1. Mapping transcription factor interactome networks using HaloTag protein arrays.

    PNAS 113(29):E4238 (2016) PMID 27357687 PMCID PMC4961138

    Protein microarrays enable investigation of diverse biochemical properties for thousands of proteins in a single experiment, an unparalleled capacity. Using a high-density system called HaloTag nucleic acid programmable protein array (HaloTag-NAPPA), we created high-density protein arrays compri...
  2. The transcription factor ERG recruits CCR4-NOT to control mRNA decay and mitotic progression.

    Nature Structural & Molecular Biology 23(7):663 (2016) PMID 27273514

    Control of mRNA levels, a fundamental aspect in the regulation of gene expression, is achieved through a balance between mRNA synthesis and decay. E26-related gene (Erg) proteins are canonical transcription factors whose previously described functions are confined to the control of mRNA synthesi...
  3. An extended set of yeast-based functional assays accurately identifies human disease mutations.

    Genome Research 26(5):670 (2016) PMID 26975778 PMCID PMC4864455

    We can now routinely identify coding variants within individual human genomes. A pressing challenge is to determine which variants disrupt the function of disease-associated genes. Both experimental and computational methods exist to predict pathogenicity of human genetic variation. However, a s...
  4. Pooled-matrix protein interaction screens using Barcode Fusion Genetics.

    Molecular Systems Biology 12(4):863 (2016) PMID 27107012 PMCID PMC4848762

    High-throughput binary protein interaction mapping is continuing to extend our understanding of cellular function and disease mechanisms. However, we remain one or two orders of magnitude away from a complete interaction map for humans and other major model organisms. Completion will require scr...
  5. An inter-species protein-protein interaction network across vast evolutionary distance.

    Molecular Systems Biology 12(4):865 (2016) PMID 27107014 PMCID PMC4848758

    In cellular systems, biophysical interactions between macromolecules underlie a complex web of functional interactions. How biophysical and functional networks are coordinated, whether all biophysical interactions correspond to functional interactions, and how such biophysical-versus-functional ...
  6. Survey of variation in human transcription factors reveals prevalent DNA binding changes.

    Science 351(6280):1450 (2016) PMID 27013732 PMCID PMC4825693

    Sequencing of exomes and genomes has revealed abundant genetic variation affecting the coding sequences of human transcription factors (TFs), but the consequences of such variation remain largely unexplored. We developed a computational, structure-based approach to evaluate TF variants for their...
  7. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.

    Cell 164(4):805 (2016) PMID 26871637 PMCID PMC4882190

    While alternative splicing is known to diversify the functional characteristics of some genes, the extent to which protein isoforms globally contribute to functional complexity on a proteomic scale remains unknown. To address this systematically, we cloned full-length open reading frames of alte...
  8. MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy.

    Cancer Discovery 6(1):45 (2016) PMID 26546296 PMCID PMC4775099

    An unbiased genome-scale screen for unmutated genes that drive cancer growth when overexpressed identified methyl cytosine-guanine dinucleotide (CpG) binding protein 2 (MECP2) as a novel oncogene. MECP2 resides in a region of the X-chromosome that is significantly amplified across 18% of cancers...
  9. The Xenopus ORFeome: A resource that enables functional genomics.

    Developmental Biology 408(2):345 (2015) PMID 26391338 PMCID PMC4684507

    Functional characterisation of proteins and large-scale, systems-level studies are enabled by extensive sets of cloned open reading frames (ORFs) in an easily-accessible format that enables many different applications. Here we report the release of the first stage of the Xenopus ORFeome, which c...
  10. Widespread macromolecular interaction perturbations in human genetic disorders.

    Cell 161(3):647 (2015) PMID 25910212 PMCID PMC4441215

    How disease-associated mutations impair protein activities in the context of biological networks remains mostly undetermined. Although a few renowned alleles are well characterized, functional information is missing for over 100,000 disease-associated variants. Here we functionally profile sever...
  11. Human gene-centered transcription factor networks for enhancers and disease variants.

