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1. Full Text Natural Variation in Gene Expression Modulates the Severity of Mutant Phenotypes
by Vu, Victoria and Verster, Adrian J and Schertzberg, Michael and Chuluunbaatar, Tungalag and Spensley, Mark and Pajkic, Djina and Hart, G. Traver and Moffat, Jason and Fraser, Andrew G
Cell, ISSN 0092-8674, 07/2015, Volume 162, Issue 2, pp. 391 - 402
Many mutations cause genetic disorders. However, two people inheriting the same mutation often have different severity of symptoms, and this is partly genetic.... 
RNA INTERFERENCE | PENETRANCE | MODIFIER | IDENTIFY | CAENORHABDITIS-ELEGANS | GENOTYPE | BIOCHEMISTRY & MOLECULAR BIOLOGY | MARFAN-SYNDROME | DISEASE | C-ELEGANS | CYSTIC-FIBROSIS | CELL BIOLOGY | Genetic Variation | Caenorhabditis elegans - classification | Phenotype | Animals | RNA Interference | Caenorhabditis elegans - genetics | Mutation | Gene Knockdown Techniques | Molecular genetics | Analysis | Genes | Genetic aspects | Gene expression | Cells
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2. Full Text BAGEL: a computational framework for identifying essential genes from pooled library screens
by Hart, Traver and Moffat, Jason
BMC bioinformatics, 04/2016, Volume 17, p. 164
The adaptation of the CRISPR-Cas9 system to pooled library gene knockout screens in mammalian cells represents a major technological leap over RNA... 
Computational Biology - methods | Epithelial Cells - metabolism | Gene Library | HCT116 Cells | Humans | Gene Knockout Techniques | Genes, Essential | Machine Learning | Genetic Fitness | Glioblastoma - genetics | RNA Interference | Sensitivity and Specificity | Cell Line, Tumor | Models, Genetic | HeLa Cells
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3. Full Text A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality
by Hart, G. Traver and Lee, Insuk and Marcotte, Edward R
BMC Bioinformatics, ISSN 1471-2105, 07/2007, Volume 8, Issue 1, pp. 236 - 236
Background: Identifying all protein complexes in an organism is a major goal of systems biology. In the past 18 months, the results of two genome-scale tandem... 
INTERACTION NETWORKS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | SACCHAROMYCES-CEREVISIAE | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | INTERACTOME | Gene Expression Regulation, Fungal | Multiprotein Complexes | Proteome | Saccharomyces cerevisiae - metabolism | Protein Interaction Mapping - methods | Algorithms | Databases, Protein | Mass Spectrometry | Bayes Theorem | Proteomics | Saccharomyces cerevisiae Proteins - metabolism | Genes, Fungal | Cluster Analysis | Saccharomyces cerevisiae Proteins - chemistry | Proteins | Genetic aspects | Research | Brewer's yeast | Identification and classification
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4. Full Text How complete are current yeast and human protein-interaction networks?
by Hart, G. Traver and Ramani, Arun K and Marcotte, Edward M
Genome Biology, ISSN 1474-7596, 12/2006, Volume 7, Issue 11, pp. 120 - 120
We estimate the full yeast protein-protein interaction network to contain 37,800-75,500 interactions and the human network 154,000-369,000, but owing to a high... 
ORGANIZATION | DATABASE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | ESCHERICHIA-COLI | GENETICS & HEREDITY | INTERACTION MAP | UPDATE | SACCHAROMYCES-CEREVISIAE | SYSTEMATIC IDENTIFICATION | GENE-FUNCTION | RESOURCE | REVEALS | Saccharomyces cerevisiae - metabolism | Protein Binding | Databases, Protein | Humans | Saccharomyces cerevisiae Proteins - metabolism | Protein Interaction Mapping | Opinion
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5. Full Text Chemogenetic interactions in human cancer cells
by Colic, Medina and Hart, Traver
Computational and Structural Biotechnology Journal, ISSN 2001-0370, 2019, Volume 17, pp. 1318 - 1325
Chemogenetic profiling enables the identification of genes that enhance or suppress the phenotypic effect of chemical compounds. Using this approach in cancer... 
