The computational capabilities of many-to-many protein interaction networks.

[1]  M. Elowitz,et al.  Combinatorial expression motifs in signaling pathways , 2022, bioRxiv.

[2]  M. Elowitz,et al.  A synthetic protein-level neural network in mammalian cells , 2022, bioRxiv.

[3]  Supravat Dey,et al.  Gene copy number and negative feedback differentially regulate transcriptional variability of segmentation clock genes , 2022, iScience.

[4]  N. Neff,et al.  Comprehensive characterization of the transcriptional response to COVID-19 in multiple organs reveals shared signatures across tissues , 2022, bioRxiv.

[5]  R. Jerala,et al.  Designed protease-based signaling networks. , 2022, Current opinion in chemical biology.

[6]  R. Mann,et al.  Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors , 2022, Nature Communications.

[7]  Christopher A. Voigt,et al.  Genetic circuit design automation with Cello 2.0 , 2022, Nature Protocols.

[8]  J. Collins,et al.  Engineering living therapeutics with synthetic biology , 2021, Nature Reviews Drug Discovery.

[9]  A. Murphy,et al.  Anti-ACVR1 antibodies exacerbate heterotopic ossification in fibrodysplasia ossificans progressiva (FOP) by activating FOP-mutant ACVR1 , 2021, bioRxiv.

[10]  M. Elowitz,et al.  Programmable protein circuit design , 2021, Cell.

[11]  M. Elowitz,et al.  Synthetic multistability in mammalian cells , 2021, bioRxiv.

[12]  Yaron E. Antebi,et al.  Ligand-receptor promiscuity enables cellular addressing , 2020, bioRxiv.

[13]  Yaron E. Antebi,et al.  The context-dependent, combinatorial logic of BMP signaling , 2020, bioRxiv.

[14]  A. Ay,et al.  Segmentation clock gene pairing drives robust pattern formation , 2020, Nature.

[15]  David E. Gloriam,et al.  Combinatorial expression of GPCR isoforms affects signalling and drug responses , 2020, Nature.

[16]  Wei Zheng,et al.  Saracatinib is an efficacious clinical candidate for fibrodysplasia ossificans progressiva , 2020, bioRxiv.

[17]  R. Haltiwanger,et al.  Canonical Notch ligands and Fringes have distinct effects on NOTCH1 and NOTCH2 , 2020, The Journal of Biological Chemistry.

[18]  Paul W Anderson,et al.  A Human IgSF Cell-Surface Interactome Reveals a Complex Network of Protein-Protein Interactions , 2020, Cell.

[19]  Yu Zhang,et al.  The changing mouse embryo transcriptome at whole tissue and single-cell resolution , 2020, Nature.

[20]  Zachary D. Smith,et al.  Epigenetic regulator function through mouse gastrulation , 2020, Nature.

[21]  N. Jura,et al.  Receptor tyrosine kinase activation: From the ligand perspective. , 2020, Current opinion in cell biology.

[22]  R. Kageyama,et al.  Oscillatory expression of Hes1 regulates cell proliferation and neuronal differentiation in the embryonic brain , 2020, Development.

[23]  D. Leckband,et al.  Cadherin Complexes are Combinatorial Mechano-Switches that Differentially Regulate Cell Mechanics , 2020 .

[24]  J. Nickel,et al.  Specification of BMP Signaling , 2019, Cells.

[25]  C. Ruppert,et al.  BMPR2 acts as a gatekeeper to protect endothelial cells from increased TGFβ responses and altered cell mechanics , 2019, PLoS biology.

[26]  Tina Lebar,et al.  A tunable orthogonal coiled-coil interaction toolbox for engineering mammalian cells , 2019, Nature Chemical Biology.

[27]  C. Heisenberg,et al.  An adhesion code ensures robust pattern formation during tissue morphogenesis , 2019, Science.

[28]  Irving L. Weissman,et al.  A molecular cell atlas of the human lung from single cell RNA sequencing , 2019, Nature.

[29]  M. Fussenegger,et al.  From synthetic biology to human therapy: engineered mammalian cells. , 2019, Current opinion in biotechnology.

[30]  R. Russell,et al.  Illuminating G-Protein-Coupling Selectivity of GPCRs , 2019, Cell.

[31]  Michael Z. Lin,et al.  A compact synthetic pathway rewires cancer signaling to therapeutic effector release , 2019, Science.

[32]  Timothy K. Lu,et al.  Engineering advanced cancer therapies with synthetic biology , 2019, Nature Reviews Cancer.

