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Tytuł :
A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity.
Autorzy :
Swaney DL; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.; J. David Gladstone Institutes, San Francisco, CA, USA.; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.
Ramms DJ; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.; Department of Pharmacology, University of California San Diego, La Jolla, CA.; Moores Cancer Center, University of California San Diego, La Jolla, CA.
Wang Z; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.; Moores Cancer Center, University of California San Diego, La Jolla, CA.
Park J; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.; Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA.
Goto Y; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.; Moores Cancer Center, University of California San Diego, La Jolla, CA.
Soucheray M; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.; J. David Gladstone Institutes, San Francisco, CA, USA.; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.
Bhola N; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
Kim K; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.; J. David Gladstone Institutes, San Francisco, CA, USA.; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.
Zheng F; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.; Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA.
Zeng Y; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
McGregor M; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.; J. David Gladstone Institutes, San Francisco, CA, USA.; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.
Herrington KA; Department of Biochemistry and Biophysics Center for Advanced Light Microscopy at UCSF, University of California San Francisco, San Francisco, CA, USA.
O'Keefe R; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
Jin N; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
VanLandingham NK; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
Foussard H; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.; J. David Gladstone Institutes, San Francisco, CA, USA.; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.
Von Dollen J; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.; J. David Gladstone Institutes, San Francisco, CA, USA.; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.
Bouhaddou M; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.; J. David Gladstone Institutes, San Francisco, CA, USA.; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.
Jimenez-Morales D; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.; J. David Gladstone Institutes, San Francisco, CA, USA.; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.
Obernier K; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.; J. David Gladstone Institutes, San Francisco, CA, USA.; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.
Kreisberg JF; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.; Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA.
Kim M; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.; J. David Gladstone Institutes, San Francisco, CA, USA.; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.
Johnson DE; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
Jura N; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.; Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.
Grandis JR; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
Gutkind JS; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.; Department of Pharmacology, University of California San Diego, La Jolla, CA.; Moores Cancer Center, University of California San Diego, La Jolla, CA.
Ideker T; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.; Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA.; Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.; Department of Computer Science, University of California San Diego, La Jolla, CA, USA.
Krogan NJ; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.; J. David Gladstone Institutes, San Francisco, CA, USA.; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA.
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Źródło :
Science (New York, N.Y.) [Science] 2021 Oct; Vol. 374 (6563), pp. eabf2911. Date of Electronic Publication: 2021 Oct 01.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms :
Protein Interaction Maps*
Carcinoma, Squamous Cell/*metabolism
Class I Phosphatidylinositol 3-Kinases/*genetics
Class I Phosphatidylinositol 3-Kinases/*metabolism
Drug Resistance, Neoplasm/*genetics
Head and Neck Neoplasms/*metabolism
Animals ; Carcinoma, Squamous Cell/genetics ; Cell Line, Tumor ; Cell Movement ; Female ; Head and Neck Neoplasms/genetics ; Humans ; Intracellular Signaling Peptides and Proteins/metabolism ; Mice ; Mice, Nude ; Microfilament Proteins/metabolism ; Mutation ; Receptor, Fibroblast Growth Factor, Type 3/metabolism ; Xenograft Model Antitumor Assays
Czasopismo naukowe
Tytuł :
A protein interaction landscape of breast cancer.
Autorzy :
Kim M; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.; Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
Park J; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.; Department of Medicine, University of California, San Diego, CA, USA.
Bouhaddou M; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.; Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
Kim K; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.; Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
Rojc A; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.; Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
Modak M; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.; Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
Soucheray M; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.; Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
McGregor MJ; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.; Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
O'Leary P; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.; Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.
Wolf D; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.; Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.
Stevenson E; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.; Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
Foo TK; Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.
Mitchell D; Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.; Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.; Division of Hematology/Oncology, University of California, San Francisco, CA, USA.
Herrington KA; Department of Biochemistry and Biophysics, Center for Advanced Light Microscopy, University of California, San Francisco, CA, USA.
Muñoz DP; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.; Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.
Tutuncuoglu B; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.; Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
Chen KH; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.; Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
Zheng F; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.; Department of Medicine, University of California, San Diego, CA, USA.
Kreisberg JF; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.; Department of Medicine, University of California, San Diego, CA, USA.
Diolaiti ME; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.; Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.
Gordan JD; Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.; Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.; Division of Hematology/Oncology, University of California, San Francisco, CA, USA.
Coppé JP; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.; Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.
