Automated identification of reference genes based on RNA-seq data.

Abstract:

BACKGROUND:Gene expression analyses demand appropriate reference genes (RGs) for normalization, in order to obtain reliable assessments. Ideally, RG expression levels should remain constant in all cells, tissues or experimental conditions under study. Housekeeping genes traditionally fulfilled this requirement, but they have been reported to be less invariant than expected; therefore, RGs should be tested and validated for every particular situation. Microarray data have been used to propose new RGs, but only a limited set of model species and conditions are available; on the contrary, RNA-seq experiments are more and more frequent and constitute a new source of candidate RGs. RESULTS:An automated workflow based on mapped NGS reads has been constructed to obtain highly and invariantly expressed RGs based on a normalized expression in reads per mapped million and the coefficient of variation. This workflow has been tested with Roche/454 reads from reproductive tissues of olive tree (Olea europaea L.), as well as with Illumina paired-end reads from two different accessions of Arabidopsis thaliana and three different human cancers (prostate, small-cell cancer lung and lung adenocarcinoma). Candidate RGs have been proposed for each species and many of them have been previously reported as RGs in literature. Experimental validation of significant RGs in olive tree is provided to support the algorithm. CONCLUSION:Regardless sequencing technology, number of replicates, and library sizes, when RNA-seq experiments are designed and performed, the same datasets can be analyzed with our workflow to extract suitable RGs for subsequent PCR validation. Moreover, different subset of experimental conditions can provide different suitable RGs.

journal_name

Biomed Eng Online

authors

Carmona R,Arroyo M,Jiménez-Quesada MJ,Seoane P,Zafra A,Larrosa R,Alché JD,Claros MG

doi

10.1186/s12938-017-0356-5

subject

Has Abstract

pub_date

2017-08-18 00:00:00

pages

65

issue

Suppl 1

issn

1475-925X

pii

10.1186/s12938-017-0356-5

journal_volume

16

pub_type

杂志文章
  • In memorium: Herman p. Schwan [1915-2005].

    abstract::Herman P. Schwan [1915-2005] was a distinguished scientist and engineer, and a founding father of the field of biomedical engineering. A man of integrity, Schwan influenced the lives of many, including his wife and children, and his many students and colleagues. Active in science until nearly the end of his life, he w...

    journal_title:Biomedical engineering online

    pub_type: 传,历史文章,杂志文章

    doi:10.1186/1475-925X-4-21

    authors: Foster KR

    更新日期:2005-03-25 00:00:00

  • Challenges, issues and trends in fall detection systems.

    abstract::Since falls are a major public health problem among older people, the number of systems aimed at detecting them has increased dramatically over recent years. This work presents an extensive literature review of fall detection systems, including comparisons among various kinds of studies. It aims to serve as a referenc...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章,评审

    doi:10.1186/1475-925X-12-66

    authors: Igual R,Medrano C,Plaza I

    更新日期:2013-07-06 00:00:00

  • Regional differences in APD restitution can initiate wavebreak and re-entry in cardiac tissue: a computational study.

    abstract:BACKGROUND:Regional differences in action potential duration (APD) restitution in the heart favour arrhythmias, but the mechanism is not well understood. METHODS:We simulated a 150 x 150 mm 2D sheet of cardiac ventricular tissue using a simplified computational model. We investigated wavebreak and re-entry initiated b...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/1475-925X-4-54

    authors: Clayton RH,Taggart P

    更新日期:2005-09-20 00:00:00

  • Automatic lumen segmentation in IVOCT images using binary morphological reconstruction.

    abstract:BACKGROUND:Atherosclerosis causes millions of deaths, annually yielding billions in expenses round the world. Intravascular Optical Coherence Tomography (IVOCT) is a medical imaging modality, which displays high resolution images of coronary cross-section. Nonetheless, quantitative information can only be obtained with...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/1475-925X-12-78

    authors: Moraes MC,Cardenas DA,Furuie SS

    更新日期:2013-08-09 00:00:00

  • Development and mechanical testing of a short intramedullary nail for fixation of femoral rotational osteotomy in cerebral palsy patients.

    abstract:BACKGROUND:Rotational osteotomy is frequently indicated to correct excessive femoral anteversion in cerebral palsy patients. Angled blade plate is the standard fixation device used when performed in the proximal femur, but extensile exposure is required for plate accommodation. The authors developed a short locked intr...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/1475-925X-10-57

    authors: Pagnano RG,Okubo R,Volpon JB

    更新日期:2011-06-28 00:00:00

  • Effects of 8-week swimming training on carotid arterial stiffness and hemodynamics in young overweight adults.

