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Humanization of yeast genes with multiple human orthologs reveals functional divergence between paralogs.
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- PLoS Biology, 2020, v. 18, n. 5, p. 1, doi. 10.1371/journal.pbio.3000627
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- Article
Many Nuanced Evolutionary Consequences of Duplicated Genes.
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- Molecular Biology & Evolution, 2019, v. 36, n. 2, p. 304, doi. 10.1093/molbev/msy210
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- Article
Discovery of new vascular disrupting agents based on evolutionarily conserved drug action, pesticide resistance mutations, and humanized yeast.
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- Genetics, 2021, v. 219, n. 1, p. 1, doi. 10.1093/genetics/iyab101
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- Article
Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex.
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- eLife, 2022, p. 1, doi. 10.7554/eLife.81977
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- Publication type:
- Article
Predictability of Genetic Interactions from Functional Gene Modules.
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- G3: Genes | Genomes | Genetics, 2017, v. 7, n. 2, p. 617, doi. 10.1534/g3.116.035915
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- Article
Towards Consensus Gene Ages.
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- Genome Biology & Evolution, 2016, v. 8, n. 6, p. 1812, doi. 10.1093/gbe/evw113
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- Article
Improving integrative 3D modeling into low‐ to medium‐resolution electron microscopy structures with evolutionary couplings.
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- Protein Science: A Publication of the Protein Society, 2021, v. 30, n. 5, p. 1006, doi. 10.1002/pro.4067
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- Publication type:
- Article
Amino acid sequence assignment from single molecule peptide sequencing data using a two-stage classifier.
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- PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011157
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- Article
Protein abundances are more conserved than mRNA abundances across diverse taxa.
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- Proteomics, 2010, v. 10, n. 23, p. 4209, doi. 10.1002/pmic.201000327
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- Article
Insights into the regulation of protein abundance from proteomic and transcriptomic analyses.
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- Nature Reviews Genetics, 2012, v. 13, n. 4, p. 227, doi. 10.1038/nrg3185
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- Article
HumanNet v3: an improved database of human gene networks for disease research.
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- Nucleic Acids Research, 2022, v. 50, n. D1, p. D632, doi. 10.1093/nar/gkab1048
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- Article
HumanNet v2: human gene networks for disease research.
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- Nucleic Acids Research, 2019, v. 47, n. D1, p. D573, doi. 10.1093/nar/gky1126
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- Publication type:
- Article
GWAB: a web server for the network-based boosting of human genome-wide association data.
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- Nucleic Acids Research, 2017, v. 45, n. W1, p. W154, doi. 10.1093/nar/gkx284
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- Publication type:
- Article
MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates.
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- Nucleic Acids Research, 2016, v. 44, n. 1, p. D848, doi. 10.1093/nar/gkv1155
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- Publication type:
- Article
MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network.
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- Nucleic Acids Research, 2014, v. 42, n. W1, p. W147, doi. 10.1093/nar/gku434
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- Publication type:
- Article
Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics.
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- PLoS Biology, 2009, v. 7, n. 10, p. 1, doi. 10.1371/journal.pbio.1000213
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- Publication type:
- Article
Group II Intron Protein Localization and Insertion Sites Are Affected by Polyphosphate.
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- PLoS Biology, 2008, v. 6, n. 6, p. e150, doi. 10.1371/journal.pbio.0060150
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- Publication type:
- Article
Functional expression of opioid receptors and other human GPCRs in yeast engineered to produce human sterols.
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- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-30570-7
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- Publication type:
- Article
Super.Complex: A supervised machine learning pipeline for molecular complex detection in protein-interaction networks.
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- PLoS ONE, 2021, v. 16, n. 12, p. 1, doi. 10.1371/journal.pone.0262056
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- Publication type:
- Article
Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence.
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- PLoS Computational Biology, 2008, v. 4, n. 11, p. 1, doi. 10.1371/journal.pcbi.1000232
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- Publication type:
- Article
Computational discovery of pathway-level genetic vulnerabilities in non-small-cell lung cancer.
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- Bioinformatics, 2016, v. 32, n. 9, p. 1373, doi. 10.1093/bioinformatics/btw010
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- Publication type:
- Article
Ribosome stalk assembly requires the dual-specificity phosphatase Yvh1 for the exchange of Mrt4 with P0.
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- Journal of Cell Biology, 2009, v. 186, n. 6, p. 849, doi. 10.1083/jcb.200904110
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- Article
A role for central spindle proteins in cilia structure and function.
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- Cytoskeleton, 2011, v. 68, n. 2, p. 112, doi. 10.1002/cm.20498
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- Article
Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness.
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- Nature Chemical Biology, 2014, v. 10, n. 3, p. 178, doi. 10.1038/nchembio.1450
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- Article
A highly parallel strategy for storage of digital information in living cells.