Swaney DL; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.; Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
Xia B; Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA.
van 't Veer L; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.; Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.
Ashworth A; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.; Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.
Ideker T; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.; Department of Medicine, University of California, San Diego, CA, USA.; Department of Bioengineering, University of California, San Diego, CA, USA.
Krogan NJ; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.; Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
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Źródło :
Science (New York, N.Y.) [Science] 2021 Oct; Vol. 374 (6563), pp. eabf3066. Date of Electronic Publication: 2021 Oct 01.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms :
Protein Interaction Maps*
Breast Neoplasms/*metabolism
Neoplasm Proteins/*metabolism
Breast Neoplasms/genetics ; Cell Line, Tumor ; Female ; Humans ; Mass Spectrometry ; Mutation ; Neoplasm Proteins/genetics ; Neoplasm Proteins/isolation & purification ; Tandem Affinity Purification
Czasopismo naukowe
Tytuł :
Yeast proteins do not practice social distancing as species hybridize.
Autorzy :
Berger CM; Département de Biologie, Faculté des sciences et de génie, Université Laval, Quebec, QC, G1V0A6, Canada. .; Département de Biochimie, Microbiologie et Bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec, QC, G1V0A6, Canada. .; Le réseau québécois de recherche sur la fonction, la structure et l'ingénierie de protéines, PROTEO, Université Laval, Quebec, QC, G1V0A6, Canada. .; Centre de Recherche en Données Massives (CRDM), Université Laval, Quebec, QC, G1V0A6, Canada. .
Landry CR; Département de Biologie, Faculté des sciences et de génie, Université Laval, Quebec, QC, G1V0A6, Canada.; Département de Biochimie, Microbiologie et Bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec, QC, G1V0A6, Canada.; Le réseau québécois de recherche sur la fonction, la structure et l'ingénierie de protéines, PROTEO, Université Laval, Quebec, QC, G1V0A6, Canada.; Centre de Recherche en Données Massives (CRDM), Université Laval, Quebec, QC, G1V0A6, Canada.
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Źródło :
Current genetics [Curr Genet] 2021 Oct; Vol. 67 (5), pp. 755-759. Date of Electronic Publication: 2021 May 04.
Typ publikacji :
Journal Article; Review
MeSH Terms :
Hybridization, Genetic*
Protein Interaction Maps*
Fungal Proteins/*metabolism
Saccharomyces/*metabolism
Saccharomyces cerevisiae/*metabolism
Animals ; Fungal Proteins/chemistry ; Fungal Proteins/genetics ; Proteomics ; Saccharomyces/chemistry ; Saccharomyces/classification ; Saccharomyces/genetics ; Saccharomyces cerevisiae/chemistry ; Saccharomyces cerevisiae/genetics
Czasopismo naukowe
Tytuł :
A novel link prediction algorithm for protein-protein interaction networks by attributed graph embedding.
Autorzy :
Nasiri E; Department of Information Technology and Communications, Azarbaijan Shahid Madani University, Tabriz, Iran. Electronic address: .
Berahmand K; School of Computer Sciences, Department of Science and Engineering, Queensland University of Technology, Brisbane, Australia. Electronic address: .
Rostami M; Department of Computer Engineering, University of Kurdistan, Sanandaj, Iran. Electronic address: .
Dabiri M; Department of Plant Biotechnology, University of Kurdistan, Sanandaj, Iran. Electronic address: .
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Źródło :
Computers in biology and medicine [Comput Biol Med] 2021 Oct; Vol. 137, pp. 104772. Date of Electronic Publication: 2021 Aug 18.
Typ publikacji :
Journal Article
MeSH Terms :
Algorithms*
Protein Interaction Maps*
Proteins
Czasopismo naukowe
Tytuł :
The transcription regulator BrsR serves as a network hub of natural competence protein-protein interactions in Streptococcus mutans .
Autorzy :
Qin H; Department of Restorative Dentistry, Oregon Health and Science University, Portland, OR 97239.
Zou Z; Department of Restorative Dentistry, Oregon Health and Science University, Portland, OR 97239.
Anderson D; Department of Restorative Dentistry, Oregon Health and Science University, Portland, OR 97239.
Sang Y; Department of Restorative Dentistry, Oregon Health and Science University, Portland, OR 97239.
Higashi D; Department of Restorative Dentistry, Oregon Health and Science University, Portland, OR 97239.
Kreth J; Department of Restorative Dentistry, Oregon Health and Science University, Portland, OR 97239.; Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239.
