List of works - Judith Klein-Seetharaman

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

scientific article

A minimal ligand binding pocket within a network of correlated mutations identified by multiple sequence and structural analysis of G protein coupled receptors ⬇️

scientific article published on June 29, 2012

A mitochondria-targeted inhibitor of cytochrome c peroxidase mitigates radiation-induced death

journal article published in 2011

A mitochondrial pathway for biosynthesis of lipid mediators

journal article published in 2014

A mixture of feature experts approach for protein-protein interaction prediction

scientific article

Additive effects of chlorin e6 and metal ion binding on the thermal stability of rhodopsin in vitro

scientific article published in March 2009

Adsorption of surfactant lipids by single-walled carbon nanotubes in mouse lung upon pharyngeal aspiration

journal article published in 2012

Allosteric Modulation of G Protein Coupled Receptors by Cytoplasmic, Transmembrane and Extracellular Ligands

scientific article published on October 2010

Alternative paths in HIV-1 targeted human signal transduction pathways

scientific article

BIPS: BIANA Interolog Prediction Server. A tool for protein–protein interaction inference ⬇️

scientific article published on June 11, 2012

Biodegradation of single-walled carbon nanotubes by eosinophil peroxidase

journal article published in 2013

Carbon nanotubes degraded by neutrophil myeloperoxidase induce less pulmonary inflammation

journal article published in 2010

Cardiolipin Interactions with Proteins

scientific article

Cardiolipin externalization to the outer mitochondrial membrane acts as an elimination signal for mitophagy in neuronal cells

journal article published in 2013

Cardiolipin signaling mechanisms: collapse of asymmetry and oxidation

journal article published in 2015

Characterization of membrane protein non-native states. 1. Extent of unfolding and aggregation of rhodopsin in the presence of chemical denaturants

scientific article published on August 2010

Characterization of membrane protein non-native states. 2. The SDS-unfolded states of rhodopsin

scientific article published on August 2010

Characterization of the simultaneous decay kinetics of metarhodopsin states II and III in rhodopsin by solution-state NMR spectroscopy

scientific article published on 6 February 2014

Chlorophyll-Derivative Modulation of Rhodopsin Signaling Properties through Evolutionarily Conserved Interaction Pathways

scientific article published on 12 December 2017

Combined inhibition of PLC{gamma}-1 and c-Src abrogates epidermal growth factor receptor-mediated head and neck squamous cell carcinoma invasion

scientific article

Comparing human-Salmonella with plant-Salmonella protein-protein interaction predictions

scientific article published on 28 January 2015

Comparison of probabilistic combination methods for protein secondary structure prediction

scientific article

Comparison of the molecular properties of retinitis pigmentosa P23H and N15S amino acid replacements in rhodopsin.

scientific article published on 17 May 2019

Determining confidence of predicted interactions between HIV-1 and human proteins using conformal method ⬇️

scientific article published on January 1, 2012

Dichotomous roles for externalized cardiolipin in extracellular signaling: promotion of phagocytosis and attenuation of innate immunity

journal article published in 2015

Differential dynamics in the G protein-coupled receptor rhodopsin revealed by solution NMR.

scholarly article

Differential dynamics of extracellular and cytoplasmic domains in denatured States of rhodopsin

scientific article

Discovering pathways by orienting edges in protein interaction networks

scientific article

Dual function of mitochondrial Nm23-H4 protein in phosphotransfer and intermembrane lipid transfer: a cardiolipin-dependent switch

journal article published in 2013

Dual role of interactions between membranous and soluble portions of helical membrane receptors for folding and signaling

scientific article

Dynamics in rhodopsin

scientific article

Early integration of the individual student in academic activities: a novel classroom concept for graduate education in molecular biophysics and structural biology

scientific article

Evaluation of different biological data and computational classification methods for use in protein interaction prediction

scientific article

Flexibility of the cytoplasmic domain of the phototaxis transducer II from Natronomonas pharaonis

scientific article

Glutamic acid-rich proteins of rod photoreceptors are natively unfolded

scientific article published on 9 November 2005

Heterolytic reduction of fatty acid hydroperoxides by cytochrome c/cardiolipin complexes: antioxidant function in mitochondria.

