Segmentation of biological multivariate time-series data.

Abstract:

:Time-series data from multicomponent systems capture the dynamics of the ongoing processes and reflect the interactions between the components. The progression of processes in such systems usually involves check-points and events at which the relationships between the components are altered in response to stimuli. Detecting these events together with the implicated components can help understand the temporal aspects of complex biological systems. Here we propose a regularized regression-based approach for identifying breakpoints and corresponding segments from multivariate time-series data. In combination with techniques from clustering, the approach also allows estimating the significance of the determined breakpoints as well as the key components implicated in the emergence of the breakpoints. Comparative analysis with the existing alternatives demonstrates the power of the approach to identify biologically meaningful breakpoints in diverse time-resolved transcriptomics data sets from the yeast Saccharomyces cerevisiae and the diatom Thalassiosira pseudonana.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Omranian N,Mueller-Roeber B,Nikoloski Z

doi

10.1038/srep08937

subject

Has Abstract

pub_date

2015-03-11 00:00:00

pages

8937

issn

2045-2322

pii

srep08937

journal_volume

5

pub_type

杂志文章
  • Optimal timing of initiating continuous renal replacement therapy in septic shock patients with acute kidney injury.

    abstract::Acute kidney injury (AKI) in patients with septic shock is associated with high mortality, but the appropriate timing for initiating continuous renal replacement therapy (CRRT) is controversial. We retrospectively enrolled 158 septic shock patients with AKI in the medical intensive care unit (ICU) from July 2016 to Ap...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-48418-4

    authors: Yoon BR,Leem AY,Park MS,Kim YS,Chung KS

    更新日期:2019-08-19 00:00:00

  • Self-assembled Collagen-Fibrin Hydrogel Reinforces Tissue Engineered Adventitia Vessels Seeded with Human Fibroblasts.

    abstract::Efforts for tissue engineering vascular grafts focuses on the tunica media and intima, although the tunica adventitia serves as the primary structural support for blood vessels. In surgery, during endarterectomies, surgeons can strip the vessel, leaving the adventitia as the main strength layer to close the vessel. He...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-21681-7

    authors: Patel B,Xu Z,Pinnock CB,Kabbani LS,Lam MT

    更新日期:2018-02-19 00:00:00

  • Geometry- and Length Scale-Dependent Deformation and Recovery on Micro- and Nanopatterned Shape Memory Polymer Surfaces.

    abstract::Micro- and nanoscale surface textures, when optimally designed, present a unique approach to improve surface functionalities. Coupling surface texture with shape memory polymers may generate reversibly tuneable surface properties. A shape memory polyetherurethane is used to prepare various surface textures including 2...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep23686

    authors: Lee WL,Low HY

    更新日期:2016-03-30 00:00:00

  • Strategically positioning cooperators can facilitate the contagion of cooperation.

    abstract::The spreading of cooperation in structured population is a challenging problem which can be observed at different scales of social and biological organization. Generally, the problem is studied by evaluating the chances that few initial invading cooperators, randomly appearing in a network, can lead to the spreading o...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-80770-8

    authors: Yang G,Cavaliere M,Zhu C,Perc M

    更新日期:2021-01-13 00:00:00

  • Spatially oriented plasmonic 'nanograter' structures.

    abstract::One of the key motivations in producing 3D structures has always been the realization of metamaterials with effective constituent properties that can be tuned in all propagation directions at various frequencies. Here, we report the investigation of spatially oriented "Nanograter" structures with orientation-dependent...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep28764

    authors: Liu Z,Cui A,Gong Z,Li H,Xia X,Shen TH,Li J,Yang H,Li W,Gu C

    更新日期:2016-06-30 00:00:00

  • Inferences of drug responses in cancer cells from cancer genomic features and compound chemical and therapeutic properties.

    abstract::Accurately predicting the response of a cancer patient to a therapeutic agent is a core goal of precision medicine. Existing approaches were mainly relied primarily on genomic alterations in cancer cells that have been treated with different drugs. Here we focus on predicting drug response based on integration of the ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep32679

    authors: Wang Y,Fang J,Chen S

    更新日期:2016-09-20 00:00:00

  • Author Correction: Resistance training regulates gene expression of molecules associated with intramyocellular lipids, glucose signaling and fiber size in old rats.

    abstract::A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper. ...

    journal_title:Scientific reports

    pub_type: 已发布勘误

    doi:10.1038/s41598-019-42462-w

    authors: Ribeiro MBT,Guzzoni V,Hord JM,Lopes GN,de Cássia Marqueti R,de Andrade RV,Selistre-de-Araujo HS,Durigan JLQ