    abstract:BACKGROUND:Exercise has been found to either reduce or increase arterial stiffness. Land-based exercise modalities have been documented as effective physical therapies to decrease arterial stiffness. However, these land-based exercise modalities may not be suitable for overweight individuals, in terms of risks of joint...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/s12938-016-0274-y

    authors: Yuan WX,Liu HB,Gao FS,Wang YX,Qin KR

    更新日期:2016-12-28 00:00:00

  • EZ Entropy: a software application for the entropy analysis of physiological time-series.

    abstract:BACKGROUND:Entropy analysis has been attracting increasing attentions in the recent two or three decades. It assesses complexity, or irregularity, of time-series which is extraordinarily relevant to physiology and diseases as demonstrated by tremendous studies. However, the complexity can hardly be appreciated by tradi...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/s12938-019-0650-5

    authors: Li P

    更新日期:2019-03-20 00:00:00

  • Examination of ceramic restoration adhesive coverage in cusp-replacement premolar using acoustic emission under fatigue testing.

    abstract:BACKGROUND:This study investigates CAD/CAM ceramic cusp-replacing restoration resistance with and without buccal cusp replacement under static and dynamic cyclic loads, monitored using the acoustic emission (AE) technique. METHOD:The cavity was designed in a typical MODP (mesial-occlusal-distal-palatal) restoration fa...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/1475-925X-13-165

    authors: Chang YH,Yu JJ,Lin CL

    更新日期:2014-12-13 00:00:00

  • Influence of head models on EEG simulations and inverse source localizations.

    abstract:BACKGROUND:The structure of the anatomical surfaces, e.g., CSF and gray and white matter, could severely influence the flow of volume currents in a head model. This, in turn, will also influence the scalp potentials and the inverse source localizations. This was examined in detail with four different human head models....

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/1475-925X-5-10

    authors: Ramon C,Schimpf PH,Haueisen J

    更新日期:2006-02-08 00:00:00

  • Integrated EIT system for functional lung ventilation imaging.

    abstract:BACKGROUND:Electrical impedance tomography (EIT) has been used for functional lung imaging of regional air distributions during mechanical ventilation in intensive care units (ICU). From numerous clinical and animal studies focusing on specific lung functions, a consensus about how to use the EIT technique has been for...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/s12938-019-0701-y

    authors: Jang GY,Ayoub G,Kim YE,Oh TI,Chung CR,Suh GY,Woo EJ

    更新日期:2019-07-25 00:00:00

  • 16-Channel biphasic current-mode programmable charge balanced neural stimulation.

    abstract:BACKGROUND:Neural stimulation is an important method used to activate or inhibit action potentials of the neuronal anatomical targets found in the brain, central nerve and peripheral nerve. The neural stimulator system produces biphasic pulses that deliver balanced charge into tissue from single or multichannel electro...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/s12938-017-0385-0

    authors: Li X,Zhong S,Morizio J

    更新日期:2017-08-14 00:00:00

  • Image based evaluation of mediastinal constraints for the development of a pulsatile total artificial heart.

    abstract:BACKGROUND:Good anatomical compatibility is an important aspect in the development of cardiovascular implants. This work analyzes the interaction of the pump unit of an electrically driven pulsatile Total Artificial Heart (TAH) and the mediastinum. For an adequate compliance, both overall dimensions and alignment of in...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/1475-925X-12-81

    authors: Fritschi AJ,Laumen M,Spiliopoulos S,Finocchiaro T,Egger C,Schmitz-Rode T,Tenderich G,Koerfer R,Steinseifer U

    更新日期:2013-08-14 00:00:00

  • An artifacts removal post-processing for epiphyseal region-of-interest (EROI) localization in automated bone age assessment (BAA).

    abstract:BACKGROUND:Segmentation is the most crucial part in the computer-aided bone age assessment. A well-known type of segmentation performed in the system is adaptive segmentation. While providing better result than global thresholding method, the adaptive segmentation produces a lot of unwanted noise that could affect the ...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/1475-925X-10-87

    authors: Chai HY,Wee LK,Swee TT,Salleh ShH,Chea LY

    更新日期:2011-09-28 00:00:00

  • The effect of inlet and outlet boundary conditions in image-based CFD modeling of aortic flow.

