UniBic: Sequential row-based biclustering algorithm for analysis of gene expression data.

Abstract:

:Biclustering algorithms, which aim to provide an effective and efficient way to analyze gene expression data by finding a group of genes with trend-preserving expression patterns under certain conditions, have been widely developed since Morgan et al. pioneered a work about partitioning a data matrix into submatrices with approximately constant values. However, the identification of general trend-preserving biclusters which are the most meaningful substructures hidden in gene expression data remains a highly challenging problem. We found an elementary method by which biologically meaningful trend-preserving biclusters can be readily identified from noisy and complex large data. The basic idea is to apply the longest common subsequence (LCS) framework to selected pairs of rows in an index matrix derived from an input data matrix to locate a seed for each bicluster to be identified. We tested it on synthetic and real datasets and compared its performance with currently competitive biclustering tools. We found that the new algorithm, named UniBic, outperformed all previous biclustering algorithms in terms of commonly used evaluation scenarios except for BicSPAM on narrow biclusters. The latter was somewhat better at finding narrow biclusters, the task for which it was specifically designed.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Wang Z,Li G,Robinson RW,Huang X

doi

10.1038/srep23466

subject

Has Abstract

pub_date

2016-03-22 00:00:00

pages

23466

issn

2045-2322

pii

srep23466

journal_volume

6

pub_type

杂志文章
  • Why one-size-fits-all vaso-modulatory interventions fail to control glioma invasion: in silico insights.

    abstract::Gliomas are highly invasive brain tumours characterised by poor prognosis and limited response to therapy. There is an ongoing debate on the therapeutic potential of vaso-modulatory interventions against glioma invasion. Prominent vasculature-targeting therapies involve tumour blood vessel deterioration and normalisat...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep37283

    authors: Alfonso JC,Köhn-Luque A,Stylianopoulos T,Feuerhake F,Deutsch A,Hatzikirou H

    更新日期:2016-11-23 00:00:00

  • Serum anion gap at admission as a predictor of mortality in the pediatric intensive care unit.

    abstract::An accurate method to predict the mortality in the intensive care unit (ICU) patients has been required, especially in children. The aim of this study is to evaluate the value of serum anion gap (AG) for predicting mortality in pediatric ICU (PICU). We reviewed a data of 461 pediatric patients were collected on PICU a...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-01681-9

    authors: Kim MJ,Kim YH,Sol IS,Kim SY,Kim JD,Kim HY,Kim KW,Sohn MH,Kim KE

    更新日期:2017-05-03 00:00:00

  • Colonization and diversification of the Euphorbia species (sect. Aphyllis subsect. Macaronesicae) on the Canary Islands.

    abstract::Diversification between islands and ecological radiation within islands are postulated to have occurred in the Euphorbia species (sect. Aphyllis subsect. Macaronesicae) on the Canary Islands. In this study, the biogeographical pattern of 11 species of subsect. Macaronesicae and the genetic differentiation among five s...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep34454

    authors: Sun Y,Li Y,Vargas-Mendoza CF,Wang F,Xing F

    更新日期:2016-09-29 00:00:00

  • Inter-relationship between subtropical Pacific sea surface temperature, Arctic sea ice concentration, and North Atlantic Oscillation in recent summers.

    abstract::The inter-relationship between subtropical western-central Pacific sea surface temperatures (STWCPSST), sea ice concentrations in the Beaufort Sea (SICBS), and the North Atlantic Oscillation (NAO) in summer are investigated over the period 1980-2016. It is shown that the Arctic response to the remote impact of the Pac...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-39896-7

    authors: Lim YK,Cullather RI,Nowicki SMJ,Kim KM

    更新日期:2019-03-05 00:00:00

  • Impact of hearing aid noise reduction algorithms on the speech-evoked auditory brainstem response.

    abstract::The purposes of this study are to investigate the neural representation of a speech stimulus in the auditory system of individuals with normal hearing (NH) and those with hearing aids (HAs) and to explore the impact of noise reduction algorithms (NR) on auditory brainstem response to complex sounds (cABR). Twenty NH i...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-66970-2

    authors: Seol HY,Park S,Ji YS,Hong SH,Moon IJ

    更新日期:2020-07-01 00:00:00

  • Crystallographic anisotropy of the resistivity size effect in single crystal tungsten nanowires.

    abstract::This work demonstrates an anisotropic increase in resistivity with decreasing width in single crystal tungsten (W) nanowires having a height of 21 nm. Nanowire-widths were in the range of 15-451 nm, with the anisotropy observed for widths below 50 nm. The longitudinal directions of the nanowires coincided with the <10...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep02591

    authors: Choi D,Moneck M,Liu X,Oh SJ,Kagan CR,Coffey KR,Barmak K

    更新日期:2013-01-01 00:00:00

  • Analysis of tractable allosteric sites in G protein-coupled receptors.

