S. Phanse

发表

Efficient prediction of human protein-protein interactions at a global scale

Hui Wang, Ashkan Golshani, Michael A. Langston, 2014, BMC Bioinformatics.

A Census of Human Soluble Protein Complexes

Andrei L. Turinsky, Greg W. Clark, Gabriel C. Wu, 2012, Cell.

Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli

Gary D. Bader, Gary D Bader, Ashkan Golshani, 2015, Bioinform..

Quantitative Genome-Wide Genetic Interaction Screens Reveal Global Epistatic Relationships of Protein Complexes in Escherichia coli

Philip M. Kim, A. Emili, James Vlasblom, 2014, PLoS genetics.

Ribosome-Dependent ATPase Interacts with Conserved Membrane Protein in Escherichia coli to Modulate Protein Synthesis and Oxidative Phosphorylation

A. Emili, J. Greenblatt, S. Phanse, 2011, PloS one.

The binary protein-protein interaction landscape of Escherichia coli

P. Uetz, A. Emili, James Vlasblom, 2014, Nature Biotechnology.

Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins

A. Emili, Xinghua Guo, Alberto Paccanaro, 2009, PLoS biology.

Genetic Interaction Maps in Escherichia coli Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways

A. Emili, James Vlasblom, J. Parkinson, 2011, PLoS genetics.

Mitochondria under the spotlight: On the implications of mitochondrial dysfunction and its connectivity to neuropsychiatric disorders

S. Phanse, M. Babu, Mara Zilocchi, 2020, Computational and structural biotechnology journal.

Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae

Franco J. Vizeacoumar, A. Emili, Gouqing Zhong, 2012, Nature.

Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation

Jeffrey R. Whiteaker, Ben C. Collins, Jacob J. Kennedy, 2015, Nature Methods.

Panorama of ancient metazoan macromolecular complexes

Greg W. Clark, Graham L. Cromar, A. Emili, 2015, Nature.

Global landscape of cell envelope protein complexes in Escherichia coli

Daniel J. Burnside, P. Uetz, A. Emili, 2017, Nature Biotechnology.

Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2

B. Blencowe, A. Emili, S. Wuchty, 2020, Molecular Cell.

eSGA: E. coli synthetic genetic array analysis

Huiming Ding, Andrew Emili, Gabriel Moreno-Hagelsieb, 2008, Nature Methods.

Yeast mitochondrial protein-protein interactions reveal diverse complexes and disease-relevant functional relationships.

James Vlasblom, G. Musso, P. Aloy, 2015, Journal of proteome research.

Misconnecting the dots: altered mitochondrial protein-protein interactions and their role in neurodegenerative disorders

S. Phanse, M. Babu, M. Jessulat, 2020, Expert review of proteomics.

Chemical-genetic profiling reveals cross-resistance and collateral sensitivity between antimicrobial peptides

C. Pál, S. Phanse, M. Babu, 2019, bioRxiv.

BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain.

Gary D Bader, Shayne D. Wierbowski, Graham L. Cromar, 2020, Cell systems.

Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis

Gary D Bader, Nichollas E. Scott, James Vlasblom, 2019, iScience.

Mitochondrial Targets for Pharmacological Intervention in Human Disease

James Vlasblom, G. Musso, Ke Jin, 2014, Journal of proteome research.

Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation.

Andrei L. Turinsky, Swneke D. Bailey, A. Emili, 2014, Cell reports.

A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals Molecular Determinants of Redox Homeostasis and NF- κ B Signaling

Gary D Bader, Nichollas E. Scott, Haiyuan Yu, 2017 .

Development of a Method Combining Peptidiscs and Proteomics to Identify, Stabilize, and Purify a Detergent-Sensitive Membrane Protein Assembly.