Chemogenetic screens | CRISPR | Drug-gene interactions
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6. Full Text Measuring error rates in genomic perturbation screens: gold standards for human functional genomics
by Hart, Traver and Brown, Kevin R and Sircoulomb, Fabrice and Rottapel, Robert and Moffat, Jason
Molecular Systems Biology, ISSN 1744-4292, 07/2014, Volume 10, Issue 7, pp. 733 - n/a
Technological advancement has opened the door to systematic genetics in mammalian cells. Genome‐scale loss‐of‐function screens can assay fitness defects... 
CRISPR | RNAi | cancer | shRNA | essential genes | VULNERABILITIES | POSITIVES | PROFILES | BIOCHEMISTRY & MOLECULAR BIOLOGY | SUPPRESSION | YEAST | HUMAN-DISEASE GENES | LETHALITY | INHIBITOR | REVEALS | Gold | Genomes | Genes | Genomics | Performance evaluation | Analytical methods | Medical research | Error analysis | RNA-mediated interference | Organisms | Perturbation | Gene expression | Screens | Mammalian cells | Proteins | Genotype & phenotype | Cell growth | Technology | Reagents | Genetics | Bayesian analysis | Cancer | Fitness
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7. Full Text BAGEL: A computational framework for identifying essential genes from pooled library screens
by Hart, Traver and Moffat, Jason
BMC Bioinformatics, ISSN 1471-2105, 04/2016, Volume 17, Issue 1
Background: The adaptation of the CRISPR-Cas9 system to pooled library gene knockout screens in mammalian cells represents a major technological leap over RNA... 
CRISPR | Essential genes | Genetic screens | Functional genomics | Cancer | CELLS | RNAI | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | IDENTIFICATION | WIDE CRISPR SCREEN | Research | Gene expression | Genomics | Cells
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8. Full Text Scaling up the systematic hunt for mammalian genetic interactions: three RNA interference-based methods probe genetic interactions in mammalian cells at large scale
by Hart, Traver and Moffat, Jason
Nature Methods, ISSN 1548-7091, 05/2013, Volume 10, Issue 5, p. 397
Genetic research | Genetic aspects | Research | Mammals | Methods | Cells
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9. Full Text A Census of Human Soluble Protein Complexes
by Havugimana, Pierre C and Hart, G. Traver and Nepusz, Tamás and Yang, Haixuan and Turinsky, Andrei L and Li, Zhihua and Wang, Peggy I and Boutz, Daniel R and Fong, Vincent and Phanse, Sadhna and Babu, Mohan and Craig, Stephanie A and Hu, Pingzhao and Wan, Cuihong and Vlasblom, James and Dar, Vaqaar-un-Nisa and Bezginov, Alexandr and Clark, Gregory W and Wu, Gabriel C and Wodak, Shoshana J and Tillier, Elisabeth R.M and Paccanaro, Alberto and Marcotte, Edward M and Emili, Andrew
Cell, ISSN 0092-8674, 08/2012, Volume 150, Issue 5, pp. 1068 - 1081
Cellular processes often depend on stable physical associations between proteins. Despite recent progress, knowledge of the composition of human protein... 