    abstract::Allosteric modulation of G protein-coupled receptors represent a promising mechanism of pharmacological intervention. Dramatic developments witnessed in the structural biology of membrane proteins continue to reveal that the binding sites of allosteric modulators are widely distributed, including along protein surface...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-42618-8

    authors: Wakefield AE,Mason JS,Vajda S,Keserű GM

    更新日期:2019-04-16 00:00:00

  • Species-specific antifungal activity of blue light.

    abstract::Fungal pathogens represent a significant threat to immunocompromised patients or individuals with traumatic injury. Strategies to efficiently remove fungal spores from hospital surfaces and, ideally, patient skin thus offer the prospect of dramatically reducing infections in at-risk patients. Photodynamic inactivation...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-05000-0

    authors: Trzaska WJ,Wrigley HE,Thwaite JE,May RC

    更新日期:2017-07-04 00:00:00

  • Distorting temporal fine structure by phase shifting and its effects on speech intelligibility and neural phase locking.

    abstract::Envelope (E) and temporal fine structure (TFS) are important features of acoustic signals and their corresponding perceptual function has been investigated with various listening tasks. To further understand the underlying neural processing of TFS, experiments in humans and animals were conducted to demonstrate the ef...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-12975-3

    authors: Xu Y,Chen M,LaFaire P,Tan X,Richter CP

    更新日期:2017-10-17 00:00:00

  • Long-term survival in permanent middle cerebral artery occlusion: a model of malignant stroke in rats.

    abstract::Occlusion of the middle cerebral artery (MCA) by an intraluminal filament is widely used to study focal brain ischemia in male Sprague-Dawley rats. However, permanent occlusion goes along with a high fatality. To overcome this drawback we designed a new filament carrying a bowling pin-shaped tip (BP-tip) and compared ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep28401

    authors: Shanbhag NC,Henning RH,Schilling L

    更新日期:2016-06-22 00:00:00

  • Nomogram-based prediction of rebleeding in small bowel bleeding patients: the 'PRSBB' score.

    abstract::Small bowel capsule endoscopy (SBCE) and balloon-assisted endoscopy (BAE) have revolutionized the diagnosis and treatment of small bowel bleeding (SBB), allowing access to the small bowel and identification of specific bleeding lesions. However, some patients experience rebleeding after small bowel investigation, and ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-24868-0

    authors: Uchida G,Hirooka Y,Nakamura M,Watanabe O,Yamamura T,Matsushita M,Suhara H,Ishikawa T,Furukawa K,Funasaka K,Ohno E,Kawashima H,Miyahara R,Goto H

    更新日期:2018-04-23 00:00:00

  • Image artifacts in single molecule localization microscopy: why optimization of sample preparation protocols matters.

    abstract::Single molecule localization microscopy (SMLM) techniques allow for sub-diffraction imaging with spatial resolutions better than 10 nm reported. Much has been discussed relating to different variations of SMLM and all-inclusive microscopes can now be purchased, removing the need for in-house software or hardware devel...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep07924

    authors: Whelan DR,Bell TD

    更新日期:2015-01-21 00:00:00

  • Transmembrane Helices Tilt, Bend, Slide, Torque, and Unwind between Functional States of Rhodopsin.

    abstract::The seven-helical bundle of rhodopsin and other G-protein coupled receptors undergoes structural rearrangements as the transmembrane receptor protein is activated. These structural changes are known to involve tilting and bending of various transmembrane helices. However, the cause and effect relationship among struct...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep34129

    authors: Ren Z,Ren PX,Balusu R,Yang X

    更新日期:2016-09-23 00:00:00

  • Carbon p electron ferromagnetism in silicon carbide.

    abstract::Ferromagnetism can occur in wide-band gap semiconductors as well as in carbon-based materials when specific defects are introduced. It is thus desirable to establish a direct relation between the defects and the resulting ferromagnetism. Here, we contribute to revealing the origin of defect-induced ferromagnetism usin...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep08999

    authors: Wang Y,Liu Y,Wang G,Anwand W,Jenkins CA,Arenholz E,Munnik F,Gordan OD,Salvan G,Zahn DR,Chen X,Gemming S,Helm M,Zhou S

    更新日期:2015-03-11 00:00:00

  • A new genus and two new species of freshwater mussels (Unionidae) from western Indochina.