    abstract:BACKGROUND:Computational modeling of cardiovascular flow is a growing and useful field, but such simulations usually require the researcher to guess the flow's inlet and outlet conditions since they are difficult and expensive to measure. It is critical to determine the amount of uncertainty introduced by these assumpt...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/s12938-018-0497-1

    authors: Madhavan S,Kemmerling EMC

    更新日期:2018-05-30 00:00:00

  • A specialized motion capture system for real-time analysis of mandibular movements using infrared cameras.

    abstract:BACKGROUND:In the last years, several methods and devices have been proposed to record the human mandibular movements, since they provide quantitative parameters that support the diagnosis and treatment of temporomandibular disorders. The techniques currently employed suffer from a number of drawbacks including high pr...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/1475-925X-12-17

    authors: Furtado DA,Pereira AA,Andrade Ade O,Bellomo DP Jr,da Silva MR

    更新日期:2013-02-22 00:00:00

  • PDE based scheme for multi-modal medical image watermarking.

    abstract:BACKGROUND:This work deals with copyright protection of digital images, an issue that needs protection of intellectual property rights. It is an important issue with a large number of medical images interchanged on the Internet every day. So, it is a challenging task to ensure the integrity of received images as well a...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/s12938-015-0101-x

    authors: Aherrahrou N,Tairi H

    更新日期:2015-11-25 00:00:00

  • Effect of pressure and padding on motion artifact of textile electrodes.

    abstract:BACKGROUND:With the aging population and rising healthcare costs, wearable monitoring is gaining importance. The motion artifact affecting dry electrodes is one of the main challenges preventing the widespread use of wearable monitoring systems. In this paper we investigate the motion artifact and ways of making a text...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/1475-925X-12-26

    authors: Cömert A,Honkala M,Hyttinen J

    更新日期:2013-04-08 00:00:00

  • Probability mapping of scarred myocardium using texture and intensity features in CMR images.

    abstract:BACKGROUND:The myocardium exhibits heterogeneous nature due to scarring after Myocardial Infarction (MI). In Cardiac Magnetic Resonance (CMR) imaging, Late Gadolinium (LG) contrast agent enhances the intensity of scarred area in the myocardium. METHODS:In this paper, we propose a probability mapping technique using Te...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/1475-925X-12-91

    authors: Kotu LP,Engan K,Skretting K,Måløy F,Orn S,Woie L,Eftestøl T

    更新日期:2013-09-22 00:00:00

  • Biomechanical simulation of thorax deformation using finite element approach.

    abstract:BACKGROUND:The biomechanical simulation of the human respiratory system is expected to be a useful tool for the diagnosis and treatment of respiratory diseases. Because the deformation of the thorax significantly influences airflow in the lungs, we focused on simulating the thorax deformation by introducing contraction...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/s12938-016-0132-y

    authors: Zhang G,Chen X,Ohgi J,Miura T,Nakamoto A,Matsumura C,Sugiura S,Hisada T

    更新日期:2016-02-06 00:00:00

  • Study of probe-sample distance for biomedical spectra measurement.

    abstract:BACKGROUND:Fiber-based optical spectroscopy has been widely used for biomedical applications. However, the effect of probe-sample distance on the collection efficiency has not been well investigated. METHOD:In this paper, we presented a theoretical model to maximize the illumination and collection efficiency in design...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/1475-925X-10-95

    authors: Wang B,Fan S,Li L,Wang C

    更新日期:2011-11-02 00:00:00

  • Infrared thermography fails to visualize stimulation-induced meridian-like structures: comment by Rixin Chen and Zhimai Lv and reply from Gerhard Litscher.

    abstract::A comment on G. Litscher: Infrared thermography fails to visualize stimulation-induced meridian-like structures. Biomed. Eng. OnLine 2005, 4:38 (15 June 2005), with a response by the author. ...

    journal_title:Biomedical engineering online

    pub_type: 评论,信件

    doi:10.1186/1475-925X-10-80

    authors: Chen R,Lv Z

    更新日期:2011-09-11 00:00:00

  • Effect of manufacturing and experimental conditions on the mechanical and surface properties of silicone elastomer scaffolds used in endothelial mechanobiological studies.

    abstract:BACKGROUND:Mechanobiological studies allow the characterization of cell response to mechanical stresses. Cells need to be supported by a material with properties similar to the physiological environment. Silicone elastomers have been used to produce various in vitro scaffolds of different geometries for endothelial cel...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/s12938-017-0380-5

    authors: Campeau MA,Lortie A,Tremblay P,Béliveau MO,Dubé D,Langelier È,Rouleau L

    更新日期:2017-07-14 00:00:00

  • Review of cognitive behavioural therapy mobile apps using a reference architecture embedded in the patient-provider relationship.