Merritt J; Department of Restorative Dentistry, Oregon Health and Science University, Portland, OR 97239; .; Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239.
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Źródło :
Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2021 Sep 28; Vol. 118 (39).
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms :
Gene Expression Regulation, Bacterial*
Protein Interaction Maps*
Bacterial Proteins/*metabolism
Bacteriocins/*metabolism
Streptococcus mutans/*metabolism
Transcription Factors/*metabolism
Bacterial Proteins/genetics ; Streptococcus mutans/genetics ; Streptococcus mutans/growth & development ; Transcription Factors/genetics
Czasopismo naukowe
Tytuł :
An iteration model for identifying essential proteins by combining comprehensive PPI network with biological information.
Autorzy :
Li S; College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410022, China.; Hunan Province Key Laboratory of Industrial Internet Technology and Security, Changsha University, Changsha, 410022, China.
Zhang Z; College of Electronic Information and Electrical Engineering, Changsha University, Changsha, 410022, China.
Li X; College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410022, China.; Hunan Province Key Laboratory of Industrial Internet Technology and Security, Changsha University, Changsha, 410022, China.
Tan Y; College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410022, China. .; Hunan Province Key Laboratory of Industrial Internet Technology and Security, Changsha University, Changsha, 410022, China. .
Wang L; College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410022, China.; Hunan Province Key Laboratory of Industrial Internet Technology and Security, Changsha University, Changsha, 410022, China.
Chen Z; College of Computer Engineering and Applied Mathematics, Changsha University, Changsha, 410022, China. .; Hunan Province Key Laboratory of Industrial Internet Technology and Security, Changsha University, Changsha, 410022, China. .
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Źródło :
BMC bioinformatics [BMC Bioinformatics] 2021 Sep 08; Vol. 22 (1), pp. 430. Date of Electronic Publication: 2021 Sep 08.
Typ publikacji :
Journal Article
MeSH Terms :
Computational Biology*
Protein Interaction Maps*
Algorithms ; Protein Interaction Mapping ; Proteins/genetics ; Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism
Czasopismo naukowe
Tytuł :
Expression and affinity purification of recombinant mammalian mitochondrial ribosomal small subunit (MRPS) proteins and protein-protein interaction analysis indicate putative role in tumourigenic cellular processes.
Autorzy :
Revathi Paramasivam O; Department of Molecular Oncology, Cancer Institute (WIA), Adyar, Chennai 600020, Tamil Nadu, India.
Gopisetty G; Department of Molecular Oncology, Cancer Institute (WIA), Adyar, Chennai 600020, Tamil Nadu, India.
Subramani J; Department of Molecular Oncology, Cancer Institute (WIA), Adyar, Chennai 600020, Tamil Nadu, India.
Thangarajan R; Department of Molecular Oncology, Cancer Institute (WIA), Adyar, Chennai 600020, Tamil Nadu, India.
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Źródło :
Journal of biochemistry [J Biochem] 2021 Sep 07; Vol. 169 (6), pp. 675-692.
Typ publikacji :
Journal Article
MeSH Terms :
Protein Interaction Maps*
Breast Neoplasms/*pathology
Mitochondrial Proteins/*metabolism
Recombinant Fusion Proteins/*metabolism
Ribosomal Proteins/*metabolism
Breast Neoplasms/genetics ; Breast Neoplasms/metabolism ; Chromatography, Affinity ; Female ; Glutathione Transferase/genetics ; Glutathione Transferase/metabolism ; Humans ; Mitochondrial Proteins/genetics ; Mitochondrial Proteins/isolation & purification ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/isolation & purification ; Ribosomal Proteins/genetics ; Ribosomal Proteins/isolation & purification ; Tumor Cells, Cultured
Czasopismo naukowe
Tytuł :
SMMPPI: a machine learning-based approach for prediction of modulators of protein-protein interactions and its application for identification of novel inhibitors for RBD:hACE2 interactions in SARS-CoV-2.
Autorzy :
Gupta P; NII, New Delhi 110067, India.
Mohanty D; Bioinformatics & Computational Biology research group at NII, New Delhi 110067, India.
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Źródło :
Briefings in bioinformatics [Brief Bioinform] 2021 Sep 02; Vol. 22 (5).