S. Phanse, M. Babu, L. Foster, 2022, Journal of proteome research.

Functional cooperativity between the trigger factor chaperone and the ClpXP proteolytic complex

S. Phanse, M. Babu, W. Houry, 2020, Nature communications.

Chemical-genetic profiling reveals limited cross-resistance between antimicrobial peptides with different modes of action

C. Pál, S. Phanse, M. Babu, 2019, Nature Communications.

Exploring the Impact of PARK2 Mutations on the Total and Mitochondrial Proteome of Human Skin Fibroblasts

S. Phanse, M. Babu, L. Pieroni, 2020, Frontiers in Cell and Developmental Biology.

Macromolecular Connectivity Landscape of Mammalian Brain

Gary D Bader, Shayne D. Wierbowski, A. Emili, 2018 .

Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery

A. Emili, S. Phanse, P. Havugimana, 2022, Nature Communications.

Auxotrophic and prototrophic conditional genetic networks reveal the rewiring of transcription factors in Escherichia coli

S. Phanse, M. Babu, M. Jessulat, 2022, Nature Communications.

A computational approach to rapidly design peptides that detect SARS-CoV-2 surface protein S

F. Dehne, Bahram Samanfar, M. Hooshyar, 2022, NAR genomics and bioinformatics.

Insights into SACS pathological attributes in autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS)☆.

S. Phanse, Mara Zilocchi, Khaled A. Aly, 2022, Current opinion in chemical biology.

Assembly principles of the human R2TP chaperone complex reveal the presence of R2T and R2P complexes.

S. Phanse, M. Babu, W. Houry, 2021, Structure.

Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli.

Ashkan Golshani, Omar Wagih, John Parkinson, 2016, Cell reports.

Resource Conditional Epistatic Inter actionMaps Reveal Global Functional Rewiring ofGenome Integrity Pathways in Escherichia coli Graphical

A. Emili, James Vlasblom, G. Musso, 2016 .

Identification of Human Neuronal Protein Complexes Reveals Biochemical Activities and Convergent Mechanisms of Action in Autism Spectrum Disorders.

Zhihai Ma, A. Urban, Ke Jin, 2015, Cell systems.

A dual function of the CRISPR–Cas system in bacterial antivirus immunity and DNA repair

Andrew Emili, Mohan Babu, Eugene V Koonin, 2011, Molecular microbiology.

Targeted protein identification, quantification and reporting for high-resolution nanoflow targeted peptide monitoring.

Andrew Emili, Sadhna Phanse, A. Emili, 2013, Journal of proteomics.

Insights from protein-protein interaction studies on bacterial pathogenesis

S. Phanse, M. Babu, Alla Gagarinova, 2017, Expert review of proteomics.

The conserved Tpk1 regulates non-homologous end joining double-strand break repair by phosphorylation of Nej1, a homolog of the human XLF

Daniel J. Burnside, Bahram Samanfar, M. Hooshyar, 2021, Nucleic acids research.

A multi-tiered map of EMT defines major transition points and identifies vulnerabilities

A. Emili, G. Karemore, S. Wuchty, 2021, bioRxiv.

EPIC: software toolkit for elution profile-based inference of protein complexes

Gary D Bader, Andrew Emili, Sadhna Phanse, 2019, Nature Methods.

Integrative network analysis of signaling in human CD34+ hematopoietic progenitor cells by global phosphoproteomic profiling using TiO2 enrichment combined with 2D LC‐MS/MS and pathway mapping

A. Emili, Ruth Isserlin, S. Phanse, 2013, Proteomics.

Spindle Checkpoint Factors Bub1 and Bub2 Promote DNA Double-Strand Break Repair by Nonhomologous End Joining

Daniel J. Burnside, N. Krogan, James Vlasblom, 2015, Molecular and Cellular Biology.

Spindle Checkpoint Factors Promote NHEJ 1 Spindle Checkpoint Factors Bub 1 and Bub 2 Promote DNA 1 Double Strand Break Repair by Non-Homologous End Joining 2 3

Dan, N. Krogan, James Vlasblom, 2015 .

NleH defines a new family of bacterial effector kinases.

S. Phanse, M. Babu, M. Cygler, 2014, Structure.

Systems analysis of the genetic interaction network of yeast molecular chaperones.

Sandra Zilles, S. Phanse, M. Babu, 2018, Molecular omics.

