当前位置： SCI文献检索 > COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE期刊下所有文献 > Classification-based quantitative analysis of stable isotope labeling by amino acids in cell culture (SILAC) data.

Classification-based quantitative analysis of stable isotope labeling by amino acids in cell culture (SILAC) data.

Abstract：

BACKGROUND AND OBJECTIVE:Stable isotope labeling by amino acids in cell culture (SILAC) is a practical and powerful approach for quantitative proteomic analysis. A key advantage of SILAC is the ability to simultaneously detect the isotopically labeled peptides in a single instrument run and so guarantee relative quantitation for a large number of peptides without introducing any variation caused by separate experiment. However, there are a few approaches available to assessing protein ratios and none of the existing algorithms pays considerable attention to the proteins having only one peptide hit. METHODS:We introduce new quantitative approaches to dealing with SILAC protein-level summary using classification-based methodologies, such as Gaussian mixture models with EM algorithms and its Bayesian approach as well as K-means clustering. In addition, a new approach is developed using Gaussian mixture model and a stochastic, metaheuristic global optimization algorithm, particle swarm optimization (PSO), to avoid either a premature convergence or being stuck in a local optimum. RESULTS:Our simulation studies show that the newly developed PSO-based method performs the best among others in terms of F1 score and the proposed methods further demonstrate the ability of detecting potential markers through real SILAC experimental data. CONCLUSIONS:No matter how many peptide hits the protein has, the developed approach can be applicable, rescuing many proteins doomed to removal. Furthermore, no additional correction for multiple comparisons is necessary for the developed methods, enabling direct interpretation of the analysis outcomes.

journal_name

Comput Methods Programs Biomed

journal_title

Computer methods and programs in biomedicine

authors

Kim S,Carruthers N,Lee J,Chinni S,Stemmer P

doi

10.1016/j.cmpb.2016.09.017

subject

Has Abstract

pub_date

2016-12-01 00:00:00

pages

137-148

eissn

0169-2607

issn

1872-7565

pii

S0169-2607(16)30136-5

journal_volume

137

pub_type

杂志文章

相关文献

COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE文献大全
  • A general algorithm for optimal sampling schedule design in nuclear medicine imaging.

    abstract：:Optimal sampling schedule (OSS) is of great interest in biomedical experiment design, as it can improve the physiological parameter estimation precision and significantly reduce the samples required. A number of well designed algorithms and software packages have been developed, which deal with the instantaneous measu...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/s0169-2607(00)00114-0

    authors： Li X,Feng D,Wong K

    更新日期：2001-04-01 00:00:00

  • Shape prior model via dual subspace segment projection learning.

    abstract：BACKGROUND AND OBJECTIVE:Shape prior models play a vital role for segmentation in medical image analysis. These models are most effective when shape variations can be captured by a parametric distribution, and sufficient training data is available. However, in the absence of these conditions, results are invariably muc...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/j.cmpb.2020.105760

    authors： Belous G,Busch A,Gao Y

    更新日期：2020-09-24 00:00:00

  • Improving drug dosing in hospitalized patients: automated modeling of pharmacokinetics for individualization of drug dosage regimens.

    abstract：:Many clinical useful drugs have a narrow range of blood concentrations which are both safe and efficacious. Inter-individual and intra-individual variations in drug disposition are important factors causing blood concentrations of drug to fall outside of the therapeutic range. Modeling of the pharmacokinetics of the i...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/0169-2607(89)90069-2

    authors： Lenert L,Sheiner L,Blaschke T

    更新日期：1989-10-01 00:00:00

  • Assessment of respiratory mechanical properties with constant-phase models in healthy and COPD lungs.

    abstract：:This study employs the concept of applying constant-phase models to input respiratory impedance data obtained with the non-invasive Forced Oscillation Technique (FOT) lung function test. Changes in respiratory mechanics from healthy and chronic obstructive pulmonary disease (COPD) diagnosed patients are observed with ...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/j.cmpb.2009.06.006

    authors： Ionescu C,Derom E,De Keyser R

    更新日期：2010-01-01 00:00:00

  • Pivoting approaches for bulk extraction of Entity-Attribute-Value data.

    abstract：:Entity-Attribute-Value (EAV) data, as present in repositories of clinical patient data, must be transformed (pivoted) into one-column-per-parameter format before it can be used by a variety of analytical programs. Pivoting approaches have not been described in depth in the literature, and existing descriptions are dat...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/j.cmpb.2006.02.001

    authors： Dinu V,Nadkarni P,Brandt C

    更新日期：2006-04-01 00:00:00

  • Parallelized collision detection with applications in virtual bone machining.

