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Systems Biology

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  • MultiCellDS: a standard and a community for sharing multicellular data
    Samuel H. Friedman, Alexander R. A. Anderson, David M. Bortz, Alexander G. Fletcher, Hermann B. Frieboes, Ahmadreza Ghaffarizadeh, David Robert Grimes, Andrea Hawkins-Daarud, Stefan Hoehme, Edwin F. Juarez, Carl Kesselman, Roeland M.H. Merks, Shannon M. Mumenthaler, Paul K. Newton, Kerri-Ann Norton, Rishi Rawat, Russell C. Rockne, Daniel Ruderman, Jacob Scott, Suzanne S. Sindi, Jessica L. Sparks, Kristin Swanson, David B. Agus, Paul Macklin
    bioRxiv 090696; doi: https://doi.org/10.1101/090696
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  • MultiCellDS: a community-developed standard for curating microenvironment-dependent multicellular data
    Samuel H. Friedman, Alexander R. A. Anderson, David M. Bortz, Alexander G. Fletcher, Hermann B. Frieboes, Ahmadreza Ghaffarizadeh, David Robert Grimes, Andrea Hawkins-Daarud, Stefan Hoehme, Edwin F. Juarez, Carl Kesselman, Roeland M.H. Merks, Shannon M. Mumenthaler, Paul K. Newton, Kerri-Ann Norton, Rishi Rawat, Russell C. Rockne, Daniel Ruderman, Jacob Scott, Suzanne S. Sindi, Jessica L. Sparks, Kristin Swanson, David B. Agus, Paul Macklin
    bioRxiv 090456; doi: https://doi.org/10.1101/090456
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  • Systematic morphological profiling of human gene and allele function reveals Hippo-NF-κB pathway connectivity
    Mohammad H Rohban, Shantanu Singh, Xiaoyun Wu, Julia B Berthet, Mark-Anthony Bray, Yashaswi Shrestha, Xaralabos Varelas, Jesse S Boehm, Anne E Carpenter
    bioRxiv 092403; doi: https://doi.org/10.1101/092403
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  • A synthesis of over 9,000 mass spectrometry experiments reveals the core set of human protein complexes
    Kevin Drew, Chanjae Lee, Ryan L. Huizar, Fan Tu, Blake Borgeson, Claire D. McWhite, Yun Ma, John B. Wallingford, Edward M. Marcotte
    bioRxiv 092361; doi: https://doi.org/10.1101/092361
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  • Investigating side effect modules in the interactome and their use in drug adverse effect discovery
    Emre Guney
    bioRxiv 089730; doi: https://doi.org/10.1101/089730
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  • Gene expression models based on a reference laboratory strain are bad predictors of Mycobacterium tuberculosis complex transcriptional diversity
    Alvaro Chiner-Oms, Fernando González-Candelas, Iñaki Comas
    bioRxiv 091082; doi: https://doi.org/10.1101/091082
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  • Inferring Fitness Landscapes and Selection on Phenotypic States from Single-Cell Genealogical Data
    Takashi Nozoe, Edo Kussell, Yuichi Wakamoto
    bioRxiv 069260; doi: https://doi.org/10.1101/069260
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  • Dissection of the contribution of regulation mode to the properties of feedforward and feedback gene regulatory motifs
    Bharat Ravi Iyengar, Beena Pillai, K.V. Venkatesh, Chetan J. Gadgil
    bioRxiv 065698; doi: https://doi.org/10.1101/065698
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  • Integrative epigenomics, transcriptomics and proteomics of patient chondrocytes reveal genes and pathways involved in osteoarthritis
    Julia Steinberg, Graham R. S. Ritchie, Theodoros I. Roumeliotis, Raveen L. Jayasuriya, Roger A. Brooks, Abbie L. A. Binch, Karan M. Shah, Rachael Coyle, Mercedes Pardo, Christine L. Le Maitre, Yolande F. M. Ramos, Rob G. H. H. Nelissen, Ingrid Meulenbelt, Andrew W. McCaskie, Jyoti S. Choudhary, J. Mark Wilkinson, Eleftheria Zeggini
    bioRxiv 038067; doi: https://doi.org/10.1101/038067
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  • NaviCom: A web application to create interactive molecular network portraits using multi-level omics data
    Mathurin Dorel, Emmanuel Barillot, Andrei Zinovyev, Inna Kuperstein
    bioRxiv 089367; doi: https://doi.org/10.1101/089367
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