    abstract::The systematics of Oriental freshwater mussels (Bivalvia: Unionidae) is poorly known. Here, we present an integrative revision of the genus Trapezoideus Simpson, 1900 to further understanding of freshwater mussel diversity in the region. We demonstrate that Trapezoideus as currently circumscribed is non-monophyletic, ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-39365-1

    authors: Konopleva ES,Pfeiffer JM,Vikhrev IV,Kondakov AV,Gofarov MY,Aksenova OV,Lunn Z,Chan N,Bolotov IN

    更新日期:2019-03-11 00:00:00

  • Approach to multifunctional device platform with epitaxial graphene on transition metal oxide.

    abstract::Heterostructures consisting of two-dimensional materials have shown new physical phenomena, novel electronic and optical properties, and new device concepts not observed in bulk material systems or purely three dimensional heterostructures. These new effects originated mostly from the van der Waals interaction between...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep14374

    authors: Park J,Back T,Mitchel WC,Kim SS,Elhamri S,Boeckl J,Fairchild SB,Naik R,Voevodin AA

    更新日期:2015-09-23 00:00:00

  • Mechanism of the antigen-independent cytokinergic SPE-7 IgE activation of human mast cells in vitro.

    abstract::Release of pro-inflammatory mediators by mast cells is a key feature of allergic disease. The 'dogma' is that IgE molecules merely sensitise mast cells by binding FcεRI prior to cross-linking by multivalent allergen, receptor aggregation and mast cell activation. However, certain monoclonal IgE antibodies have been sh...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep09538

    authors: Bax HJ,Bowen H,Dodev TS,Sutton BJ,Gould HJ

    更新日期:2015-04-20 00:00:00

  • Classification of Tandem Mass Spectra for Identification of N- and O-linked Glycopeptides.

    abstract::Analysis of intact glycopeptides by mass spectrometry is essential to determining the microheterogeneity of protein glycosylation. Higher-energy collisional dissociation (HCD) fragmentation of glycopeptides generates mono- or disaccharide ions called oxonium ions that carry information about the structure of the fragm...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep37189

    authors: Toghi Eshghi S,Yang W,Hu Y,Shah P,Sun S,Li X,Zhang H

    更新日期:2016-11-21 00:00:00

  • The BMP2 nuclear variant, nBMP2, is expressed in mouse hippocampus and impacts memory.

    abstract::The novel nuclear protein nBMP2 is synthesized from the BMP2 gene by translational initiation at an alternative start codon. We generated a targeted mutant mouse, nBmp2NLStm, in which the nuclear localization signal (NLS) was inactivated to prevent nuclear translocation of nBMP2 while still allowing the normal synthes...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep46464

    authors: Cordner RD,Friend LN,Mayo JL,Badgley C,Wallmann A,Stallings CN,Young PL,Miles DR,Edwards JG,Bridgewater LC

    更新日期:2017-04-18 00:00:00

  • Role of flagella and type four pili in the co-migration of Burkholderia terrae BS001 with fungal hyphae through soil.

    abstract::Burkholderia terrae BS001 has previously been found to be able to disperse along with growing fungal hyphae in soil, with the type-3 secretion system having a supportive role in this movement. In this study, we focus on the role of two motility- and adherence-associated appendages, i.e. type-4 pili (T4P) and flagella....

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-02959-8

    authors: Yang P,Zhang M,van Elsas JD

    更新日期:2017-06-07 00:00:00

  • Association between alcohol consumption pattern and the incidence risk of type 2 diabetes in Korean men: A 12-years follow-up study.

    abstract::Moderate alcohol consumption is generally associated with reduced risk of type 2 diabetes. However, this beneficial effects of alcohol intake remains controversial due to inconsistent results across studies. The analysis was performed using data from the Ansung-Ansan cohort study. We categorized the participants into ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-07549-2

    authors: Lee DY,Yoo MG,Kim HJ,Jang HB,Kim JH,Lee HJ,Park SI

    更新日期:2017-08-04 00:00:00

  • Fabry-Pérot modes associated with hyperbolic-like dispersion in dielectric photonic crystals and demonstration of a bending angle sensor at microwave frequencies.

    abstract::The dispersion properties of metamaterials and photonic crystals (PhCs) lead to an intensive research in the development of cavity resonators for the confinement of electromagnetic (e-m) radiation. In this work, we investigate the formation of Fabry-Pérot (FP) modes associated with hyperbolic-like dispersion (HLD) reg...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-67965-9

    authors: Darthy RR,Venkateswaran C,Subramanian V,Ouyang Z,Yogesh N

    更新日期:2020-07-06 00:00:00

  • Factors associated with smoking susceptibility among high school students in western Spain.