[33]  Rob Phillips,et al.  Combinatorial Control through Allostery , 2018, bioRxiv.

[34]  Robert A. Langan,et al.  Programmable design of orthogonal protein heterodimers , 2018, Nature.

[35]  J. Babon,et al.  The molecular details of cytokine signaling via the JAK/STAT pathway , 2018, Protein science : a publication of the Protein Society.

[36]  George Mountoufaris,et al.  Writing, Reading, and Translating the Clustered Protocadherin Cell Surface Recognition Code for Neural Circuit Assembly. , 2018, Annual review of cell and developmental biology.

[37]  James T. Webber,et al.  Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris , 2018, Nature.

[38]  Michael B Elowitz,et al.  Programmable protein circuits in living cells , 2018, Science.

[39]  D. Stainier,et al.  A molecular mechanism for Wnt ligand-specific signaling , 2018, Science.

[40]  K. Ebnet,et al.  Junctional adhesion molecule-A: functional diversity through molecular promiscuity , 2018, Cellular and Molecular Life Sciences.

[41]  Ron Weiss,et al.  Programming gene and engineered-cell therapies with synthetic biology , 2018, Science.

[42]  T. Hughes,et al.  The Human Transcription Factors , 2018, Cell.

[43]  Ursula Klingmüller,et al.  Resolving the Combinatorial Complexity of Smad Protein Complex Formation and Its Link to Gene Expression. , 2017, Cell systems.

[44]  Marion B Johnson,et al.  Engineering multicellular systems: using synthetic biology to control tissue self-organization. , 2017, Current opinion in biomedical engineering.

[45]  V. Taylor,et al.  Differential interactions between Notch and ID factors control neurogenesis by modulating Hes factor autoregulation , 2017, Development.

[46]  Michael B. Elowitz,et al.  Combinatorial Signal Perception in the BMP Pathway , 2017, Cell.

[47]  Y. Saeys,et al.  Evolution and diversity of cadherins and catenins. , 2017, Experimental cell research.

[48]  M. Boutros,et al.  Mapping of Wnt-Frizzled interactions by multiplex CRISPR targeting of receptor gene families , 2017, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[49]  R. Nusse,et al.  Wnt/β-Catenin Signaling, Disease, and Emerging Therapeutic Modalities , 2017, Cell.

[50]  A. Keating,et al.  Combinatorial bZIP dimers display complex DNA-binding specificity landscapes , 2017, eLife.

[51]  Jens Timmer,et al.  L1 regularization facilitates detection of cell type-specific parameters in dynamical systems , 2016, Bioinform..

[52]  Yanhui Hu,et al.  Mapping signaling pathway cross-talk in Drosophila cells , 2016, Proceedings of the National Academy of Sciences.

[53]  Ursula Klingmüller,et al.  Identification of Cell Type-Specific Differences in Erythropoietin Receptor Signaling in Primary Erythroid and Lung Cancer Cells , 2016, PLoS Comput. Biol..

[54]  Robert A. Langan,et al.  De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity , 2016, Science.

[55]  Russell M. Gordley,et al.  Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors , 2016, Cell.

[56]  C. Cox,et al.  Comparative analysis of zebrafish bone morphogenetic proteins 2, 4 and 16: molecular and evolutionary perspectives , 2016, Cellular and Molecular Life Sciences.

[57]  Hugo J. Bellen,et al.  Control of Synaptic Connectivity by a Network of Drosophila IgSF Cell Surface Proteins , 2015, Cell.

[58]  A. Waage,et al.  Activin A inhibits BMP-signaling by binding ACVR2A and ACVR2B , 2015, Cell Communication and Signaling.

[59]  Geoffrey E. Hinton,et al.  Deep Learning , 2015, Nature.

[60]  N. Itoh,et al.  The Fibroblast Growth Factor signaling pathway , 2015, Wiley interdisciplinary reviews. Developmental biology.

[61]  John Ingraham,et al.  Galactose metabolic genes in yeast respond to a ratio of galactose and glucose , 2015, Proceedings of the National Academy of Sciences.

[62]  Michael B Elowitz,et al.  Synthetic biology of multicellular systems: new platforms and applications for animal cells and organisms. , 2014, ACS synthetic biology.

[63]  D. Corey,et al.  Sorting out a promiscuous superfamily: towards cadherin connectomics. , 2014, Trends in cell biology.

[64]  J. Tapia,et al.  Single-Cell Identity Generated by Combinatorial Homophilic Interactions between α, β, and γ Protocadherins , 2014, Cell.