    abstract：BACKGROUND AND OBJECTIVES:Virtual reality surgery simulators have been proved effective for training in several surgical disciplines. Nevertheless, this technology is presently underutilized in orthopaedics, especially for bone machining procedures, due to the limited realism in haptic simulation of bone interactions. ...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/j.cmpb.2019.105263

    authors： Faieghi M,Tutunea-Fatan OR,Eagleson R

    更新日期：2020-05-01 00:00:00

  • Fast unsupervised nuclear segmentation and classification scheme for automatic allred cancer scoring in immunohistochemical breast tissue images.

    abstract：BACKGROUND AND OBJECTIVE:This paper presents an improved scheme able to perform accurate segmentation and classification of cancer nuclei in immunohistochemical (IHC) breast tissue images in order to provide quantitative evaluation of estrogen or progesterone (ER/PR) receptor status that will assist pathologists in can...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/j.cmpb.2018.08.005

    authors： Mouelhi A,Rmili H,Ali JB,Sayadi M,Doghri R,Mrad K

    更新日期：2018-10-01 00:00:00

  • Magneto rotating flow of hybrid nanofluid with entropy generation.

    abstract：BACKGROUND:Study of nanofluids has been enormously increased for the last couple of years. Regardless of some irregularity in the revealed outcomes and lacking consistency, yet the mechanisms of heat transport have been emerged as highly efficient. In the continuation of nanomaterials research, the investigators and an...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/j.cmpb.2019.105093

    authors： Ijaz Khan M,Hafeez MU,Hayat T,Imran Khan M,Alsaedi A

    更新日期：2020-01-01 00:00:00

  • An expert system for the nutritional management of the critically ill.

    abstract：:While there have been considerable advances in the last several years in the nutritional management of the critically ill, these improvements are not always recognized in intensive care environments. In this paper we describe the development and testing of an expert system, NUTRITIONAL ADVISOR, which would be be an ai...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/0169-2607(90)90040-g

    authors： Fraser RB,Turney SZ

    更新日期：1990-11-01 00:00:00

  • Design of crossover microcomputer program and application on drug bioequivalence data.

    abstract：:A simple microcomputer crossover program in BASIC is designed for the purpose of drug bioequivalence studies and other related fields of statistical investigation. An illustration of the application of the program is presented to compare the bioavailability of ibuprofen when administered alone or followed by colestipo...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 临床试验,杂志文章

    doi：10.1016/0169-2607(95)01695-3

    authors： Abdullah ME,El-Sayed YM

    更新日期：1995-12-01 00:00:00

  • The IBIS project: data collection in London. Improved Monitoring for Brain Dysfunction during Intensive Care and Surgery.

    abstract：:The primary aim of the Improved Monitoring for Brain Dysfunction during Intensive Care and Surgery (IBIS) project was to create a unique and comprehensively annotated data library (DL) of multiple physiological, including neurophysiological, signals. Data collection was undertaken in Kuopio, Finland and London, UK, an...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/s0169-2607(00)00107-3

    authors： Mandersloot GF,Pottinger RC,Weller PR,Prior PF,Morgan C,Smith NJ,Langford RM

    更新日期：2000-11-01 00:00:00

  • Fast parallel vessel segmentation.

    abstract：BACKGROUND AND OBJECTIVE:Accurate and fast vessel segmentation from liver slices remain challenging and important tasks for clinicians. The algorithms from the literature are slow and less accurate. We propose fast parallel gradient based seeded region growing for vessel segmentation. Seeded region growing is tedious w...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/j.cmpb.2020.105430

    authors： Satpute N,Naseem R,Palomar R,Zachariadis O,Gómez-Luna J,Cheikh FA,Olivares J

    更新日期：2020-08-01 00:00:00

  • Correlation analysis of respiratory signals by using parallel coordinate plots.

    abstract：BACKGROUND AND OBJECTIVES:The understanding of the bonds and the relationships between the respiratory signals, i.e. the airflow, the mouth pressure, the relative temperature and the relative humidity during breathing may provide the improvement on the measurement methods of respiratory mechanics and sensor designs or ...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/j.cmpb.2017.10.003

    authors： Saatci E

    更新日期：2018-01-01 00:00:00

  • Machine learning-based assessment tool for imbalance and vestibular dysfunction with virtual reality rehabilitation system.

    abstract：BACKGROUND AND OBJECTIVE:Dizziness is a major consequence of imbalance and vestibular dysfunction. Compared to surgery and drug treatments, balance training is non-invasive and more desired. However, training exercises are usually tedious and the assessment tool is insufficient to diagnose patient's severity rapidly. ...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/j.cmpb.2014.04.014

    authors： Yeh SC,Huang MC,Wang PC,Fang TY,Su MC,Tsai PY,Rizzo A

    更新日期：2014-10-01 00:00:00

  • Quantile planes without crossing via nonlinear programming.

