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   Detecting Novel Sequence Signals in Targeting Peptides Using Deep Learning

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   Sufficiency analysis of estrogen responsive enhancers using synthetic activators

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   biorxiv.org/content/10.1101/479709v2

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   Mechanistic Insights into the Protective Roles of Polyphosphate Against Amyloid Cytotoxicity

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   biorxiv.org/content/10.1101/704882v1

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   Evolutionarily-conserved chromatin crosstalk generates a DOT1L-dose dependency in thymic lymphoma caused by loss of HDAC1

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   biorxiv.org/content/10.1101/509976v1

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   Biologically indeterminate yet ordered promiscuous gene expression in single medullary thymic epithelial cells

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   Combinatorial prediction of gene-marker panels from single-cell transcriptomic data.

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   biorxiv.org/content/10.1101/655753v2

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   High affinity interactions and signal transduction between Aβ oligomers and TREM2

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   Pannexin-1 Channels govern the Generation of Necroptotic small Extracellular Vesicles

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    The Israeli Acute Paralysis Virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs.

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    Long-term expanding human airway organoids for disease modelling.

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    Plasma proteome profiling to detect and avoid sample-related biases in biomarker studies

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    Estrogen receptor alpha controls gene expression via translational offsetting

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    Paralog dependency indirectly affects the robustness of human cells

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    Endogenous fluctuations of OCT4 and SOX2 bias pluripotent cell fate decisions

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    S-acylated Golga7b stabilises DHHC5 at the plasma membrane to regulate desmosome assembly and cell adhesion.

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    An integrated workflow for cross-linking/mass spectrometry

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    biorxiv.org/content/10.1101/355396v2

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    Elucidation of the viral disassembly switch of tobacco mosaic virus

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    biorxiv.org/content/10.1101/569178v1

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    Endogenous RNAi pathway evolutionarily shapes the destiny of the antisense lncRNAs transcriptome

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    biorxiv.org/content/10.1101/612630v2

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    let-7 controls the transition to adulthood by releasing select transcriptional regulators from repression by LIN41

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    Ncl1 mediated metabolic rewiring is critical during metabolic stress

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    Kinesin-8B controls basal body function and flagellum formation and is key to malaria parasite transmission

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    XIAP controls RIPK2 signaling by preventing its deposition in speck-like structures

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    Tumor-Intrinsic Response to IFNgamma Shapes the Tumor Microenvironment and Anti-PD-1 Response in NSCLC

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    The WT1-BASP1 complex is required to maintain the differentiated state of taste receptor cells

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    Molecular characterization of Chlamydomonas reinhardtii telomeres and telomerase mutants

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    Molecular characterization of CHAD domains as inorganic polyphosphate binding modules

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    Hierarchical organization of the human cell from a cancer coessentiality network

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    BZLF1 interacts with the chromatin remodeler INO80 promoting escape from latent infections with Epstein-Barr virus

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    The chaperone-client network subordinates cell-cycle entry to growth and stress

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    Maternal Circulating MicroRNAs Control the Placental Response to Alcohol

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    Human CST suppresses origin licensing and promotes AND-1/Ctf4 chromatin association

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    Intra-individual methylomics detects the impact of early-life adversity

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    Human DNA polymerase delta is a pentameric complex with dimeric p12 subunit: Implications in enzyme architecture and PCNA interaction

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    PISD is a mitochondrial disease gene causing skeletal dysplasia, cataracts and white matter changes

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    Expanding the repertoire of glucocorticoid receptor target genes by engineering genomic response elements

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    Worldwide genetic variation of the IGHV and TRBV immune receptor gene families in humans

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    The small and large ribosomal subunits depend on each other for stability and accumulation

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    Main constraints for RNAi induced by expressed long dsRNA in mouse cells

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    MiR-146a wild-type 3\' sequence identity is dispensable for proper innate immune function in vivo

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    Mitochondrial acetyl-CoA reversibly regulates locus-specific histone acetylation and gene expression

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    A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs

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    Rab1b and ARF5 are novel RNA-binding proteins involved in IRES-driven RNA localization

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    Direct binding of Cdt2 to PCNA is important for targeting the CRL4Cdt2 E3 ligase activity to Cdt1

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    Mouse REC114 is essential for meiotic DNA double-strand break formation and forms a complex with MEI4

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    An integrative machine learning approach for prediction of toxicity-related drug safety