scientific article published in August 2009

Human immunodeficiency virus type 1 Vpr: oligomerization is an essential feature for its incorporation into virus particles

scientific article

Identification of Motions in Membrane Proteins by Elastic Network Models and Their Experimental Validation ⬇️

scientific article published on January 1, 2012

Identification of core amino acids stabilizing rhodopsin

scientific article

Isotope Labeling in Insect Cells ⬇️

scientific article published on January 1, 2012

Isotope Labeling in Mammalian Cells ⬇️

scientific article published on January 1, 2012

Isotope labeling of mammalian GPCRs in HEK293 cells and characterization of the C-terminus of bovine rhodopsin by high resolution liquid NMR spectroscopy

scientific article published on 13 November 2007

Known unknowns of cardiolipin signaling: the best is yet to come

journal article published in 2017

Ligand-independent antiapoptotic function of estrogen receptor-beta in lung cancer cells

scientific article published on 21 July 2010

Lipid bodies containing oxidatively truncated lipids block antigen cross-presentation by dendritic cells in cancer

scientific article

Long-range interactions within a nonnative protein

scientific article published in March 2002

Mechanistic investigations of horseradish peroxidase-catalyzed degradation of single-walled carbon nanotubes

journal article published in 2009

Mitochondrial redox opto-lipidomics reveals mono-oxygenated cardiolipins as pro-apoptotic death signals

journal article published in 2016

Mitochondrial targeting of electron scavenging antioxidants: regulation of selective oxidation vs random chain reactions

journal article published in 2009

Molecular speciation and dynamics of oxidized triacylglycerols in lipid droplets: mass spectrometry and coarse-grained simulations

journal article published in 2014

Multitask Matrix Completion for Learning Protein Interactions Across Diseases

scientific article

Multitask learning for host-pathogen protein interactions

scientific article published on July 2013

NMR spectroscopy of phosphorylated wild-type rhodopsin: mobility of the phosphorylated C-terminus of rhodopsin in the dark and upon light activation

scientific article published in February 2004

NMR-based screening of membrane protein ligands

scientific article published on March 2010

Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis

scientific article

Oxidized lipids block antigen cross-presentation by dendritic cells in cancer

scientific article

Prediction and comparison of Salmonella-human and Salmonella-Arabidopsis interactomes

scientific article published on May 2012

Prediction of interactions between HIV-1 and human proteins by information integration.

scientific article published on January 2009

Preferential binding of allosteric modulators to active and inactive conformational states of metabotropic glutamate receptors

scientific article

Protein complex identification by supervised graph local clustering

scientific article published on July 2008

Refining literature curated protein interactions using expert opinions

scientific article published on January 2015

Retinal proteins as model systems for membrane protein folding

scientific article published on 12 December 2013

Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins ⬇️

scientific article published on September 15, 2010

Shape and oligomerization state of the cytoplasmic domain of the phototaxis transducer II from Natronobacterium pharaonis

scholarly article

Similarity of the non-amyloid-β component and C-terminal tail of monomeric and tetrameric alpha-synuclein with 14-3-3 sigma

scientific article published on 14 September 2021

Specificity of lipoprotein-associated phospholipase A(2) toward oxidized phosphatidylserines: liquid chromatography-electrospray ionization mass spectrometry characterization of products and computer modeling of interactions

journal article published in 2012

Structural and Functional Consequences of the Weak Binding of Chlorin e6 to Bovine Rhodopsin

scientific article published on 12 March 2019

Structural characterization of cardiolipin-driven activation of cytochrome C into a peroxidase and membrane perturbation

journal article published in 2018

Structure and dynamics of the insulin receptor: implications for receptor activation and drug discovery.