    abstract：BACKGROUND AND OBJECTIVE:In this note we propose a nonlinear programming approach for simultaneous fitting of quantile regression models for two or more quantiles. The approach is straightforward, flexible and practical. We apply this approach to a dataset of lactic acid values from a screening dataset in childhood mal...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/j.cmpb.2017.10.019

    authors： Hutson AD

    更新日期：2018-01-01 00:00:00

  • Development of an automatic muscle atrophy measuring algorithm to calculate the ratio of supraspinatus in supraspinous fossa using deep learning.

    abstract：BACKGROUND AND OBJECTIVE:Rotator cuff muscle tear is one of the most frequent reason of operations in orthopedic surgery. There are several clinical indicators such as Goutallier grade and occupation ratio in the diagnosis and surgery of these diseases, but subjective intervention of the diagnosis is an obstacle in acc...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/j.cmpb.2019.105063

    authors： Kim JY,Ro K,You S,Nam BR,Yook S,Park HS,Yoo JC,Park E,Cho K,Cho BH,Kim IY

    更新日期：2019-12-01 00:00:00

  • Three dimensional imaging of tracheobronchial system using spiral CT.

    abstract：:The purpose of this study was to evaluate the clinical efficacy of 3D reconstruction of the tracheobronchial system using spiral CT. A total of 25 patients with tracheobronchial abnormalities, stenosis (n = 21) and fistula with esophagus (n = 4), underwent a single breathhold spiral CT (5 mm collision, 5 mm)/s increme...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 临床试验,杂志文章

    doi：10.1016/s0169-2607(98)00053-4

    authors： Kozuka T,Minaguchi K,Yamaguchi R,Yamaguchi M,Taniguchi Y

    更新日期：1998-08-01 00:00:00

  • Predicting daily outcomes in acetaminophen-induced acute liver failure patients with machine learning techniques.

    abstract：BACKGROUND/OBJECTIVE:Assessing prognosis for acetaminophen-induced acute liver failure (APAP-ALF) patients during the first week of hospitalization often presents significant challenges. Current models such as the King's College Criteria (KCC) and the Acute Liver Failure Study Group (ALFSG) Prognostic Index are develop...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/j.cmpb.2019.04.012

    authors： Speiser JL,Karvellas CJ,Wolf BJ,Chung D,Koch DG,Durkalski VL

    更新日期：2019-07-01 00:00:00

  • Unique parameter identification for cardiac diagnosis in critical care using minimal data sets.

    abstract：:Lumped parameter approaches for modelling the cardiovascular system typically have many parameters of which a significant percentage are often not identifiable from limited data sets. Hence, significant parts of the model are required to be simulated with little overall effect on the accuracy of data fitting, as well ...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/j.cmpb.2010.01.002

    authors： Hann CE,Chase JG,Desaive T,Froissart CB,Revie J,Stevenson D,Lambermont B,Ghuysen A,Kolh P,Shaw GM

    更新日期：2010-07-01 00:00:00

  • PROforma: a general technology for clinical decision support systems.

    abstract：:The need for flexible and well understood knowledge representations which are capable of capturing clinical guidelines and protocols for decision support systems is widely recognised. The PROforma method for specifying clinical guidelines and protocols comprises a graphical notation for their design, and a formal know...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/s0169-2607(97)00034-5

    authors： Fox J,Johns N,Lyons C,Rahmanzadeh A,Thomson R,Wilson P

    更新日期：1997-09-01 00:00:00

  • Semi-supervised learning for automatic segmentation of the knee from MRI with convolutional neural networks.

    abstract：BACKGROUND AND OBJECTIVE:Segmentation is a crucial step in multiple biomechanics and orthopedics applications. The time-intensiveness and expertise requirements of medical image segmentation present a significant bottleneck for corresponding workflows. The current study develops and evaluates convolutional neural netwo...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/j.cmpb.2020.105328

    authors： Burton W 2nd,Myers C,Rullkoetter P

    更新日期：2020-06-01 00:00:00

  • Development and evaluation of PC-based HIS-RIS-modality-PACS coupling: the results of evaluation of initial stage with personal computer application.