[65]  Evgeny Katz,et al.  Notes on stochastic (bio)-logic gates: computing with allosteric cooperativity , 2014, Scientific Reports.

[66]  Zhaowu Ma,et al.  Evolution, functional divergence and conserved exon–intron structure of bHLH/PAS gene family , 2014, Molecular Genetics and Genomics.

[67]  S. Zipursky,et al.  The molecular basis of self-avoidance. , 2013, Annual review of neuroscience.

[68]  S. Warming,et al.  Context-dependent signaling defines roles of BMP9 and BMP10 in embryonic and postnatal development , 2013, Proceedings of the National Academy of Sciences.

[69]  Sarah Marzen,et al.  Statistical mechanics of Monod-Wyman-Changeux (MWC) models. , 2013, Journal of molecular biology.

[70]  Johannes Jaeger,et al.  Evolution and expression of BMP genes in flies , 2013, Development Genes and Evolution.

[71]  Andrew Mugler,et al.  Protein logic: a statistical mechanical study of signal integration at the single-molecule level. , 2012, Biophysical journal.

[72]  J. Nickel,et al.  Promiscuity and specificity in BMP receptor activation , 2012, FEBS letters.

[73]  Frank Jülicher,et al.  Topology and Dynamics of the Zebrafish Segmentation Clock Core Circuit , 2012, PLoS biology.

[74]  A. Bhattacharya,et al.  A Network of Broadly Expressed HLH Genes Regulates Tissue-Specific Cell Fates , 2011, Cell.

[75]  Greg M. Delgoffe,et al.  Interpreting mixed signals: the cell's cytokine conundrum. , 2011, Current opinion in immunology.

[76]  Olivier Pourquié,et al.  Vertebrate Segmentation: From Cyclic Gene Networks to Scoliosis , 2011, Cell.

[77]  S. Hughes,et al.  Cdkn1c drives muscle differentiation through a positive feedback loop with Myod. , 2011, Developmental biology.

[78]  Javier Macía,et al.  Distributed biological computation with multicellular engineered networks , 2011, Nature.

[79]  D. Schreiner,et al.  Combinatorial homophilic interaction between γ-protocadherin multimers greatly expands the molecular diversity of cell adhesion , 2010, Proceedings of the National Academy of Sciences.

[80]  D. Robertson,et al.  Genome-Wide Classification and Evolutionary Analysis of the bHLH Family of Transcription Factors in Arabidopsis, Poplar, Rice, Moss, and Algae1[W] , 2010, Plant Physiology.

[81]  Daniel E. Newburger,et al.  A Multiparameter Network Reveals Extensive Divergence between C. elegans bHLH Transcription Factors , 2009, Cell.

[82]  David L Robertson,et al.  Choose your partners: dimerization in eukaryotic transcription factors. , 2008, Trends in biochemical sciences.

[83]  V. D’Agati,et al.  Receptor for Advanced Glycation Endproducts (RAGE): a formidable force in the pathogenesis of the cardiovascular complications of diabetes & aging. , 2007, Current molecular medicine.

[84]  Ingmar H Riedel-Kruse,et al.  Synchrony Dynamics During Initiation, Failure, and Rescue of the Segmentation Clock , 2007, Science.

[85]  Erich Bornberg-Bauer,et al.  A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network , 2007, BMC Systems Biology.

[86]  Olivier Cinquin,et al.  Repressor Dimerization in the Zebrafish Somitogenesis Clock , 2007, PLoS Comput. Biol..

[87]  R. Kishony,et al.  Functional classification of drugs by properties of their pairwise interactions , 2006, Nature Genetics.

[88]  W. Van Hul,et al.  Extracellular regulation of BMP signaling in vertebrates: a cocktail of modulators. , 2002, Developmental biology.

[89]  D. Bray.  Protein molecules as computational elements in living cells , 1995, Nature.

[90]  J. Ross,et al.  Computational functions in biochemical reaction networks. , 1994, Biophysical journal.

[91]  Barbara Wold,et al.  HLH forced dimers: Tethering MyoD to E47 generates a dominant positive myogenic factor insulated from negative regulation by Id , 1993, Cell.

[92]  L. B. Milstein,et al.  Spread spectrum for mobile communications , 1991 .

[93]  Sergei Maslov,et al.  Topological and Dynamical Properties of Protein Interaction Networks , 2008, Protein-protein Interactions and Networks.

[94]  Gordon L. Stüber.  Principles of mobile communication , 1996 .

[95]  J. Massagué,et al.  The transforming growth factor-beta family. , 1990, Annual review of cell biology.