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Machine Learning*
Protein Interaction Maps*
Angiotensin-Converting Enzyme 2/*antagonists & inhibitors
Proteins/*metabolism
SARS-CoV-2/*metabolism
Angiotensin-Converting Enzyme 2/metabolism ; Humans
Czasopismo naukowe
Tytuł :
Analyzing host-viral interactome of SARS-CoV-2 for identifying vulnerable host proteins during COVID-19 pathogenesis.
Autorzy :
Das JK; Department of Pediatrics, School of Medicine, Johns Hopkins University, MD, USA.
Roy S; Network Reconstruction & Analysis (NetRA) Lab, Department of Computer Applications, Sikkim University, Gangtok, India. Electronic address: .
Guzzi PH; Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy. Electronic address: .
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Źródło :
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases [Infect Genet Evol] 2021 Sep; Vol. 93, pp. 104921. Date of Electronic Publication: 2021 May 15.
Typ publikacji :
Journal Article
MeSH Terms :
Protein Interaction Maps*/genetics
COVID-19/*metabolism
Host-Pathogen Interactions/*physiology
SARS-CoV-2/*pathogenicity
Gene Ontology ; Humans ; Proteins/genetics ; Proteins/metabolism ; Viral Proteins/metabolism
Czasopismo naukowe
Tytuł :
A New Sequential Forward Feature Selection (SFFS) Algorithm for Mining Best Topological and Biological Features to Predict Protein Complexes from Protein-Protein Interaction Networks (PPINs).
Autorzy :
Younis H; School of Professional Advancement, University of Management and Technology, Lahore, Pakistan.; Department of Computer Science, COMSATS University Islamabad, Lahore, Pakistan.
Anwar MW; Department of Computer Science, COMSATS University Islamabad, Lahore, Pakistan. .
Khan MUG; Department of Computer Science and Engineering, University of Engineering and Technology, Lahore, Pakistan.
Sikandar A; Govt. Girls Post Graduate College No.1 Abbottabad, Abbottabad, Pakistan.
Bajwa UI; Department of Computer Science, COMSATS University Islamabad, Lahore, Pakistan.
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Źródło :
Interdisciplinary sciences, computational life sciences [Interdiscip Sci] 2021 Sep; Vol. 13 (3), pp. 371-388. Date of Electronic Publication: 2021 May 06.
Typ publikacji :
Journal Article
MeSH Terms :
Data Mining*
Protein Interaction Maps*
Animals ; Databases, Factual ; Mice ; Proteins
Czasopismo naukowe
Tytuł :
alfaNET: A Database of Alfalfa-Bacterial Stem Blight Protein-Protein Interactions Revealing the Molecular Features of the Disease-causing Bacteria.
Autorzy :
Kataria R; Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA.
Kaundal R; Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA.; Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA.; Department of Computer Science, College of Science, Utah State University, Logan, UT 84322, USA.
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Źródło :
International journal of molecular sciences [Int J Mol Sci] 2021 Aug 03; Vol. 22 (15). Date of Electronic Publication: 2021 Aug 03.
Typ publikacji :
Journal Article
MeSH Terms :
Databases, Protein*
Host-Pathogen Interactions*
Protein Interaction Maps*
Bacterial Proteins/*metabolism
Medicago sativa/*metabolism
Plant Diseases/*immunology
Pseudomonas syringae/*pathogenicity
Medicago sativa/immunology ; Medicago sativa/microbiology ; Plant Diseases/microbiology
Czasopismo naukowe
Tytuł :
DIA-Based Quantitative Proteomics Reveals the Protein Regulatory Networks of Floral Thermogenesis in Nelumbo nucifera .
Autorzy :
Sun Y; State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China.
Zou Y; State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China.
Jin J; Department of Biotechnology, College of Life Sciences, Guizhou University, Guiyang 550025, China.
Chen H; Institute of Vegetables, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China.
Liu Z; State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China.
Zi Q; State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China.
Xiong Z; State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China.
Wang Y; State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China.
Li Q; State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China.
Peng J; Institute of Vegetables, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China.
Ding Y; State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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Źródło :
International journal of molecular sciences [Int J Mol Sci] 2021 Jul 31; Vol. 22 (15). Date of Electronic Publication: 2021 Jul 31.