SYSTEMATIC ANALYSIS | INTERACTION NETWORK | ORGANIZATION | 8Q24 | BIOCHEMISTRY & MOLECULAR BIOLOGY | GENES | SCALE | MUTATIONS | CELL | MAP | DISCOVERY | CELL BIOLOGY | Molecular genetics | Children's hospitals | Oncology, Experimental | Genes | Disease susceptibility | Research | Chromatography | Cells | Proteins | Computer science | Analysis | Physiological aspects | Mass spectrometry | Cancer
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10. Full Text Genome-wide CRISPR screens reveal a Wnt-FZD5 signaling circuit as a druggable vulnerability of RNF43-mutant pancreatic tumors
by Steinhart, Zachary and Pavlovic, Zvezdan and Chanashekhar, Megha and Hart, Traver and Wang, Xiaowei and Zhang, Xiaoyu and Robitaille, Mélanie and Brown, Kevin R and Jaksani, Sridevi and Overmeer, René and Boj, Sylvia F and Adams, Jarrett and Pan, James and Clevers, Hans and Sidhu, Sachdev and Moffat, Jason and Angers, Stéphane
Nature Medicine, ISSN 1078-8956, 01/2017, Volume 23, Issue 1, pp. 60 - 68
Forward genetic screens with CRISPR-Cas9 genome editing enable high-resolution detection of genetic vulnerabilities in cancer cells. We conducted genome-wide... 
Medicine(all) | Biochemistry, Genetics and Molecular Biology(all) | Journal Article | MEDICINE, RESEARCH & EXPERIMENTAL | RNF43 | HUMAN-CELLS | BIOCHEMISTRY & MOLECULAR BIOLOGY | MECHANISMS | CANCER | CELL BIOLOGY | ESSENTIAL GENES | INHIBITION | GROWTH | MUTATIONAL LANDSCAPE | WNT | RECEPTORS | Frizzled Receptors - antagonists & inhibitors | Neoplasm Transplantation | Oncogene Proteins - genetics | Pancreatic Neoplasms - metabolism | Colorectal Neoplasms - genetics | Humans | Carcinoma, Pancreatic Ductal - metabolism | Molecular Targeted Therapy | RNA, Messenger - metabolism | Carcinoma, Pancreatic Ductal - genetics | Adenocarcinoma - metabolism | Flow Cytometry | Organoids - metabolism | Clustered Regularly Interspaced Short Palindromic Repeats | Adenocarcinoma - genetics | Real-Time Polymerase Chain Reaction | Colorectal Neoplasms - metabolism | Frizzled Receptors - metabolism | Pancreatic Neoplasms - genetics | DNA-Binding Proteins - genetics | Mice, SCID | Reverse Transcriptase Polymerase Chain Reaction | Antibodies - pharmacology | Animals | Wnt Signaling Pathway - drug effects | Wnt Signaling Pathway - genetics | Cell Cycle Checkpoints - drug effects | Fluorescent Antibody Technique | Organoids - drug effects | Cell Line, Tumor | Mice | Care and treatment | Pancreatic cancer | Innovations | Development and progression | Genotype | Genetic engineering | Cellular signal transduction | Genetic aspects | Health aspects | Proteins | Viral antibodies | Genomics | Colorectal cancer | Antibodies | Genomes | Genetic screening | Cell proliferation | Adenocarcinoma | CRISPR | Therapy | Immunoglobulins | Wnt protein | Frizzled protein | Xenotransplantation | Colorectal carcinoma | Cell surface | Signaling | Receptors | Organoids | Xenografts | Inhibition | Mutation | Pancreas | Tumors | Recombinant
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11. Full Text Finding the active genes in deep RNA-seq gene expression studies
by Hart, Traver and Komori, H K and LaMere, Sarah and Podshivalova, Katie and Salomon, Daniel R
BMC Genomics, ISSN 1471-2164, 11/2013, Volume 14, Issue 1, pp. 778 - 778
Background: Early application of second-generation sequencing technologies to transcript quantitation (RNA-seq) has hinted at a vast mammalian transcriptome,... 