    abstract:BACKGROUND:Mobile health apps (mHealth apps) are increasing in popularity and utility for the management of many chronic diseases. Although the current reimbursement structure for mHealth apps is lagging behind the rapidly improving functionality, more clinicians will begin to recommend these apps as they prove their c...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/s12938-018-0611-4

    authors: Lan A,Lee A,Munroe K,McRae C,Kaleis L,Keshavjee K,Guergachi A

    更新日期:2018-12-17 00:00:00

  • A perceptual map for gait symmetry quantification and pathology detection.

    abstract:BACKGROUND:The gait movement is an essential process of the human activity and the result of collaborative interactions between the neurological, articular and musculoskeletal systems, working efficiently together. This explains why gait analysis is important and increasingly used nowadays for the diagnosis of many dif...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/s12938-015-0097-2

    authors: Moevus A,Mignotte M,de Guise JA,Meunier J

    更新日期:2015-10-29 00:00:00

  • Collaborative and secure transmission of medical data applied to mobile healthcare.

    abstract:PURPOSE:We propose a collaborative and secure transmission scheme in order to safely and efficiently transmit medical data and provide telemedicine services, lighten the load on wireless access networks, and improve the quality of medical treatment such as surgery. METHODS:First, the transmission technology based on o...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/s12938-019-0674-x

    authors: Chen W,Chen Z,Cui F

    更新日期:2019-05-20 00:00:00

  • S-EMG signal compression based on domain transformation and spectral shape dynamic bit allocation.

    abstract:BACKGROUND:Surface electromyographic (S-EMG) signal processing has been emerging in the past few years due to its non-invasive assessment of muscle function and structure and because of the fast growing rate of digital technology which brings about new solutions and applications. Factors such as sampling rate, quantiza...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/1475-925X-13-22

    authors: Trabuco MH,Costa MV,Nascimento FA

    更新日期:2014-02-27 00:00:00

  • Development of a mathematical model to estimate intra-tumor oxygen concentrations through multi-parametric imaging.

    abstract:BACKGROUND:Tumor hypoxia is involved in every stage of solid tumor development: formation, progression, metastasis, and apoptosis. Two types of hypoxia exist in tumors-chronic hypoxia and acute hypoxia. Recent studies indicate that the regional hypoxia kinetics is closely linked to metastasis and therapeutic responses,...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/s12938-016-0235-5

    authors: Lee CW,Stantz KM

    更新日期:2016-10-12 00:00:00

  • Evaluation of three force-position hybrid control methods for a robot-based biological joint-testing system.

    abstract:BACKGROUND:Robot-based joint-testing systems (RJTS) can be used to perform unconstrained laxity tests, measuring the stiffness of a degree of freedom (DOF) of the joint at a fixed flexion angle while allowing the other DOFs unconstrained movement. Previous studies using the force-position hybrid (FPH) control method pr...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/s12938-016-0195-9

    authors: Hsieh HJ,Hu CC,Lu TW,Lu HL,Kuo MY,Kuo CC,Hsu HC

    更新日期:2016-06-07 00:00:00

  • The approximate entropy of the electromyographic signals of tremor correlates with the osmotic fragility of human erythrocytes.

    abstract:BACKGROUND:The main problem of tremor is the damage caused to the quality of the life of patients, especially those at more advanced ages. There is not a consensus yet about the origins of this disorder, but it can be examined in the correlations between the biological signs of aging and the tremor characteristics. ME...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/1475-925X-9-29

    authors: Mansur PH,Cury LK,Leite JO,Pereira AA,Penha-Silva N,Andrade AO

    更新日期:2010-06-22 00:00:00

  • Reviewing the connection between speech and obstructive sleep apnea.

    abstract:BACKGROUND:Sleep apnea (OSA) is a common sleep disorder characterized by recurring breathing pauses during sleep caused by a blockage of the upper airway (UA). The altered UA structure or function in OSA speakers has led to hypothesize the automatic analysis of speech for OSA assessment. In this paper we critically rev...

    journal_title:Biomedical engineering online

    pub_type: 杂志文章

    doi:10.1186/s12938-016-0138-5

    authors: Espinoza-Cuadros F,Fernández-Pozo R,Toledano DT,Alcázar-Ramírez JD,López-Gonzalo E,Hernández-Gómez LA

    更新日期:2016-02-20 00:00:00