A supervised learning framework for chromatin loop detection in genome-wide contact maps.

abstract：:Aberrant metabolism of cancer cells is well appreciated, but the identification of cancer subsets with specific metabolic vulnerabilities remains challenging. We conducted a chemical biology screen and identified a subset of neuroendocrine tumors displaying a striking pattern of sensitivity to inhibition of the choles...

journal_title：Nature communications

authors： Mahoney CE,Pirman D,Chubukov V,Sleger T,Hayes S,Fan ZP,Allen EL,Chen Y,Huang L,Liu M,Zhang Y,McDonald G,Narayanaswamy R,Choe S,Chen Y,Gross S,Cianchetta G,Padyana AK,Murray S,Liu W,Marks KM,Murtie J,Dorsch M,

更新日期：2019-01-09 00:00:00

abstract：:Developmental plasticity describes the influence of environmental factors on phenotypic variation. An important mediator of developmental plasticity in many animals is parental care. Here, we examine the consequences of maternal care on offspring after the initial mass provisioning of brood in the small carpenter bee,...

journal_title：Nature communications

authors： Arsenault SV,Hunt BG,Rehan SM

更新日期：2018-08-27 00:00:00

abstract：:Identifying genes regulating the pace of epigenetic ageing represents a new frontier in genome-wide association studies (GWASs). Here using 1,796 brain samples from 1,163 individuals, we carry out a GWAS of two DNA methylation-based biomarkers of brain age: the epigenetic ageing rate and estimated proportion of neuron...

journal_title：Nature communications

authors： Lu AT,Hannon E,Levine ME,Crimmins EM,Lunnon K,Mill J,Geschwind DH,Horvath S

更新日期：2017-05-18 00:00:00

abstract：:Genomic changes observed across treatment may result from either clonal evolution or geographically disparate sampling of heterogeneous tumors. Here we use computational modeling based on analysis of fifteen primary breast tumors and find that apparent clonal change between two tumor samples can frequently be explaine...

journal_title：Nature communications

authors： Caswell-Jin JL,McNamara K,Reiter JG,Sun R,Hu Z,Ma Z,Ding J,Suarez CJ,Tilk S,Raghavendra A,Forte V,Chin SF,Bardwell H,Provenzano E,Caldas C,Lang J,West R,Tripathy D,Press MF,Curtis C

更新日期：2019-02-08 00:00:00

abstract：:Mapping neuroanatomy is a foundational goal towards understanding brain function. Electron microscopy (EM) has been the gold standard for connectivity analysis because nanoscale resolution is necessary to unambiguously resolve synapses. However, molecular information that specifies cell types is often lost in EM recon...

journal_title：Nature communications

authors： Shen FY,Harrington MM,Walker LA,Cheng HPJ,Boyden ES,Cai D

更新日期：2020-09-15 00:00:00

abstract：:Microvilli on T cells have been proposed to survey surfaces of antigen-presenting cells (APC) or facilitate adhesion under flow; however, whether they serve essential functions during T cell activation remains unclear. Here we show that antigen-specific T cells deposit membrane particles derived from microvilli onto t...

journal_title：Nature communications

authors： Kim HR,Mun Y,Lee KS,Park YJ,Park JS,Park JH,Jeon BN,Kim CH,Jun Y,Hyun YM,Kim M,Lee SM,Park CS,Im SH,Jun CD

更新日期：2018-09-07 00:00:00

abstract：:Tandem organic solar cells are based on the device structure monolithically connecting two solar cells to broaden overall absorption spectrum and utilize the photon energy more efficiently. Herein, we demonstrate a simple strategy of inserting a double bond between the central core and end groups of the small molecule...

journal_title：Nature communications

authors： Jia Z,Qin S,Meng L,Ma Q,Angunawela I,Zhang J,Li X,He Y,Lai W,Li N,Ade H,Brabec CJ,Li Y

更新日期：2021-01-08 00:00:00

abstract：:Sign epistasis is a central evolutionary constraint, but its causal factors remain difficult to predict. Here we use the notion of parameterised optima to explain epistasis within a signalling cascade, and test these predictions in Escherichia coli. We show that sign epistasis arises from the benefit of tuning phenoty...

journal_title：Nature communications

authors： Nghe P,Kogenaru M,Tans SJ

更新日期：2018-04-13 00:00:00

abstract：:The main advantage of organic transistors with dual gates/bases is that the threshold voltages can be set as a function of the applied second gate/base bias, which is crucial for the application in logic gates and integrated circuits. However, incorporating a dual gate/base structure into an ultra-short channel vertic...

journal_title：Nature communications

authors： Guo E,Wu Z,Darbandy G,Xing S,Wang SJ,Tahn A,Göbel M,Kloes A,Leo K,Kleemann H

更新日期：2020-09-18 00:00:00

abstract：:MAVS and MITA are essential adaptor proteins mediating innate antiviral immune responses against RNA and DNA viruses, respectively. Here we show that RNF115 plays dual roles in response to RNA or DNA virus infections by catalyzing distinct types of ubiquitination of MAVS and MITA at different phases of viral infection...