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    Phosphorylation of Arp2 is not essential for Arp2/3 complex activity in fission yeast

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    Specificity for deubiquitination of monoubiquitinated FANCD2 is driven by the N-terminus of USP1

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    Novel organelle anion channels formed by chromogranin B drive normal granule maturation in endocrine cells

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    Cumulative regulatory potential of clustered methyl-arginine protein modifications

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    Loss of Wt1 in the murine spinal cord alters interneuron composition and locomotion

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    CHRAC/ACF Contribute to the Repressive Ground State of Chromatin

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    Role of Cnot6l in maternal mRNA turnover

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    JIP2 haploinsufficiency contributes to neurodevelopmental abnormalities in human pluripotent stem cell-derived neural progenitors and cortical neurons.

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    The repressive and alleviating nature of FACT shapes the transcriptional landscape in ES cells

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    The histone chaperone FACT modulates nucleosome structure by tethering its components

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    Dynamic m6A methylation facilitates mRNA triaging to stress granules

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    DHX15 regulates CMTR1-dependent gene expression and cell proliferation

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    Co-existing feedback loops generate tissue-specific circadian rhythms

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    Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers

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    The expansion in lymphoid organs of IL-4+ BATF+ T follicular helper cells is linked to IgG4 class switching in vivo

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    The TRAPP complex mediates secretion arrest induced by stress granule assembly

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    Endo-lysosomal sorting and degradation of Tau mediates glucocorticoid-driven hippocampalmalfunction

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    Actin filaments regulate microtubule growth at the centrosome.

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    Sphingolipid metabolic flow controls phosphoinositide turnover at thetrans Golgi network

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    The β3-integrin endothelial adhesome regulates microtubule dependent cell migration

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    Mapping In Vivo O-Glycoproteome Using Site-specific Extraction of O-linked glycopeptides (EXoO)

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    Nuclear RNA export factor variant initiates piRNA-guided co-transcriptional silencing

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    F-actin patches associated with glutamatergic synapses control positioning of dendritic lysosomes

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    A genetic system for generating single-sex progeny in mice

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    Multiple C2 domains and Transmembrane region Proteins (MCTPs) tether membranes at plasmodesmata

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    Functional systemic CD4 immunity is a differential factor for clinical responses to PD-L1/PD-1 blockade therapy in lung cancer

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    Disentangling bacterial invasiveness from lethality in an experimental host-pathogen system

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    RASSF1A Is Required For The Maintenance Of Nuclear Actin Levels

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    Stalk-mediated communication in the dynein motor domain

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    Euchromatic histone methyltransferases regulate peripheral heterochromatin tethering via histone and non-histone protein methylations

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    Drug-induced increase in lysobisphosphatidic acid reduces the cholesterol overload in Niemann-Pick type C cells and mice

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    PP4-dependent HDAC3 dephosphorylation discriminates between axonal regeneration and regenerative failure

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    LRX- and FER-dependent extracellular sensing coordinates vacuolar size for cytosol homeostasis

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    The nucleoporin ELYS regulates nuclear size by controlling NPC number and nuclear import capacity

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    Absolute quantification of translational regulation and burden using combined sequencing approaches

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    Triggering MSR1 promotes JNK-mediated inflammation in IL-4 activated macrophages

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    Mechanistic causes of constrained phenotypic variation revealed by synthetic gene regulatory networks

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    The fitness cost and benefit of phase separated protein deposits

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    Defining the RNA Interactome by Total RNA-Associated Protein Purification

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    SWI/SNF chromatin remodeling controls Notch-responsive enhancer accessibility

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    Asymmetric Distribution of Glucose Transporter mRNA Provides Growth Advantage

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    Evidence that the cell cycle is a series of uncoupled, memoryless phases

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    The fungal root endophyte Serendipita indica modifies extracellular nucleotides to subvert plant immunity

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    netDx: Patient classification using integrated patient similarity networks

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    SSU72 phosphatase is a telomere replication terminator

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    De novo Gene Signature Identification from Single-Cell RNA-Seq with Hierarchical Poisson Factorization

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    Quantification and discovery of sequence determinants of protein per mRNA amount in 29 human tissues

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    A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

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    Structures of the heart specific SERCA2a Ca2+-ATPase

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     Choreography of budding yeast chromosomes during the cell cycle

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     Length-independent telomere damage drives cardiomyocyte senescence

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     Widespread inter-individual gene expression variability in Arabidopsis thaliana