Typ publikacji :
Journal Article
MeSH Terms :
Adaptation, Physiological*
Gene Regulatory Networks*
Protein Interaction Maps*
Flowers/*metabolism
Nelumbo/*genetics
Proteome/*metabolism
Citrate (si)-Synthase/genetics ; Citrate (si)-Synthase/metabolism ; Citric Acid Cycle ; Flowers/genetics ; Gene Expression Regulation, Plant ; Mitochondrial Proteins/genetics ; Mitochondrial Proteins/metabolism ; Nelumbo/growth & development ; Nelumbo/metabolism ; Oxidoreductases/genetics ; Oxidoreductases/metabolism ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Proteome/genetics ; Temperature
Czasopismo naukowe
Tytuł :
A split protease-E. coli ClpXP system quantifies protein-protein interactions in Escherichia coli cells.
Autorzy :
Wang S; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China.
Zhang F; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China.
Mei M; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China.
Wang T; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China.
Yun Y; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China.
Yang S; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China.
Zhang G; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China. .
Yi L; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China. .
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Źródło :
Communications biology [Commun Biol] 2021 Jul 06; Vol. 4 (1), pp. 841. Date of Electronic Publication: 2021 Jul 06.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Protein Interaction Maps*
Endopeptidase Clp/*metabolism
Escherichia coli/*metabolism
Escherichia coli Proteins/*metabolism
Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; CRISPR-Cas Systems ; Endopeptidase Clp/genetics ; Enterovirus/enzymology ; Enterovirus/genetics ; Escherichia coli/genetics ; Escherichia coli Proteins/genetics ; Green Fluorescent Proteins/genetics ; Green Fluorescent Proteins/metabolism ; Histidine Kinase/genetics ; Histidine Kinase/metabolism ; Humans ; Models, Molecular ; Protein Binding ; Protein Conformation ; Proteolysis ; Serine Endopeptidases/chemistry ; Serine Endopeptidases/genetics ; Serine Endopeptidases/metabolism ; Viral Proteins/genetics ; Viral Proteins/metabolism
SCR Organism :
Rhinovirus B
Czasopismo naukowe
Tytuł :
Identification of key miRNAs and their targets in peripheral blood mononuclear cells of IgA nephropathy using bioinformatics analysis.
Autorzy :
Liu L; Department of Nephrology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical Universtiy, Tiyuchang Road 453#, Hangzhou, Zhejiang, China.
Yang Y
Yu D
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Źródło :
Medicine [Medicine (Baltimore)] 2021 Jul 02; Vol. 100 (26), pp. e26495.
Typ publikacji :
Journal Article
MeSH Terms :
Glomerulonephritis, IGA*/blood
Glomerulonephritis, IGA*/diagnosis
Glomerulonephritis, IGA*/genetics
MicroRNAs*/analysis
MicroRNAs*/classification
Protein Interaction Maps*
Leukocytes, Mononuclear/*physiology
Computational Biology/methods ; Databases, Genetic ; Disease Progression ; Gene Expression Profiling ; Gene Regulatory Networks ; Genetic Association Studies ; Genome-Wide Association Study ; Humans ; Prognosis
Czasopismo naukowe
Tytuł :
An engineered protein-phosphorylation toggle network with implications for endogenous network discovery.
Autorzy :
Mishra D; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
Bepler T; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.; Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA.; Simons Machine Learning Center, New York Structural Biology Center, New York, NY, USA.
Teague B; Department of Biology, University of Wisconsin, Stout, WI, USA.
Berger B; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.; Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA.; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA.
Broach J; Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA.
Weiss R; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.; Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA.; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Źródło :
Science (New York, N.Y.) [Science] 2021 Jul 02; Vol. 373 (6550).
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms :
Bioengineering*
Protein Interaction Maps*
Saccharomyces cerevisiae/*metabolism
Saccharomyces cerevisiae Proteins/*metabolism
Mitogen-Activated Protein Kinases/genetics ; Mitogen-Activated Protein Kinases/metabolism ; Phosphorylation ; Saccharomyces cerevisiae Proteins/genetics
Czasopismo naukowe
Tytuł :
Arena3Dweb: interactive 3D visualization of multilayered networks.
Autorzy :
Karatzas E; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari, Greece.
Baltoumas FA; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari, Greece.
Panayiotou NA; School of Mechanical Engineering, Section of Industrial Management and Operational Research, National Technical University of Athens, Zografou, Athens, Greece.
Schneider R; University of Luxembourg, Luxembourg Centre for Systems Biomedicine, Bioinformatics Core, Esch-sur-Alzette, Luxembourg.