scientific article

Systematic prediction of human membrane receptor interactions

scientific article

TMpro web server and web service: transmembrane helix prediction through amino acid property analysis

scientific article published on 27 August 2007

Techniques for transferring host-pathogen protein interactions knowledge to new tasks

scientific article published on 02 February 2015

Techniques to cope with missing data in host–pathogen protein interaction prediction ⬇️

scientific article published on September 15, 2012

The Cytoplasmic Rhodopsin-Protein Interface: Potential for Drug Discovery ⬇️

scientific article published on January 1, 2012

The brown adipocyte protein CIDEA promotes lipid droplet fusion via a phosphatidic acid-binding amphipathic helix

scientific article

The current Salmonella‐host interactome ⬇️

scientific article published on December 27, 2011

The effect of loops on the structural organization of alpha-helical membrane proteins

scientific article published on March 2009

The enzymatic oxidation of graphene oxide

journal article published in 2011

The importance of valine 114 in ligand binding in beta(2)-adrenergic receptor

scientific article published on January 2010

Topography of tyrosine residues and their involvement in peroxidation of polyunsaturated cardiolipin in cytochrome c/cardiolipin peroxidase complexes

journal article published in 2011

Towards personalised molecular feedback for weight loss

scientific article published on 06 May 2019

Transmembrane helix prediction using amino acid property features and latent semantic analysis

scientific article

Vibrational resonance, allostery, and activation in rhodopsin-like G protein-coupled receptors

scientific article

Virus interactions with human signal transduction pathways

scientific article

X-ray structure, thermodynamics, elastic properties and MD simulations of cardiolipin/dimyristoylphosphatidylcholine mixed membranes

scientific article

pH-dependent interaction of rhodopsin with cyanidin-3-glucoside. 1. Structural aspects

scientific article published on 19 January 2009

pH-dependent interaction of rhodopsin with cyanidin-3-glucoside. 2. Functional aspects

scientific article published in March 2009

List of works by Judith Klein-Seetharaman

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

A minimal ligand binding pocket within a network of correlated mutations identified by multiple sequence and structural analysis of G protein coupled receptors ⬇️

A mitochondria-targeted inhibitor of cytochrome c peroxidase mitigates radiation-induced death

A mitochondrial pathway for biosynthesis of lipid mediators

A mixture of feature experts approach for protein-protein interaction prediction

Additive effects of chlorin e6 and metal ion binding on the thermal stability of rhodopsin in vitro

Adsorption of surfactant lipids by single-walled carbon nanotubes in mouse lung upon pharyngeal aspiration

Allosteric Modulation of G Protein Coupled Receptors by Cytoplasmic, Transmembrane and Extracellular Ligands

Alternative paths in HIV-1 targeted human signal transduction pathways

BIPS: BIANA Interolog Prediction Server. A tool for protein–protein interaction inference ⬇️

Biodegradation of single-walled carbon nanotubes by eosinophil peroxidase

Carbon nanotubes degraded by neutrophil myeloperoxidase induce less pulmonary inflammation

Cardiolipin Interactions with Proteins

Cardiolipin externalization to the outer mitochondrial membrane acts as an elimination signal for mitophagy in neuronal cells

Cardiolipin signaling mechanisms: collapse of asymmetry and oxidation

Characterization of membrane protein non-native states. 1. Extent of unfolding and aggregation of rhodopsin in the presence of chemical denaturants

Characterization of membrane protein non-native states. 2. The SDS-unfolded states of rhodopsin

Characterization of the simultaneous decay kinetics of metarhodopsin states II and III in rhodopsin by solution-state NMR spectroscopy

Chlorophyll-Derivative Modulation of Rhodopsin Signaling Properties through Evolutionarily Conserved Interaction Pathways

Combined inhibition of PLC{gamma}-1 and c-Src abrogates epidermal growth factor receptor-mediated head and neck squamous cell carcinoma invasion

Comparing human-Salmonella with plant-Salmonella protein-protein interaction predictions

Comparison of probabilistic combination methods for protein secondary structure prediction

Comparison of the molecular properties of retinitis pigmentosa P23H and N15S amino acid replacements in rhodopsin.

Determining confidence of predicted interactions between HIV-1 and human proteins using conformal method ⬇️

Dichotomous roles for externalized cardiolipin in extracellular signaling: promotion of phagocytosis and attenuation of innate immunity

Differential dynamics in the G protein-coupled receptor rhodopsin revealed by solution NMR.