CELLS | HUMAN GENOME | TRANSCRIPTOME | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | QUANTIFICATION | GENETICS & HEREDITY | Animals | Humans | RNA, Messenger - genetics | Transcriptome | Genome | High-Throughput Nucleotide Sequencing - methods | Chromatin - genetics | RNA sequencing | Gene expression | Research | Chromatin | Cells | Studies | Proteins | Genomes
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12. Full Text The shieldin complex mediates 53BP1-dependent DNA repair
by Noordermeer, Sylvie M and Adam, Salomé and Setiaputra, Dheva and Barazas, Marco and Pettitt, Stephen J and Ling, Alexanda K and Olivieri, Michele and Álvarez-Quilón, Alejandro and Moatti, Nathalie and Zimmermann, Michal and Annunziato, Stefano and Krastev, Dragomir B and Song, Feifei and Brandsma, Inger and Frankum, Jessica and Brough, Rachel and Sherker, Alana and Landry, Sébastien and Szilard, Rachel K and Munro, Meagan M and McEwan, Andrea and de Rugy, Théo Goullet and Lin, Zhen-Yuan and Hart, Traver and Moffat, Jason and Gingras, Anne-Claude and Martin, Alberto and van Attikum, Haico and Jonkers, Jos and Lord, Christopher J and Rottenberg, Sven and Durocher, Daniel
Nature, ISSN 0028-0836, 2018, Volume 560, Issue 7716, pp. 117 - 121
53BP1 is a chromatin-binding protein that regulates the repair of DNA double-strand breaks by suppressing the nucleolytic resection of DNA termini(1,2). This... 
5' END RESECTION | BREAST-CANCER | BRCA1-DEFICIENT CELLS | MAMMARY-TUMORS | 53BP1 | MULTIDISCIPLINARY SCIENCES | RESISTANCE | HOMOLOGOUS RECOMBINATION | BRCA1 | INHIBITOR | MASS SPECTROMETRY DATA | Immunoglobulins | Research | DNA repair | Protein binding | Chromatin | Single-stranded DNA | DNA damage | Homologous recombination | Poly(ADP-ribose) | Homology | Genomes | ADP | Proteins | Restoration | Ribose | Repair | Deoxyribonucleic acid--DNA | CRISPR | Integrated software | BRCA1 protein | Poly(ADP-ribose) polymerase | Breast cancer | Gene expression | Class switching | Domains | Polymerase | Non-homologous end joining | Proteomics | Scientific imaging | Mutation | Mass spectrometry | Cancer | Tumors
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13. Full Text CRISPR screens identify genomic ribonucleotides as a source of PARP-trapping lesions
by Zimmermann, Michal and Murina, Olga and Reijns, Martin A. M and Agathanggelou, Angelo and Challis, Rachel and Tarnauskaite, Žygimante and Muir, Morwenna and Fluteau, Adeline and Aregger, Michael and McEwan, Andrea and Yuan, Wei and Clarke, Matthew and Lambros, Maryou B and Paneesha, Shankara and Moss, Paul and Chandrashekhar, Megha and Angers, Stephane and Moffat, Jason and Brunton, Valerie G and Hart, Traver and De Bono, Johann and Stankovic, Tatjana and Jackson, Andrew P and Durocher, Daniel
Nature, ISSN 0028-0836, 07/2018, Volume 559, Issue 7713, pp. 285 - 289
The observation that BRCA1-and BRCA2-deficient cells are sensitive to inhibitors of poly(ADP-ribose) polymerase (PARP) has spurred the development of cancer... 