    abstract::The Expanded Susceptibility to Smoking Index (ESSI) is based on the combination of susceptibility to smoking and curiosity about smoking. The ESSI can identify young people who are at risk of starting to smoke cigarettes and related products. The objective of this study was to analyse the ESSI results and to examine f...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-021-81723-5

    authors: Santano-Mogena E,Franco-Antonio C,Chimento-Díaz S,Rico-Martín S,Cordovilla-Guardia S

    更新日期:2021-01-21 00:00:00

  • Activation of the unfolded protein response promotes axonal regeneration after peripheral nerve injury.

    abstract::Although protein-folding stress at the endoplasmic reticulum (ER) is emerging as a driver of neuronal dysfunction in models of spinal cord injury and neurodegeneration, the contribution of this pathway to peripheral nerve damage remains poorly explored. Here we targeted the unfolded protein response (UPR), an adaptive...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep21709

    authors: Oñate M,Catenaccio A,Martínez G,Armentano D,Parsons G,Kerr B,Hetz C,Court FA

    更新日期:2016-02-24 00:00:00

  • Advanced maternal age compromises fetal growth and induces sex-specific changes in placental phenotype in rats.

    abstract::Advanced maternal age is associated with an increased risk of pregnancy complications. It programmes sex-specific cardiovascular dysfunction in rat offspring, however the intrauterine mechanisms involved remain unknown. This study in the rat assessed the impact of advanced maternal age on placental phenotype in relati...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-53199-x

    authors: Napso T,Hung YP,Davidge ST,Care AS,Sferruzzi-Perri AN

    更新日期:2019-11-28 00:00:00

  • Mechanical interlocking of cotton fibers on slightly textured surfaces of metallic cylinders.

    abstract::Mechanical interlocking is widely applied in industry and general lives of human beings. In this work, we realized the control of locking or sliding states of cotton fibers on the metal surfaces with slightly different textures through traditional machining. Three types of sliding states, i.e., locking, one-way slidin...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep25403

    authors: Zhang Y,Tian Y,Meng Y

    更新日期:2016-05-09 00:00:00

  • Characterization of Conserved and Novel microRNAs in Lilium lancifolium Thunb. by High-Throughput Sequencing.

    abstract::MicroRNAs (miRNAs) are among the class of noncoding small RNA molecules and play a crucial role in post-transcriptional regulation in plants. Although Lilium is one of the most popular ornamental flowers worldwide, however, there is no report on miRNAs identification. In the present study, therefore, miRNAs and their ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-21193-4

    authors: He X,Shenkute AG,Wang W,Xu S

    更新日期:2018-02-13 00:00:00

  • Confirmation of ovulation from urinary progesterone analysis: assessment of two automated assay platforms.

    abstract::Urinary concentrations of the major progesterone (P4) metabolite pregnanediol-3-glucuronide (PDG) are used to confirm ovulation. We aimed to determine whether automated immunoassay of urinary P4 was as efficacious as PDG to confirm ovulation. Daily urine samples from 20 cycles in 14 healthy women in whom ovulation was...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-36051-6

    authors: Gifford RM,Howie F,Wilson K,Johnston N,Todisco T,Crane M,Greeves JP,Skorupskaite K,Woods DR,Reynolds RM,Anderson RA

    更新日期:2018-12-04 00:00:00

  • Identification of brain antigens recognized by autoantibodies in experimental autoimmune encephalomyelitis-induced animals treated with etomoxir or interferon-β.

    abstract::Multiple sclerosis (MS) is a neurodegenerative autoimmune disease, where chronic inflammation plays an essential role in its pathology. A feature of MS is the production of autoantibodies stimulated by an altered-peptide-ligand response and epitope spreading, resulting in loss of tolerance for self-proteins. The invol...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-25391-y

    authors: Mørkholt AS,Kastaniegaard K,Trabjerg MS,Gopalasingam G,Niganze W,Larsen A,Stensballe A,Nielsen S,Nieland JD

    更新日期:2018-05-04 00:00:00

  • MLH1 single-nucleotide variant in circulating tumor DNA predicts overall survival of patients with hepatocellular carcinoma.

    abstract::Liquid biopsy can provide a strong basis for precision medicine. We aimed to identify novel single-nucleotide variants (SNVs) in circulating tumor DNA (ctDNA) in patients with hepatocellular carcinoma (HCC). Deep sequencing of plasma-derived ctDNA from 59 patients with HCC was performed using a panel of 2924 SNVs in 6...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-74494-y

    authors: Kim SS,Eun JW,Choi JH,Woo HG,Cho HJ,Ahn HR,Suh CW,Baek GO,Cho SW,Cheong JY

    更新日期:2020-10-20 00:00:00