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  1. No Access


    Programmatic Retrieval of Small Molecule Information from PubChem Using PUG-REST

    PubChem ( is an open archive which contains information on small molecules as well as other chemical entities such as lipids, carb...

    Sunghwan Kim, Paul A. Thiessen, Evan E. Bolton (2019)

  2. No Access


    Predicting Tumor Growth and Ligand Dependence from mRNA by Combining Machine Learning with Mechanistic Modeling

    For successful treatment of cancer patients, it is crucial to identify subgroups that respond to certain types of targeted therapy. A key element for tumor growth is the abundance of receptors and binding of g...

    Helge Hass, Andreas Raue (2019)

  3. No Access


    Image-based Identification of Chemical Compounds Capable of Trapping FOXO in the Cell Nucleus

    Forkhead box O (FOXO) factors are tumor suppressor proteins commonly inactivated in human tumors. Furthermore, genetic variation within the FOXO3a gene is consistently associated with human longevity. FOXO pro...

    Susana Machado, Catarina Raposo, Bibiana I. Ferreira in FOXO Transcription Factors (2019)

  4. No Access


    High-Resolution Mapping of N 6-Methyladenosine Using m6A Crosslinking Immunoprecipitation Sequencing (m6A-CLIP-Seq)

    N 6-Methyladenosine, an abundant chemical modification in mRNA, plays crucial roles in regulating gene expression and biological processes. Research on m6A and its functions has progressed rapidly in the past fe...

    Phillip J. Hsu, Chuan He in Epitranscriptomics (2019)

  5. No Access


    Transgene Recombineering in Bacterial Artificial Chromosomes

    Bacterial Artificial Chromosome (BAC) libraries are a valuable research resource. Any one of the clones in these libraries can carry hundreds of thousands of base pairs of genetic information. Often the entire...

    Michael G. Zeidler, Thomas L. Saunders in Microinjection (2019)

  6. No Access


    Live Cell Imaging of Hepatitis C Virus Trafficking in Hepatocytes

    Standard fixed cell confocal microscopy is inherently limited in visualizing dynamic processes involving two- and three-dimensional movement. To overcome these limitations, live cell imaging approaches have be...

    Yasmine Baktash, Glenn Randall in Hepatitis C Virus Protocols (2019)

  7. No Access


    A Protocol to Study T-Cell Signaling in an Immune Synapse by Microscopy

    The immune synapse is a complex cellular structure that enables cell–cell communications between immune cells, mainly at the interface of an effector T-cell and an antigen-presenting cell (APC) that expresses ...

    Mobashar Hussain Urf Turabe Fazil, Pankaj Kumar, Navin Kumar Verma in T-Cell Motility (2019)

  8. No Access


    Monitoring of Interferon Response Triggered by Cells Infected by Hepatitis C Virus or Other Viruses Upon Cell–Cell Contact

    Plasmacytoid dendritic cells (pDCs) constitute a unique DC subset specialized in rapid and massive secretion of cytokines, including type I interferon (i.e., IFNα and IFNβ), known to be pivotal for both innate...

    Séverin Coléon, Sonia Assil, Marlène Dreux in Hepatitis C Virus Protocols (2019)

  9. No Access


    Single-Cell Library Preparation of iPSC-Derived Neural Stem Cells

    Single-cell RNA-seq technology allows for the identification of heterogeneous cell populations, measures stochastic gene expressions, and identifies highly variable genes. Thus, with this technology it is poss...

    Jeffrey Kim, Marcel M. Daadi in Neural Stem Cells (2019)

  10. No Access


    Chemical Synthesis of an Asymmetric Mimic of the Nitrogenase Active Site

    The synthetic inorganic chemistry of metal–sulfur (M-S, M = metals) clusters has played an important, complementary role to the biochemical analyses of nitrogenase toward a better understanding of the enzyme a...