    更新日期:2019-04-17 00:00:00

  • His-tag protein monitoring by a fast mix-and-measure immunoassay.

    abstract::Here, we present a fast mix-and-measure immunoassay for the specific semiquantitative detection of His-tagged proteins, for example in E. coli cell lysate. The assay is based on Förster resonance energy transfer (FRET) between a lanthanide dye-labeled low-affinity His-peptide and an acceptor-labeled anti-His-tag antib...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep05613

    authors: Kreisig T,Prasse AA,Zscharnack K,Volke D,Zuchner T

    更新日期:2014-07-08 00:00:00

  • Intrauterine exposure to low-dose DBP in the mice induces obesity in offspring via suppression of UCP1 mediated ER stress.

    abstract::Dibutyl phthalate (DBP) is recognized as an environmental endocrine disruptor that has been detected in fetal and postnatal samples. Recent evidence found that in utero DBP exposure was associated with an increase of adipose tissue weight and serum lipids in offspring, but the precise mechanism is unknown. Here we aim...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-73477-3

    authors: Li H,Li J,Qu Z,Qian H,Zhang J,Wang H,Xu X,Liu S

    更新日期:2020-10-01 00:00:00

  • H727 cells are inherently resistant to the proteasome inhibitor carfilzomib, yet require proteasome activity for cell survival and growth.

    abstract::The second-in-class proteasome inhibitor (PI) carfilzomib (Kyprolis, Cfz) has contributed to a substantial advancement in multiple myeloma treatment by improving patient survival and quality of life. A considerable portion of patients however display intrinsic resistance to Cfz. Our mechanistic understanding of intrin...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-40635-1

    authors: Lee MJ,Miller Z,Park JE,Bhattarai D,Lee W,Kim KB

    更新日期:2019-03-11 00:00:00

  • Characterization of Graphene-based FET Fabricated using a Shadow Mask.

    abstract::To pattern electrical metal contacts, electron beam lithography or photolithography are commonly utilized, and these processes require polymer resists with solvents. During the patterning process the graphene surface is exposed to chemicals, and the residue on the graphene surface was unable to be completely removed b...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep25050

    authors: Tien DH,Park JY,Kim KB,Lee N,Seo Y

    更新日期:2016-05-12 00:00:00

  • Sulphur and carbon isotopes as tracers of past sub-seafloor microbial activity.

    abstract::Microbial life below the seafloor has changed over geological time, but these changes are often not obvious, as they are not recorded in the sediment. Sulphur (S) isotope values in pyrite extracted from a Plio- to Holocene sequence of the Peru Margin (Ocean Drilling Program, ODP, Site 1229) show a down-core pattern th...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-36943-7

    authors: Meister P,Brunner B,Picard A,Böttcher ME,Jørgensen BB

    更新日期:2019-01-24 00:00:00

  • Functional brain networks reveal the existence of cognitive reserve and the interplay between network topology and dynamics.

    abstract::We investigated how the organization of functional brain networks was related to cognitive reserve (CR) during a memory task in healthy aging. We obtained the magnetoencephalographic functional networks of 20 elders with a high or low CR level to analyse the differences at network features. We reported a negative corr...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-28747-6

    authors: Martínez JH,López ME,Ariza P,Chavez M,Pineda-Pardo JA,López-Sanz D,Gil P,Maestú F,Buldú JM

    更新日期:2018-07-12 00:00:00

  • High performance organic-inorganic perovskite-optocoupler based on low-voltage and fast response perovskite compound photodetector.

    abstract::Organic-inorganic hybrid photodetectors attract considerable attention because they can combine the advantages of both organic and inorganic systems. Here, a perovskite compound with a broad absorption spectrum and high power conversion efficiency is used as a photosensitive layer in an organic/inorganic hybrid hetero...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep07902

    authors: Li D,Dong G,Li W,Wang L

    更新日期:2015-01-20 00:00:00

  • High-performance thermochromic VO2-based coatings with a low transition temperature deposited on glass by a scalable technique.

    abstract::We report on high-performance thermochromic ZrO2/V0.982W0.018O2/ZrO2 coatings with a low transition temperature prepared on glass by a low-temperature scalable deposition technique. The V0.982W0.018O2 layers were deposited by a controlled high-power impulse magnetron sputtering of V target, combined with a simultaneou...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-68002-5

    authors: Kolenatý D,Vlček J,Bárta T,Rezek J,Houška J,Haviar S

    更新日期:2020-07-06 00:00:00

  • Turn-off colorimetric sensor for sequence-specific recognition of single-stranded DNA based upon Y-shaped DNA structure.