journal_title：Nature communications

authors： Zhang ZD,Xiong TC,Yao SQ,Wei MC,Chen M,Lin D,Zhong B

更新日期：2020-11-02 00:00:00

abstract：:The Gibbs energy, G, determines the equilibrium conditions of chemical reactions and materials stability. Despite this fundamental and ubiquitous role, G has been tabulated for only a small fraction of known inorganic compounds, impeding a comprehensive perspective on the effects of temperature and composition on mate...

journal_title：Nature communications

authors： Bartel CJ,Millican SL,Deml AM,Rumptz JR,Tumas W,Weimer AW,Lany S,Stevanović V,Musgrave CB,Holder AM

更新日期：2018-10-09 00:00:00

abstract：:Roughly a third (~30 ppm) of the carbon dioxide (CO2) that entered the ocean during ice ages is attributed to biological mechanisms. A leading hypothesis for the biological drawdown of CO2 is iron (Fe) fertilisation of the high latitudes, but modelling efforts attribute at most 10 ppm to this mechanism, leaving ~20 pp...

journal_title：Nature communications

authors： Buchanan PJ,Chase Z,Matear RJ,Phipps SJ,Bindoff NL

更新日期：2019-10-10 00:00:00

abstract：:Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation ...

journal_title：Nature communications

authors： Ahola V,Lehtonen R,Somervuo P,Salmela L,Koskinen P,Rastas P,Välimäki N,Paulin L,Kvist J,Wahlberg N,Tanskanen J,Hornett EA,Ferguson LC,Luo S,Cao Z,de Jong MA,Duplouy A,Smolander OP,Vogel H,McCoy RC,Qian K,Chong W

更新日期：2014-09-05 00:00:00

abstract：:The development of efficient reactions for the one-pot construction of bicyclic ring systems bearing two quaternary carbon centres at their bridgehead positions represents a significant challenge to synthetic chemistry. The development of new methods capable of overcoming this challenge is highly desirable, because th...

journal_title：Nature communications

authors： Long R,Huang J,Shao W,Liu S,Lan Y,Gong J,Yang Z

更新日期：2014-12-08 00:00:00

abstract：:Changing climate will impact species' ranges only when environmental variability directly impacts the demography of local populations. However, measurement of demographic responses to climate change has largely been limited to single species and locations. Here we show that amphibian communities are responsive to clim...

journal_title：Nature communications

authors： Miller DAW,Grant EHC,Muths E,Amburgey SM,Adams MJ,Joseph MB,Waddle JH,Johnson PTJ,Ryan ME,Schmidt BR,Calhoun DL,Davis CL,Fisher RN,Green DM,Hossack BR,Rittenhouse TAG,Walls SC,Bailey LL,Cruickshank SS,Fellers GM,G

更新日期：2018-09-25 00:00:00

abstract：:Textiles that are capable of harvesting biomechanical energy via triboelectric effects are of interest for self-powered wearable electronics. Fabrication of conformable and durable textiles with high triboelectric outputs remains challenging. Here we propose a washable skin-touch-actuated textile-based triboelectric n...

journal_title：Nature communications

authors： Xiong J,Cui P,Chen X,Wang J,Parida K,Lin MF,Lee PS

更新日期：2018-10-15 00:00:00

abstract：:β-Diguetoxin-Dc1a (Dc1a) is a toxin from the desert bush spider Diguetia canities that incapacitates insects at concentrations that are non-toxic to mammals. Dc1a promotes opening of German cockroach voltage-gated sodium (Nav) channels (BgNav1), whereas human Nav channels are insensitive. Here, by transplanting common...

journal_title：Nature communications

authors： Bende NS,Dziemborowicz S,Mobli M,Herzig V,Gilchrist J,Wagner J,Nicholson GM,King GF,Bosmans F

更新日期：2014-07-11 00:00:00

abstract：:Polymers bearing dynamic covalent bonds may exhibit dynamic properties, such as self-healing, shape memory and environmental adaptation. However, most dynamic covalent chemistries developed so far require either catalyst or change of environmental conditions to facilitate bond reversion and dynamic property change in ...

journal_title：Nature communications

authors： Ying H,Zhang Y,Cheng J

更新日期：2014-01-01 00:00:00

abstract：:The study of the high pressure phase diagram of hydrogen has continued with renewed effort for about one century as it remains a fundamental challenge for experimental and theoretical techniques. Here we employ an efficient molecular dynamics based on the quantum Monte Carlo method, which can describe accurately the e...

journal_title：Nature communications

authors： Mazzola G,Yunoki S,Sorella S

更新日期：2014-03-19 00:00:00

abstract：:Survival in complex environments necessitates a flexible navigation system that incorporates memory of recent behavior and associations. Yet, how the hippocampal spatial circuit represents latent information independent of sensory inputs and future goals has not been determined. To address this, we image the activity ...

journal_title：Nature communications

authors： Keinath AT,Nieto-Posadas A,Robinson JC,Brandon MP

更新日期：2020-06-15 00:00:00

abstract：:Deep subwavelength integration of high-definition plasmonic nanostructures is of key importance in the development of future optical nanocircuitry for high-speed communication, quantum computation and lab-on-a-chip applications. To date, the experimental realization of proposed extended plasmonic networks consisting o...