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     Complex-centric proteome profiling by SEC-SWATH-MS

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     CRISPR Cas9 searches for a protospacer adjacent motif by one-dimensional diffusion

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     High-resolution mapping of cancer cell networks using co-functional interactions

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     CDK phosphorylation of Xenopus laevis M18BP1 promotes its metaphase centromere localization

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     Activated BAX/BAK enable mitochondrial inner membrane permeabilisation and mtDNA release during cell death

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     Bimodal Spindle Orientation Drives Tissue Regularity in a Proliferating Epithelium

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     Avidity-driven polarity establishment via multivalent lipid-GTPase module interactions

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     The key protein of endosomal mRNP transport binds translational landmark sites of cargo mRNAs

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     Murine MPDZ-Linked Hydrocephalus is Caused by Hyperpermeability of the Choroid Plexus

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     S phase R-loop formation is restricted by PrimPol-mediated repriming

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     A common molecular logic determines embryonic stem cell self-renewal and reprogramming

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     Functional Compensation Between Hematopoietic Stem Cells In Vivo

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     Shelterin and subtelomeric DNA sequences control nucleosome maintenance and genome stability

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     Synergistic Recruitment of UbcH7~Ub and Phosphorylated Ubl Domain Triggers Parkin Activation

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     Synthesis and degradation of FtsZ determines the first cell division in starved bacteria

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     Yap regulates glucose utilization and sustains nucleotide synthesis to enable organ growth

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     ESCRT-mediated lysosome repair precedes lysophagy and promotes cell survival

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     Transcriptional control and exploitation of an immune-responsive family of retrotransposons in Arabidopsis

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     Fibroblasts from metastatic sites induce broad-spectrum drug desensitization via modulation of mitochondrial priming

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     Paupar LncRNA Promotes KAP1 Dependent Chromatin Changes And Regulates Subventricular Zone Neurogenesis

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     TRIP6 inhibits the Hippo signaling pathway in response to tension at adherens junctions

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     CTCF, WAPL and PDS5 proteins control the formation of TADs and loops by cohesin

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     Whole chromosome loss in tetraploid cells confers tumorigenic potential in a mouse allograft model

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     Non-canonical circadian oscillations in Drosophila S2 cells drive gene-expression cycles coupled to metabolic oscillations

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     Bicoid gradient formation mechanism and dynamics revealed by protein lifetime analysis

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     Ratiometric Distribution Of OCT4 During Stem Cell Division Controls The Balance Between Self-Renewal And Differentiation

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     Multi-Omics factor analysis disentangles heterogeneity in blood cancer

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     FAM35A co-operates with REV7 to coordinate DNA double-strand break repair pathway choice.

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     Fibroblast state switching orchestrates dermal maturation and wound healing

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     Genomics of cellular proliferation under periodic stress

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     Household triclosan and triclocarban exposure impacts the adult intestinal microbiome but not the infant intestinal microbiome

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     MODELING SIGNALING-DEPENDENT PLURIPOTENT CELL STATES WITH BOOLEAN LOGIC CAN PREDICT CELL FATE TRANSITIONS

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     Genome-wide phenotypic analysis of growth, cell morphogenesis and cellcycle events in Escherichia coli.

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     Structure of the archaellar motor and associated cytoplasmic cone in Thermococcus kodakaraensis

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     A synthesis of over 9,000 mass spectrometry experiments reveals the core set of human protein complexes

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     A two-state photoconversion model predicts the spectral response dynamics of optogenetic systems

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     Unraveling mitotic protein networks by 3D multiplexed epitope drug screening

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     Mapping DNA damage-dependent genetic interactions in yeast via orgy mating and barcode fusion genetics

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     LINE-1 repression attenuates degeneration in adult dopaminergic neurons

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     Redesigning chromosomes to optimize conformation capture (Hi-C) assays

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     The Trithorax group protein dMLL3/4 instructs the assembly of the zygotic genome at fertilization

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     GTSF-1 is required for the formation of a functional RNA-dependent RNA Polymerase complex in C. elegans

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     A temporally dynamic Foxp3 autoregulatory transcriptional circuit controls the effector Treg programme

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     X10 Expansion Microscopy Enables 25 nm Resolution on Conventional Microscopes

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     Lateral plasma membrane compartmentalization links protein function and turnover

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     Deciphering microbial interactions in synthetic human gut microbiome communities