    abstract::A novel turn-off colorimetric sensor for sequence-specific recognition of single-stranded DNA (ssDNA) was established by combining Y-shaped DNA duplex and G-quadruplex-hemin DNAzyme. A G-rich single-stranded DNA (Oligo-1) displays peroxidase mimicking catalytic activity due to the specific binding with hemin in the pr...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-30529-z

    authors: Zhang H,Li X,He F,Zhao M,Ling L

    更新日期:2018-08-13 00:00:00

  • An approximate analytical solution of the Bethe equation for charged particles in the radiotherapeutic energy range.

    abstract::Charged particles such as protons and carbon ions are an increasingly important tool in radiotherapy. There are however unresolved physics issues impeding optimal implementation, including estimation of dose deposition in non-homogeneous tissue, an essential aspect of treatment optimization. Monte Carlo (MC) methods c...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-10554-0

    authors: Grimes DR,Warren DR,Partridge M

    更新日期:2017-08-29 00:00:00

  • Leidenfrost levitation: beyond droplets.

    abstract::Friction is a major inhibitor in almost every mechanical system. Enlightened by the Leidenfrost effect - a droplet can be levitated by its own vapor layer on a sufficiently hot surface - we demonstrate for the first time that a small cart can also be levitated by Leidenfrost vapor. The levitated cart can carry certain...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep00797

    authors: Hashmi A,Xu Y,Coder B,Osborne PA,Spafford J,Michael GE,Yu G,Xu J

    更新日期:2012-01-01 00:00:00

  • Disease-free monoculture farming by fungus-growing termites.

    abstract::Fungus-growing termites engage in an obligate mutualistic relationship with Termitomyces fungi, which they maintain in monocultures on specialised fungus comb structures, without apparent problems with infectious diseases. While other fungi have been reported in the symbiosis, detailed comb fungal community analyses h...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-45364-z

    authors: Otani S,Challinor VL,Kreuzenbeck NB,Kildgaard S,Krath Christensen S,Larsen LLM,Aanen DK,Rasmussen SA,Beemelmanns C,Poulsen M

    更新日期:2019-06-19 00:00:00

  • Amyloid formation of growth hormone in presence of zinc: Relevance to its storage in secretory granules.

    abstract::Amyloids are cross-β-sheet fibrillar aggregates, associated with various human diseases and native functions such as protein/peptide hormone storage inside secretory granules of neuroendocrine cells. In the current study, using amyloid detecting agents, we show that growth hormone (GH) could be stored as amyloid in th...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep23370

    authors: Jacob RS,Das S,Ghosh S,Anoop A,Jha NN,Khan T,Singru P,Kumar A,Maji SK

    更新日期:2016-03-23 00:00:00

  • Genome-Wide Identification of Mitogen-activated Protein Kinase Cascade Genes and Transcriptional Profiling Analysis during Organ Development in Eucommia ulmoides.

    abstract::The mitogen-activated protein kinase (MAPK) cascades, which play crucial roles in plant development processes, are universal modules of signal transduction in eukaryotes and consist of a core module of three sequentially phosphorylated kinases: MAPK, MAPK kinase (MAPKK), and MAPKK kinase (MAPKKK). This is the first re...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-17615-4

    authors: Jing T,Wang L,Liu H,Wuyun TN,Du H

    更新日期:2017-12-18 00:00:00

  • Substitution rate and natural selection in parvovirus B19.

    abstract::The aim of this study was to estimate substitution rate and imprints of natural selection on parvovirus B19 genotype 1. Studied datasets included 137 near complete coding B19 genomes (positions 665 to 4851) for phylogenetic and substitution rate analysis and 146 and 214 partial genomes for selection analyses in open r...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep35759

    authors: Stamenković GG,Ćirković VS,Šiljić MM,Blagojević JV,Knežević AM,Joksić ID,Stanojević MP

    更新日期:2016-10-24 00:00:00

  • Establishment of a guided, in vivo, multi-channel, abdominal, tissue imaging approach.

    abstract::Novel tools in humane animal research should benefit the animal as well as the experimentally obtained data. Imaging technologies have proven to be versatile and also in accordance with the demands of the 3 R principle. However, most imaging technologies are either limited by the target organs, number of repetitive im...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-65950-w

    authors: Bahlmann J,Madrahimov N,Daniel F,Theidel D,DeTemple DE,Buettner M,Bleich A,Haverich A,Heisterkamp A,Kalies S