journal_title：Nature communications

authors： Huang JS,Callegari V,Geisler P,Brüning C,Kern J,Prangsma JC,Wu X,Feichtner T,Ziegler J,Weinmann P,Kamp M,Forchel A,Biagioni P,Sennhauser U,Hecht B

更新日期：2010-01-01 00:00:00

abstract：:The mobility of drops on surfaces is important in many biological and industrial processes, but the phenomena governing their adhesion, which is dictated by the morphology of the three-phase contact line, remain unclear. Here we describe a technique for measuring the dynamic behaviour of the three-phase contact line a...

journal_title：Nature communications

authors： Paxson AT,Varanasi KK

更新日期：2013-01-01 00:00:00

abstract：:AML1-ETO (AE) is a fusion transcription factor, generated by the t(8;21) translocation, that functions as a leukemia promoting oncogene. Here, we demonstrate that TATA-Box Binding Protein Associated Factor 1 (TAF1) associates with K43 acetylated AE and this association plays a pivotal role in the proliferation of AE-e...

journal_title：Nature communications

authors： Xu Y,Man N,Karl D,Martinez C,Liu F,Sun J,Martinez CJ,Martin GM,Beckedorff F,Lai F,Yue J,Roisman A,Greenblatt S,Duffort S,Wang L,Sun X,Figueroa M,Shiekhattar R,Nimer S

更新日期：2019-10-29 00:00:00

abstract：:A reliable method for recording evoked synaptic events in identified neurons in Caenorhabditis elegans would greatly accelerate our understanding of its nervous system at the molecular, cellular and network levels. Here we describe a method for recording synaptic currents and potentials from identified neurons in near...

journal_title：Nature communications

authors： Lindsay TH,Thiele TR,Lockery SR

更新日期：2011-01-01 00:00:00

abstract：:Foldamers provide an attractive medium to test the mechanisms by which biological macromolecules fold into complex three-dimensional structures, and ultimately to design novel protein-like architectures with properties unprecedented in nature. Here, we describe a large cage-like structure formed from an amphiphilic ar...

journal_title：Nature communications

authors： Pavone V,Zhang SQ,Merlino A,Lombardi A,Wu Y,DeGrado WF

更新日期：2014-04-07 00:00:00

abstract：:Increased aerobic glycolysis in endothelial cells of atheroprone areas of blood vessels has been hypothesized to drive increased inflammation and lesion burden but direct links remain to be established. Here we show that endothelial cells exposed to disturbed flow in vivo and in vitro exhibit increased levels of prote...

journal_title：Nature communications

authors： Yang Q,Xu J,Ma Q,Liu Z,Sudhahar V,Cao Y,Wang L,Zeng X,Zhou Y,Zhang M,Xu Y,Wang Y,Weintraub NL,Zhang C,Fukai T,Wu C,Huang L,Han Z,Wang T,Fulton DJ,Hong M,Huo Y

更新日期：2018-11-07 00:00:00

abstract：:Two voltage-gated calcium channel subtypes-CaV1.2 and CaV1.3-underlie the major L-type Ca(2+) currents in the mammalian central nervous system. Owing to their high sequence homology, the two channel subtypes share similar pharmacological properties, and at high doses classic calcium channel blockers, such as dihydropy...

journal_title：Nature communications

authors： Huang H,Ng CY,Yu D,Zhai J,Lam Y,Soong TW

更新日期：2014-07-24 00:00:00

abstract：:In certain regions of the predominantly nitrogen limited ocean, microbes can become co-limited by phosphorus. Within such regions, a proportion of the dissolved organic phosphorus pool can be accessed by microbes employing a variety of alkaline phosphatase (APase) enzymes. In contrast to the PhoA family of APases that...

journal_title：Nature communications

authors： Browning TJ,Achterberg EP,Yong JC,Rapp I,Utermann C,Engel A,Moore CM

更新日期：2017-05-19 00:00:00

abstract：:Netrins, a family of laminin-related molecules, have been proposed to act as guidance cues either during nervous system development or the establishment of the vascular system. This was clearly demonstrated for netrin-1 via its interaction with the receptors DCC and UNC5s. However, mainly based on shared homologies wi...

journal_title：Nature communications

authors： Reuten R,Patel TR,McDougall M,Rama N,Nikodemus D,Gibert B,Delcros JG,Prein C,Meier M,Metzger S,Zhou Z,Kaltenberg J,McKee KK,Bald T,Tüting T,Zigrino P,Djonov V,Bloch W,Clausen-Schaumann H,Poschl E,Yurchenco PD,Eh

更新日期：2016-11-30 00:00:00

abstract：:A variety of flexible and stretchable electronics have been reported for use in flexible electronic devices or biomedical applications. The practical and wider application of such flexible electronics has been limited because commercial electronic components are difficult to be directly integrated into flexible stretc...

journal_title：Nature communications

authors： Jeong GS,Baek DH,Jung HC,Song JH,Moon JH,Hong SW,Kim IY,Lee SH

更新日期：2012-01-01 00:00:00