Pavlopoulos GA; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari, Greece.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2021 Jul 02; Vol. 49 (W1), pp. W36-W45.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Algorithms*
Data Visualization*
Internet*
Protein Interaction Maps*
Software*
COVID-19/drug therapy ; COVID-19/metabolism ; Color ; Drug Repositioning ; Humans ; Melanoma/drug therapy ; Melanoma/metabolism ; Programming Languages ; Receptors, Endothelin/metabolism ; SARS-CoV-2/metabolism ; Signal Transduction
Czasopismo naukowe
Tytuł :
StrongestPath: a Cytoscape application for protein-protein interaction analysis.
Autorzy :
Mousavian Z; Department of Computer Science, School of Mathematics, Statistics and Computer Science, College of Science, University of Tehran, Tehran, Iran. .
Khodabandeh M; School of Computing Science, Simon Fraser University, Burnaby, BC, Canada.
Sharifi-Zarchi A; Department of Computer Engineering, Sharif University of Technology, Tehran, Iran.; Department of Stem cells and Developmental Biology at the Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
Nadafian A; Department of Computer Science, School of Mathematics, Statistics and Computer Science, College of Science, University of Tehran, Tehran, Iran.
Mahmoudi A; Department of Computer Science, School of Mathematics, Statistics and Computer Science, College of Science, University of Tehran, Tehran, Iran.
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Źródło :
BMC bioinformatics [BMC Bioinformatics] 2021 Jun 29; Vol. 22 (1), pp. 352. Date of Electronic Publication: 2021 Jun 29.
Typ publikacji :
Journal Article
MeSH Terms :
Protein Interaction Maps*
Proteins*/genetics
Proteins*/metabolism
Animals ; Mice
Czasopismo naukowe
Tytuł :
MONACO: accurate biological network alignment through optimal neighborhood matching between focal nodes.
Autorzy :
Woo HM; Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA.
Yoon BJ; Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA.; TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX 77845, USA.; Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jun 16; Vol. 37 (10), pp. 1401-1410.
Typ publikacji :
Journal Article
MeSH Terms :
Protein Interaction Mapping*
Protein Interaction Maps*
Algorithms ; Computational Biology ; Diffusion ; Monaco
Czasopismo naukowe
Tytuł :
Reliable identification of protein-protein interactions by crosslinking mass spectrometry.
Autorzy :
Lenz S; Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.
Sinn LR; Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.
O'Reilly FJ; Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.
Fischer L; Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.
Wegner F; Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.
Rappsilber J; Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany. .; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK. .
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Źródło :
Nature communications [Nat Commun] 2021 Jun 11; Vol. 12 (1), pp. 3564. Date of Electronic Publication: 2021 Jun 11.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Protein Interaction Maps*/genetics
Mass Spectrometry/*methods
Protein Interaction Mapping/*methods
Escherichia coli/genetics ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/metabolism ; Proteome
Czasopismo naukowe
Tytuł :
Protein functional module identification method combining topological features and gene expression data.
Autorzy :
Zhao Z; School of Computer and Information, Anhui Agricultural University, Hefei, Anhui, 230036, China.
Xu W; School of Computer and Information, Anhui Agricultural University, Hefei, Anhui, 230036, China.
Chen A; School of Computer and Information, Anhui Agricultural University, Hefei, Anhui, 230036, China.
Han Y; School of Computer and Information, Anhui Agricultural University, Hefei, Anhui, 230036, China.
Xia S; School of Computer and Information, Anhui Agricultural University, Hefei, Anhui, 230036, China.
Xiang C; School of Computer and Information, Anhui Agricultural University, Hefei, Anhui, 230036, China.
Wang C; School of Computer and Information, Anhui Agricultural University, Hefei, Anhui, 230036, China.
Jiao J; School of Computer and Information, Anhui Agricultural University, Hefei, Anhui, 230036, China.
Wang H; School of Computer and Information, Anhui Agricultural University, Hefei, Anhui, 230036, China.
Yuan X; Department of Computer Science and Engineering, University of North Texas, Denton, TX, 76203, United States.
Gu L; School of Computer and Information, Anhui Agricultural University, Hefei, Anhui, 230036, China. .
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Źródło :
BMC genomics [BMC Genomics] 2021 Jun 08; Vol. 22 (1), pp. 423. Date of Electronic Publication: 2021 Jun 08.
Typ publikacji :
Journal Article
MeSH Terms :
Protein Interaction Mapping*
Protein Interaction Maps*
Algorithms ; Cluster Analysis ; Gene Expression ; Proteins/genetics ; Proteins/metabolism
Czasopismo naukowe

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