RNASE H2 | CELLS | REPLICATION | MULTIDISCIPLINARY SCIENCES | PROSTATE-CANCER | DNA-DAMAGE | ANTIANDROGEN RESISTANCE | LINEAGE PLASTICITY | GENES | TRANSCRIPTION | TOPOISOMERASE-I | Humans | Genome - genetics | Male | Synthetic Lethal Mutations | DNA Repair - genetics | Leukemia, Lymphocytic, Chronic, B-Cell - genetics | Ribonucleotides - genetics | Neoplasms - genetics | Poly (ADP-Ribose) Polymerase-1 - deficiency | Female | Genes, BRCA1 | BRCA1 Protein - deficiency | Prostatic Neoplasms - drug therapy | Ribonuclease H - genetics | DNA Damage - drug effects | Cell Line | Prostatic Neoplasms - pathology | DNA Topoisomerases, Type I - metabolism | Ribonuclease H - deficiency | Neoplasms - enzymology | DNA Replication | Poly (ADP-Ribose) Polymerase-1 - metabolism | Piperazines - pharmacology | Gene Editing | Leukemia, Lymphocytic, Chronic, B-Cell - pathology | Neoplasms - drug therapy | Xenograft Model Antitumor Assays | BRCA1 Protein - genetics | Phthalazines - pharmacology | Poly(ADP-ribose) Polymerase Inhibitors - pharmacology | Leukemia, Lymphocytic, Chronic, B-Cell - enzymology | Animals | CRISPR-Cas Systems | Prostatic Neoplasms - enzymology | Mice | HeLa Cells | Leukemia, Lymphocytic, Chronic, B-Cell - drug therapy | Neoplasms - pathology | Poly (ADP-Ribose) Polymerase-1 - genetics | Ribonuclease H - metabolism | DNA polymerases | Physiological aspects | Ribonucleotides | Genetic aspects | Ionizing radiation | DNA replication | Genes | Genomics | Development and progression | Ribonuclease | Health aspects | Prostate cancer | Sugars | Monosaccharides | Toxicity | Leukemia | Homologous recombination | DNA damage | Poly(ADP-ribose) | Cytotoxicity | Homology | Genomes | Kinases | ADP | Metastases | Ribonuclease H2 | Proteins | Dwarfism | Genotype & phenotype | Clonal deletion | Ribose | Cell cycle | Deletion | Inhibition | Lesions | Repair | Deoxyribonucleic acid--DNA | Adducts | BRCA2 protein | CRISPR | Enzymes | Chronic lymphatic leukemia | BRCA1 protein | Anemia | Hypersensitivity | Poly(ADP-ribose) polymerase | Breast cancer | Screens | Substrates | Polymerase | DNA biosynthesis | Poly(ADP-ribose) Polymerase 1 | Trapping | Inhibitors | Mutation | DNA adducts | Prostate | Cancer
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14. Full Text High-throughput immunofluorescence microscopy using yeast spheroplast cell-based microarrays
by Niu, Wei and Niu, Wei and Hart, G Traver and Traver Hart, G and Marcotte, Edward M and Marcotte, Edward M
Methods in molecular biology (Clifton, N.J.), ISSN 1064-3745, 2011, Volume 706, pp. 83 - 95
We have described a protocol for performing high-throughput immunofluorescence microscopy on microarrays of yeast cells. This approach employs immunostaining... 
Yeast | Microtubule | Cell microarrays | Immunofluorescence | High-throughput microscopy | Yeasts - genetics | Microtubules - metabolism | Spindle Apparatus - metabolism | Down-Regulation | Tetracycline - pharmacology | Spindle Apparatus - pathology | Genes, Fungal | Tissue Array Analysis - methods | Microscopy, Fluorescence | High-Throughput Screening Assays - methods | Spheroplasts - genetics | microtubule | cell microarrays | high-throughput microscopy | immunofluorescence
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15. Full Text Scaling up the systematic hunt for mammalian genetic interactions
by Hart, Traver and Moffat, Jason
Nature Methods, ISSN 1548-7091, 05/2013, Volume 10, Issue 5, pp. 397 - 399
  Hart and Moffat comment on three recent studies introducing different approaches, all based on RNA interference (RNAi), to genetic interaction assays in... 
HUMAN GENOME | OVARIAN-CANCER | CELL | BIOCHEMICAL RESEARCH METHODS | RNA Interference | Humans | Animals | Biotechnology | Genetics | Ribonucleic acid--RNA | Biological assays | Mammals
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