EPIC: software toolkit for elution profile-based inference of protein complexes

Gary D Bader, A. Fraser, A. Emili, 2019, Nature Methods.

Systematic Genetic Screens Reveal the Dynamic Global Functional Organization of the Bacterial Translation Machinery.

Ashkan Golshani, Andrew Emili, Mohan Babu, 2016, Cell reports.

A Gaussian process-based definition reveals new and bona fide genetic interactions compared to a multiplicative model in the Gram-negative Escherichia coli

Sandra Zilles, Ashwani Kumar, Mohan Babu, 2019, Bioinform..

Features of the Chaperone Cellular Network Revealed through Systematic Interaction Mapping.

James Vlasblom, C. Myers, Charles Boone, 2017, Cell reports.

Development of a Method Combining Peptidiscs and Proteomics to Identify, Stabilize and Purify a Detergent-Sensitive Membrane Protein Assembly

S. Phanse, M. Babu, L. Foster, 2022, bioRxiv.

A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling.

Gary D Bader, Nichollas E. Scott, Haiyuan Yu, 2017, Cell systems.

AMap of HumanMitochond rial Protein Interactions Linked toNeurodegenerationRevealsNewMechanisms of Redox Homeostasis and NFk B Signaling Graphical

Gary D Bader, Nichollas E. Scott, Haiyuan Yu, 2017 .

Extracting high confidence protein interactions from affinity purification data: at the crossroads.

Andrei L. Turinsky, Shoshana J. Wodak, James Vlasblom, 2015, Journal of proteomics.

ZapG (YhcB/DUF1043), a novel cell division protein in gamma-proteobacteria linking the Z-ring to septal peptidoglycan synthesis

P. Uetz, G. Montelione, S. Phanse, 2021, The Journal of biological chemistry.

YhcB (DUF1043), a novel cell division protein conserved across gamma-proteobacteria

P. Uetz, G. Montelione, S. Phanse, 2021, bioRxiv.

Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes

Olga Kagan, John Parkinson, Edward M. Marcotte, 2015, Data in brief.

Human-Soybean Allergies: Elucidation of the Seed Proteome and Comprehensive Protein-Protein Interaction Prediction.

Daniel J. Burnside, Le Hoa Tan, F. Dehne, 2021, Journal of proteome research.

From fuzziness to precision medicine: on the rapidly evolving proteomics with implications in mitochondrial connectivity to rare human disease

S. Phanse, M. Babu, Khaled A. Aly, 2021, iScience.

Bacteriome.org—an integrated protein interaction database for E. coli

Chong Su, John Parkinson, Andrew Emili, 2007, Nucleic Acids Res..

Author Correction: Functional cooperativity between the trigger factor chaperone and the ClpXP proteolytic complex

S. Phanse, M. Babu, W. Houry, 2021, Nature Communications.

ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores

L. Kay, S. Phanse, M. Babu, 2019, Communications Biology.

Acyldepsipeptide Analogs Dysregulate Human Mitochondrial ClpP Protease Activity and Cause Apoptotic Cell Death.

S. Phanse, M. Babu, W. Houry, 2018, Cell chemical biology.

Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT

A. Emili, G. Karemore, S. Wuchty, 2023, Nature Communications.

Poly(GR) interacts with key stress granule factors promoting its assembly into cytoplasmic inclusions.

C. Brangwynne, A. Emili, L. Petrucelli, 2023, Cell reports.

In vitro toxicity screening of amorphous silica nanoparticles using mitochondrial fraction exposure followed by MS-based proteomic analysis.

S. Phanse, H. Aoki, Nazila Nazemof, 2022, The Analyst.

HDL functionality is dependent on hepatocyte stress defense factors Nrf1 and Nrf2

S. Phanse, S. Widenmaier, Mohan Babu, 2023, Frontiers in physiology.

Complementary gene regulation by NRF1 and NRF2 protects against hepatic cholesterol overload.

S. Phanse, S. Widenmaier, Qingzhou Zhang, 2023, Cell reports.