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     FAM35A associates with REV7 and modulates DNA damage responses of normal and BRCA1-defective cells

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     Expression variation and covariation impair analog and enable binary signaling control

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     Strong homeostatic TCR signals induce formation of self-tolerant virtual memory CD8 T cells

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     Timing of gene expression in a cell-fate decision system

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     Thermal proteome profiling of breast cancer cells reveals proteasomal activation by CDK4/6 inhibitor palbociclib

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     Real-time observation of flexible domain movements in Cas9

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     Structural centrosome aberrations promote non-cell-autonomous invasiveness

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     Structure of the human pro-myostatin precursor and determinants of growth factor latency

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     Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism

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     A Map Of Genetic Interactions In Cancer Cells

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     Structure of the eukaryotic cytoplasmic pre-40S ribosomal subunit

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     Antisense transcription-dependent chromatin signature modulates sense transcription and transcript dynamics

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     Small interfering RNAs based on huntingtin trinucleotide repeats are highly toxic to cancer cells

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     High-throughput identification of RNA nuclear enrichment sequences

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     Tolloid cleavage activates latent GDF8 by priming the pro-complex for dissociation

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     Assigning Function To Natural Allelic Variation Via Dynamic Modeling Of Gene Network Induction

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     Mapping protein interactions of sodium channel NaV1.7 using epitope-tagged gene targeted mice

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     Expanding the Atlas of Functional Missense Variation for Human Genes

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     WDR11-mediated Hedgehog signalling defects underlie a new ciliopathy related to Kallmann syndrome

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     Resolving Drug Effects In Patient-Derived Cancer Cells Links Organoid Responses To Genome Alterations

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     A Mechanism of Cohesin-Dependent Loop Extrusion Organizes Zygotic Genome Architecture

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     The Landscape Of Human Mutually Exclusive Splicing

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     From word models to executable models of signaling networks using automated assembly

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     Aubergine And piRNAs Repress The Proto-Oncogene Cbl For Germline Stem Cell Self-Renewal

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     An "invisible" ubiquitin conformation is required for efficient phosphorylation by PINK1

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     Real-time detection of condensin-driven DNA compaction reveals a multistep binding mechanism

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     Initiation of DNA replication requires actin dynamics and formin activity

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     Combinatorial Regulation Of The Balance Between Dynein Microtubule End Accumulation And Initiation Of Directed Motility

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     CRISPR/Cas9 screening using unique molecular identifiers

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     In Situ Genotyping Of A Pooled Strain Library After Characterizing Complex Phenotypes

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     A Theory That Predicts Behaviors Of Disordered Cytoskeletal Networks

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     Cytosolic ribosomes on the surface of mitochondria

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     Remodeling of ER-exit sites initiates a membrane supply pathway forautophagosome biogenesis

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     Structural and Functional analysis of the GABARAP Interaction Motif (GIM).

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     Structural and functional dissection of the interplay between lipid and Notch binding by human Notch ligands

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     High-throughput CRISPRi phenotyping in Streptococcus pneumoniae identifies new essential genes involved in cell wall synthesis and competence development

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     In vivo structures of an intact type VI secretion system revealed by electron cryotomography

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     Structure of the Legionella Dot/Icm type IV secretion system in situ by electron cryotomography

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     DNA sequence properties that predict susceptibility to epiallelic switching

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     A living vector field reveals constraints on galactose network induction in yeast

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     An RNA-binding tropomyosin recruits kinesin-1 dynamically to oskar mRNPs

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     Distinct Cellular States Determine Calcium Signaling Response

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     Polarized Cortical Tension drives Zebrafish Epiboly Movements

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     An Atlas of Human Kinase Regulation

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     A population-based temporal logic gate for timing and recording chemical events

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     Tyrosination of α-Tubulin Controls The Initiation of Processive Dynein-Dynactin Motility

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     Determinants of RNA metabolism in the Schizosaccharomyces pombe genome

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     Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress

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     Efficient Search, Mapping, and Optimization of Multi-protein Genetic Systems in Diverse Bacteria

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     Measuring error rates in genomic perturbation screens: gold standards for human functional genomics

     1

     1. EMBOpress 22 Sep 2019

        in EMBO Press

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        PeerReviewed EMBOPress Molecular Systems Biology Systems Biology

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     • Molecular Systems Biology

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     URL

     biorxiv.org/content/10.1101/003327v1

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