    Cell 161(3):661 (2015) PMID 25910213 PMCID PMC4409666

    Gene regulatory networks (GRNs) comprising interactions between transcription factors (TFs) and regulatory loci control development and physiology. Numerous disease-associated mutations have been identified, the vast majority residing in non-coding regions of the genome. As current GRN mapping m...
  12. Protein domain-level landscape of cancer-type-specific somatic mutations.

    PLoS computational biology 11(3):e1004147 (2015) PMID 25794154 PMCID PMC4368709

    Identifying driver mutations and their functional consequences is critical to our understanding of cancer. Towards this goal, and because domains are the functional units of a protein, we explored the protein domain-level landscape of cancer-type-specific somatic mutations. Specifically, we syst...
  13. Spatiotemporal 16p11.2 protein network implicates cortical late mid-fetal brain development and KCTD13-Cul3-RhoA pathway in psychiatric diseases.

    Neuron 85(4):742 (2015) PMID 25695269 PMCID PMC4335356

    The psychiatric disorders autism and schizophrenia have a strong genetic component, and copy number variants (CNVs) are firmly implicated. Recurrent deletions and duplications of chromosome 16p11.2 confer a high risk for both diseases, but the pathways disrupted by this CNV are poorly defined. H...
  14. Multiplex single-molecule interaction profiling of DNA-barcoded proteins.

    Nature 515(7528):554 (2014) PMID 25252978 PMCID PMC4246050

    In contrast with advances in massively parallel DNA sequencing, high-throughput protein analyses are often limited by ensemble measurements, individual analyte purification and hence compromised quality and cost-effectiveness. Single-molecule protein detection using optical methods is limited by...
  15. A proteome-scale map of the human interactome network.

    Cell 159(5):1212 (2014) PMID 25416956 PMCID PMC4266588

    Just as reference genome sequences revolutionized human genetics, reference maps of interactome networks will be critical to fully understand genotype-phenotype relationships. Here, we describe a systematic map of ?14,000 high-quality human binary protein-protein interactions. At equal quality, ...
  16. Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage.

    Genes & Development 28(17):1957 (2014) PMID 25184681 PMCID PMC4197947

    BRCA1 is a breast and ovarian tumor suppressor. Given its numerous incompletely understood functions and the possibility that more exist, we performed complementary systematic screens in search of new BRCA1 protein-interacting partners. New BRCA1 functions and/or a better understanding of existi...
  17. Systematic identification of pathological lamin A interactors.

    Molecular Biology of the Cell 25(9):1493 (2014) PMID 24623722 PMCID PMC4004598

    Laminopathies are a collection of phenotypically diverse diseases that include muscular dystrophies, cardiomyopathies, lipodystrophies, and premature aging syndromes. Laminopathies are caused by >300 distinct mutations in the LMNA gene, which encodes the nuclear intermediate filament proteins la...
  18. Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism.

    Nature Communications 5:3650 (2014) PMID 24722188 PMCID PMC3996537

    Increased risk for autism spectrum disorders (ASD) is attributed to hundreds of genetic loci. The convergence of ASD variants have been investigated using various approaches, including protein interactions extracted from the published literature. However, these datasets are frequently incomplete...
  19. Mycobacterium tuberculosis type VII secreted effector EsxH targets host ESCRT to impair trafficking.

    PLoS Pathogens 9(10):e1003734 (2013) PMID 24204276 PMCID PMC3814348

    Mycobacterium tuberculosis (Mtb) disrupts anti-microbial pathways of macrophages, cells that normally kill bacteria. Over 40 years ago, D'Arcy Hart showed that Mtb avoids delivery to lysosomes, but the molecular mechanisms that allow Mtb to elude lysosomal degradation are poorly understood. Spec...
  20. Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network.

    Molecular Cell 51(1):116 (2013) PMID 23791784 PMCID PMC3794439

    Gene duplication results in two identical paralogs that diverge through mutation, leading to loss or gain of interactions with other biomolecules. Here, we comprehensively characterize such network rewiring for C. elegans transcription factors (TFs) within and across four newly delineated molecu...