    abstract：:A PC-based HIS/RIS/Modality/PACS coupling was developed and operated where hospital-wide PACS was closely cooperated with the HIS and RIS. Three workstations with a magneto-optical disk (MOD) juke-box for each one were used as PACS servers to collect images from eight computed radiography systems and three CT scanners...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/s0169-2607(98)00046-7

    authors： Kondoh H,Washiashi T,Sasagaki M,Arisawa J,Nakamura H,Inamura K

    更新日期：1998-08-01 00:00:00

  • Connecting high-dimensional mRNA and miRNA expression data for binary medical classification problems.

    abstract：:In modern molecular biology, high-throughput experiments allow the simultaneous study of expression levels of thousands of biopolymers such as mRNAs, miRNAs or proteins. A typical goal of such experiments is to find molecular signatures that can distinguish between different types of tissue or that can predict a thera...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/j.cmpb.2013.05.013

    authors： Fuchs M,Beißbarth T,Wingender E,Jung K

    更新日期：2013-09-01 00:00:00

  • IT-based evaluation and automatic improvement of the quality of intraoral radiographs.

    abstract：:The quality of intraoral radiographs made in dental practices is too often not adequate for diagnostic purposes. This necessitates standardized measures for the quality of intraoral radiographs and controlled techniques for automatic image improvement. For the evaluation of the quality of digitized intraoral radiograp...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/0169-2607(94)01597-9

    authors： Koch S,Wagner IV,Seipel S,Schneider W

    更新日期：1995-01-01 00:00:00

  • Automated expert multiexponential biomodeling interactively over the Internet.

    abstract：:DIMSUM, an acronym for DIMension of a SUM of exponentials, is a highly automated expert system for fitting multiexponential models of increasing dimension to time series data. Up to now, a researcher has needed an individual copy of DIMSUM on his or her own computer as well as support to learn how to use it. W3DIMSUM,...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/j.cmpb.2005.03.008

    authors： Harless C,Distefano JJ 3rd

    更新日期：2005-08-01 00:00:00

  • Automated detection of conduct disorder and attention deficit hyperactivity disorder using decomposition and nonlinear techniques with EEG signals.

    abstract：BACKGROUND AND OBJECTIVES:Attention deficit hyperactivity disorder (ADHD) is often presented with conduct disorder (CD). There is currently no objective laboratory test or diagnostic method to discern between ADHD and CD, and diagnosis is further made difficult as ADHD is a common neuro-developmental disorder often pre...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/j.cmpb.2021.105941

    authors： Tor HT,Ooi CP,Lim-Ashworth NS,Wei JKE,Jahmunah V,Oh SL,Acharya UR,Fung DSS

    更新日期：2021-01-14 00:00:00

  • Darcy-Forchheimer hybrid (MoS2, SiO2) nanofluid flow with entropy generation.

    abstract：BACKGROUND:The aim of this articles is to investigate the entropy optimization in Darcy-Forchheimer hybrid nanofluids flow towards a stretchable surface. The flow is caused due to stretching of surface. Energy equation is discussed through heat generation/absorption, viscous dissipation and heat flux. Here molybdenum d...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/j.cmpb.2019.105152

    authors： Khan SA,Khan MI,Hayat T,Alsaedi A

    更新日期：2020-03-01 00:00:00

  • Classification of nervous system withdrawn and approved drugs with ToxPrint features via machine learning strategies.

    abstract：BACKGROUND AND OBJECTIVES:Early-phase virtual screening of candidate drug molecules plays a key role in pharmaceutical industry from data mining and machine learning to prevent adverse effects of the drugs. Computational classification methods can distinguish approved drugs from withdrawn ones. We focused on 6 data set...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/j.cmpb.2017.02.004

    authors： Onay A,Onay M,Abul O

    更新日期：2017-04-01 00:00:00

  • Computer-assisted predictive mathematical relationship among electroshock voltage and duration and occurrence of convulsion in mice.

    abstract：:A microcomputer program in BASIC for predicting percentage of occurrence of electroshock-induced convulsion in mice was designed. A formula published by the author to express the mathematical relationship among the drug dose, the time, and the biological response was used in this program. Analysis of the actual, and t...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/0169-2607(89)90177-6

    authors： Chung SJ

    更新日期：1989-01-01 00:00:00

  • An advanced method in fetal phonocardiography.

    abstract：:The long-term variability of the fetal heart rate (FHR) provides valuable information on the fetal health status. The routine clinical FHR measurements are usually carried out by the means of ultrasound cardiography. Although the frequent FHR monitoring is recommendable, the high quality ultrasound devices are so expe...

    journal_title：Computer methods and programs in biomedicine

    pub_type： 杂志文章

    doi：10.1016/s0169-2607(02)00111-6

    authors： Várady P,Wildt L,Benyó Z,Hein A

    更新日期：2003-07-01 00:00:00