    Kazuki Tanifuji, Yasuhiro Ohki in Metalloproteins (2019)

  11. No Access


    An In Vitro Three-Dimensional Organotypic Model to Analyze Peripancreatic Fat Invasion in Pancreatic Cancer: A Culture System Based on Collagen Gel Embedding

    Three-dimensional culture systems reflect biological environments better than conventional two-dimensional culture. Additionally, three-dimensional culture is a strong experimental tool to analyze direct inter...

    Takashi Okumura, Kenoki Ohuchida, Masafumi Nakamura in Pancreatic Cancer (2019)

  12. No Access


    Interface-Based Structural Prediction of Novel Host-Pathogen Interactions

    About 20% of the cancer incidences worldwide have been estimated to be associated with infections. However, the molecular mechanisms of exactly how they contribute to host tumorigenesis are still unknown. To e...

    Emine Guven-Maiorov, Chung-Jung Tsai in Computational Methods in Protein Evolution (2019)

  13. No Access


    Single-Cell Analysis of Circulating Tumor Cells

    Circulating tumor cells (CTCs) are rare cells that can be found in the peripheral blood of cancer patients. They have been demonstrated to be useful prognostic markers in many cancer types. Within the last dec...

    Jana- A. Thiele, Pavel Pitule, James Hicks, Peter Kuhn in Tumor Profiling (2019)

  14. No Access


    In Silico-Directed Evolution Using CADEE

    Recent years have seen an explosion of interest in both sequence- and structure-based approaches toward in silico-directed evolution. We recently developed a novel computational toolkit, CADEE, which facilitat...

    Beat Anton Amrein, Ashish Runthala in Computational Methods in Protein Evolution (2019)

  15. No Access


    Rare Variant Quantitation Using Droplet Digital PCR

    Droplet digital PCR (ddPCR) allows precise quantitation of individual copies of DNA. Using allele-specific fluorescent oligonucleotide probes, ddPCR can enumerate both mutant and wild-type alleles enabling hig...

    Brian Parkin in Chronic Lymphocytic Leukemia (2019)

  16. No Access


    Modeling Long ncRNA-Mediated Regulation in the Mammalian Cell Cycle

    Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides that are not translated into proteins. They have recently gained widespread attention due to the finding that tens of thousands of lncR...

    Jomar F. Rabajante, Ricardo C. H. del Rosario in Computational Biology of Non-Coding RNA (2019)

  17. No Access


    Genome Sequencing and Analysis Methods in Chronic Lymphocytic Leukemia

    The genomic sequencing of chronic lymphocytic leukemia (CLL) samples has provided exciting new venues for the understanding and treatment of this prevalent disease. This feat is possible thanks to high-through...

    Víctor Quesada, Miguel Araujo-Voces, José G. Pérez-Silva in Chronic Lymphocytic Leukemia (2019)

  18. No Access


    Identification of Proteins on Archived 2D Gels

    Separation technology of proteins from a complex mixture by two-dimensional gel (2D gel) was invented more than 40 years ago. With a good laboratory practice, the 2D gels are likely to be dried and stored at a...

    Hiroyuki Matsumoto, Nobuaki Takemori in Electrophoretic Separation of Proteins (2019)

  19. No Access


    Tumor-Associated Macrophage Isolation and In Vivo Analysis of Their Tumor-Promoting Activity

    Characterization of individual cell populations from the tumor microenvironment is critical to understand their functional contribution to tumor progression. Magnetic bead enrichment and fluorescence-activated...

    Nicholas M. Clark, Paula D. Bos in Cancer Immunosurveillance (2019)

  20. No Access


    MHC Class I Internalization via Autophagy Proteins

    Macroautophagy is a ubiquitous degradative pathway involved in innate and adaptive immunity. Its molecular machinery has been described to deliver intracellular and extracellular antigens to MHC class II loadi...

    Monica Loi, Laure-Anne Ligeon, Christian Münz in Autophagy (2019)

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