Differential dynamics of extracellular and cytoplasmic domains in denatured States of rhodopsin

Discovering pathways by orienting edges in protein interaction networks

Dual function of mitochondrial Nm23-H4 protein in phosphotransfer and intermembrane lipid transfer: a cardiolipin-dependent switch

Dual role of interactions between membranous and soluble portions of helical membrane receptors for folding and signaling

Dynamics in rhodopsin

Early integration of the individual student in academic activities: a novel classroom concept for graduate education in molecular biophysics and structural biology

Evaluation of different biological data and computational classification methods for use in protein interaction prediction

Flexibility of the cytoplasmic domain of the phototaxis transducer II from Natronomonas pharaonis

Glutamic acid-rich proteins of rod photoreceptors are natively unfolded

Heterolytic reduction of fatty acid hydroperoxides by cytochrome c/cardiolipin complexes: antioxidant function in mitochondria.

Human immunodeficiency virus type 1 Vpr: oligomerization is an essential feature for its incorporation into virus particles

Identification of Motions in Membrane Proteins by Elastic Network Models and Their Experimental Validation ⬇️

Identification of core amino acids stabilizing rhodopsin

Isotope Labeling in Insect Cells ⬇️

Isotope Labeling in Mammalian Cells ⬇️

Isotope labeling of mammalian GPCRs in HEK293 cells and characterization of the C-terminus of bovine rhodopsin by high resolution liquid NMR spectroscopy

Known unknowns of cardiolipin signaling: the best is yet to come

Ligand-independent antiapoptotic function of estrogen receptor-beta in lung cancer cells

Lipid bodies containing oxidatively truncated lipids block antigen cross-presentation by dendritic cells in cancer

Long-range interactions within a nonnative protein

Mechanistic investigations of horseradish peroxidase-catalyzed degradation of single-walled carbon nanotubes

Mitochondrial redox opto-lipidomics reveals mono-oxygenated cardiolipins as pro-apoptotic death signals

Mitochondrial targeting of electron scavenging antioxidants: regulation of selective oxidation vs random chain reactions

Molecular speciation and dynamics of oxidized triacylglycerols in lipid droplets: mass spectrometry and coarse-grained simulations

Multitask Matrix Completion for Learning Protein Interactions Across Diseases

Multitask learning for host-pathogen protein interactions

NMR spectroscopy of phosphorylated wild-type rhodopsin: mobility of the phosphorylated C-terminus of rhodopsin in the dark and upon light activation

NMR-based screening of membrane protein ligands

Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis

Oxidized lipids block antigen cross-presentation by dendritic cells in cancer

Prediction and comparison of Salmonella-human and Salmonella-Arabidopsis interactomes

Prediction of interactions between HIV-1 and human proteins by information integration.

Preferential binding of allosteric modulators to active and inactive conformational states of metabotropic glutamate receptors

Protein complex identification by supervised graph local clustering

Refining literature curated protein interactions using expert opinions

Retinal proteins as model systems for membrane protein folding

Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins ⬇️

Shape and oligomerization state of the cytoplasmic domain of the phototaxis transducer II from Natronobacterium pharaonis

Similarity of the non-amyloid-β component and C-terminal tail of monomeric and tetrameric alpha-synuclein with 14-3-3 sigma

Specificity of lipoprotein-associated phospholipase A(2) toward oxidized phosphatidylserines: liquid chromatography-electrospray ionization mass spectrometry characterization of products and computer modeling of interactions

Structural and Functional Consequences of the Weak Binding of Chlorin e6 to Bovine Rhodopsin

Structural characterization of cardiolipin-driven activation of cytochrome C into a peroxidase and membrane perturbation

Structure and dynamics of the insulin receptor: implications for receptor activation and drug discovery.

Systematic prediction of human membrane receptor interactions

TMpro web server and web service: transmembrane helix prediction through amino acid property analysis

Techniques for transferring host-pathogen protein interactions knowledge to new tasks

Techniques to cope with missing data in host–pathogen protein interaction prediction ⬇️

The Cytoplasmic Rhodopsin-Protein Interface: Potential for Drug Discovery ⬇️

The brown adipocyte protein CIDEA promotes lipid droplet fusion via a phosphatidic acid-binding amphipathic helix

The current Salmonella‐host interactome ⬇️

The effect of loops on the structural organization of alpha-helical membrane proteins

The enzymatic oxidation of graphene oxide

The importance of valine 114 in ligand binding in beta(2)-adrenergic receptor