Proteome Research	2015
26356563	Global phosphotyrosine survey in triple-negative breast cancer reveals activation of multiple tyrosine kinase signaling pathways.	Oncotarget	2015
26542228	A multi-omic analysis of human naÃ¯ve CD4+ T cells.	BMC Syst Biol	2015
26251448	The NHERF2 sequence adjacent and upstream of the ERM-binding domain affects NHERF2-ezrin binding and dexamethasone stimulated NHE3 activity.	Biochem J	2015
26032504	Ablation of Dicer leads to widespread perturbation of signaling pathways.	Biochemical and Biophysical Research Communications	2015
25056907	Identification of putative biomarkers for HIV-associated neurocognitive impairment in the CSF of HIV-infected patients under cART therapy determined by mass spectrometry.	J Neurovirol	2014
24870542	A draft map of the human proteome.	Nature	2014
25247763	Activation of diverse signalling pathways by oncogenic PIK3CA mutations.	Nat Commun	2014
24769236	Regulation of PPAR-alpha pathway by Dicer revealed through proteomic analysis.	Journal of Proteomics	2014
24657443	Identification of prosaposin and transgelin as potential biomarkers for gallbladder cancer using quantitative proteomics.	Biochem Biophys Res Commun	2014
25060758	Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis.	Mol Cell Proteomics	2014
23727491	The keratoconus corneal proteome: loss of epithelial integrity and stromal degeneration.	Journal of Proteomics	2013
24086712	Integrated proteomic and metabolic analysis of breast cancer progression.	PLoS One	2013
23785281	The Escherichia coli phosphotyrosine proteome relates to core pathways and virulence.	PLoS Pathog	2013
23521751	Quantitative proteomics for identifying biomarkers for Rabies.	Clinical Proteomics	2013
23161554	SILAC-based quantitative proteomic analysis of gastric cancer secretome.	Proteomics - Clinical Applications	2013
21597922	Transcriptomic and proteomic profiling of KEAP1 disrupted and sulforaphane-treated human breast epithelial cells reveals common expression profiles.	Breast Cancer Research and Treatment	2012
22971049	Proteomic analysis of Chinese hamster ovary cells.	J Proteome Res	2012
22345495	TSLP signaling network revealed by SILAC-based phosphoproteomics.	Mol Cell Proteomics	2012
22737227	Genome-wide profiling of pluripotent cells reveals a unique molecular signature of human embryonic germ cells.	PLoS One	2012
22539434	A proteogenomic approach to map the proteome of an unsequenced pathogen - Leishmania donovani.	Proteomics	2012