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- BMC Biotechnology, 2018, v. 18, n. 1, p. N.PAG, doi. 10.1186/s12896-018-0476-4
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- Publication type:
- Article
Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line.
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- Molecular Systems Biology, 2010, v. 6, n. 1, p. 1, doi. 10.1038/msb.2010.59
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- Article
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.
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- Molecular Systems Biology, 2008, v. 4, n. 1, p. 1, doi. 10.1038/msb.2008.19
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- Publication type:
- Article
Revisiting the negative example sampling problem for predicting protein–protein interactions.
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- Bioinformatics, 2011, v. 27, n. 21, p. 3024, doi. 10.1093/bioinformatics/btr514
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- Publication type:
- Article
Mining gene functional networks to improve mass-spectrometry-based protein identification.
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- Bioinformatics, 2009, v. 25, n. 22, p. 2955, doi. 10.1093/bioinformatics/btp461
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- Publication type:
- Article
Integrating shotgun proteomics and mRNA expression data to improve protein identification.
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- Bioinformatics, 2009, v. 25, n. 11, p. 1397, doi. 10.1093/bioinformatics/btp168
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- Publication type:
- Article
mspire: mass spectrometry proteomics in Ruby.
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- Bioinformatics, 2008, v. 24, n. 23, p. 2796, doi. 10.1093/bioinformatics/btn513
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- Article
A fast coarse filtering method for peptide identification by mass spectrometry.
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- Bioinformatics, 2006, v. 22, n. 12, p. 1524
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- Publication type:
- Article
Protein function prediction using the Protein Link EXplorer (PLEX).
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- Bioinformatics, 2005, v. 21, n. 10, p. 2558, doi. 10.1093/bioinformatics/bti313
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- Publication type:
- Article
Diametrical clustering for identifying anti-correlated gene clusters.
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- Bioinformatics, 2003, v. 19, n. 13, p. 1612, doi. 10.1093/bioinformatics/btg209
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- Publication type:
- Article
Exploiting big biology: Integrating large-scale biological data for function inference.
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- Briefings in Bioinformatics, 2001, v. 2, n. 4, p. 51, doi. 10.1093/bib/2.4.363
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- Article
RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network.
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- Genome Biology, 2012, v. 13, n. 12, p. 1, doi. 10.1186/gb-2012-13-12-r125
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- Article
Simplified geometric representations of protein structures identify complementary interaction interfaces.
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- Proteins, 2021, v. 89, n. 3, p. 348, doi. 10.1002/prot.26020
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- Article
Prediction of gene-phenotype associations in humans, mice, and plants using phenologs.
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- BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-203
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- Article
Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins.
- Published in:
- eLife, 2021, p. 1, doi. 10.7554/eLife.58662
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- Article
Temporal stability and molecular persistence of the bone marrow plasma cell antibody repertoire.
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- Nature Communications, 2016, v. 7, n. 12, p. 13838, doi. 10.1038/ncomms13838
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- Article
Modes of Interaction between Individuals Dominate the Topologies of Real World Networks.
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- PLoS ONE, 2015, v. 10, n. 3, p. 1, doi. 10.1371/journal.pone.0121248
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- Publication type:
- Article
<i>Pseudomonas aeruginosa</i> Enhances Production of a Non-Alginate Exopolysaccharide during Long-Term Colonization of the Cystic Fibrosis Lung.
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- PLoS ONE, 2013, v. 8, n. 12, p. 1, doi. 10.1371/journal.pone.0082621
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- Publication type:
- Article
Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses
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- PLoS ONE, 2013, v. 8, n. 5, p. 1, doi. 10.1371/journal.pone.0058977
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- Article
Transiently Transfected Purine Biosynthetic Enzymes Form Stress Bodies.
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- PLoS ONE, 2013, v. 8, n. 2, p. 1, doi. 10.1371/journal.pone.0056203
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- Publication type:
- Article
Human Cell Chips: Adapting DNA Microarray Spotting Technology to Cell-Based Imaging Assays.
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- PLoS ONE, 2009, v. 4, n. 10, p. 1, doi. 10.1371/journal.pone.0007088
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- Article
An open invitation to the Understudied Proteins Initiative.
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- 2022
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- Publication type:
- Letter
Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures.
- Published in:
- Nature Biotechnology, 2018, v. 36, n. 11, p. 1076, doi. 10.1038/nbt.4278
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- Article
A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans.
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- Nature Genetics, 2008, v. 40, n. 2, p. 181, doi. 10.1038/ng.2007.70
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- Article
A probabilistic view of gene function.
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- Nature Genetics, 2004, v. 36, n. 6, p. 559, doi. 10.1038/ng1370
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- Article
Flaws in evaluation schemes for pair-input computational predictions.
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- Nature Methods, 2012, v. 9, n. 12, p. 1134, doi. 10.1038/nmeth.2259
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- Article