    更新日期:2020-06-08 00:00:00

  • Computational modeling of human reasoning processes for interpretable visual knowledge: a case study with radiographers.

    abstract::Visual reasoning is critical in many complex visual tasks in medicine such as radiology or pathology. It is challenging to explicitly explain reasoning processes due to the dynamic nature of real-time human cognition. A deeper understanding of such reasoning processes is necessary for improving diagnostic accuracy and...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-77550-9

    authors: Li Y,Cao H,Allen CM,Wang X,Erdelez S,Shyu CR

    更新日期:2020-12-10 00:00:00

  • A scoring system to detect fixed airflow limitation in smokers from simple easy-to-use parameters.

    abstract::No validated screening method currently exists for Chronic Obstructive Pulmonary Disease (COPD) in smokers. Therefore, we constructed a predictive model with simple parameters that can be applied for COPD screening to detect fixed airflow limitation. This observational cross-sectional study included a random sample of...

    journal_title:Scientific reports

    pub_type: 杂志文章,随机对照试验

    doi:10.1038/s41598-018-31198-8

    authors: Román-Conejos E,Palazón-Bru A,Folgado-de la Rosa DM,Sánchez-Molla M,Rizo-Baeza MM,Gil-Guillén VF,Cortés-Castell E

    更新日期:2018-09-06 00:00:00

  • Single Crystal Growth and Spin Polarization Measurements of Diluted Magnetic Semiconductor (BaK)(ZnMn)2As2.

    abstract::Recently a new diluted magnetic semiconductor, (Ba,K)(Zn,Mn)2As2 (BZA), with high Curie temperature was discovered, showing an independent spin and charge-doping mechanism. This makes BZA a promising material for spintronics devices. We report the successful growth of a BZA single crystal for the first time in this st...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-08394-z

    authors: Zhao GQ,Lin CJ,Deng Z,Gu GX,Yu S,Wang XC,Gong ZZ,Uemura YJ,Li YQ,Jin CQ

    更新日期:2017-11-03 00:00:00

  • Synchronization Analysis of Master-Slave Probabilistic Boolean Networks.

    abstract::In this paper, we analyze the synchronization problem of master-slave probabilistic Boolean networks (PBNs). The master Boolean network (BN) is a deterministic BN, while the slave BN is determined by a series of possible logical functions with certain probability at each discrete time point. In this paper, we firstly ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep13437

    authors: Lu J,Zhong J,Li L,Ho DW,Cao J

    更新日期:2015-08-28 00:00:00

  • Forest roadsides harbour less competitive habitats for a relict mountain plant (Pulsatilla vernalis) in lowlands.

    abstract::The long-term survival of relict populations depends on the accessibility of appropriate sites (microrefugia). In recent times, due to the mass extinction of rare species that has resulted from the loss of natural habitats, the question is - Are there any human-made sites that can act as refugial habitats? We examined...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep31913

    authors: Zielińska KM,Kiedrzyński M,Grzyl A,Rewicz A

    更新日期:2016-08-18 00:00:00

  • Cytoglobin Promotes Cardiac Progenitor Cell Survival against Oxidative Stress via the Upregulation of the NFκB/iNOS Signal Pathway and Nitric Oxide Production.

    abstract::Human cardiac stem/progenitor cells (hCPCs) may serve in regenerative medicine to repair the infarcted heart. However, this approach is severely limited by the poor survival of donor cells. Recent studies suggest that the mammalian globin cytoglobin (CYGB) regulates nitric oxide (NO) metabolism and cell death. In the ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-11342-6

    authors: Zhang S,Li X,Jourd'heuil FL,Qu S,Devejian N,Bennett E,Jourd'heuil D,Cai C

    更新日期:2017-09-07 00:00:00

  • Local adaptation to temperature and precipitation in naturally fragmented populations of Cephalotaxus oliveri, an endangered conifer endemic to China.

    abstract::Cephalotaxus oliveri is an endangered tertiary relict conifer endemic to China. The species survives in a wide range from west to east with heterogeneous climatic conditions. Precipitation and temperature are main restrictive factors for distribution of C. oliveri. In order to comprehend the mechanism of adaptive evol...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep25031

    authors: Wang T,Wang Z,Xia F,Su Y

    更新日期:2016-04-26 00:00:00