Abstract:
:New genomes are being sequenced at an increasingly rapid rate, far outpacing the rate at which manual gene annotation can be performed. Automated genome annotation is thus necessitated by this growth in genome projects; however, full-fledged annotation systems are usually home-grown and customized to a particular genome. There is thus a renewed need for accurate ab initio gene prediction methods. However, it is apparent that fully ab initio methods fall short of the required level of sensitivity and specificity for a quality annotation. Evidence in the form of expressed sequences gives the single biggest improvement in accuracy when used to inform gene predictions. Here, we present a lightweight pipeline for first-pass gene prediction on newly sequenced genomes. The two main components are ASPic, a program that derives highly accurate, albeit not necessarily complete, EST-based transcript annotations from EST alignments, and GeneID, a standard gene prediction program, which we have modified to take as evidence intron annotations. The introns output by ASPic CDS predictions is given to GeneID to constrain the exon-chaining process and produce predictions consistent with the underlying EST alignments. The pipeline was successfully tested on the entire C. elegans genome and the 44 ENCODE human pilot regions.
journal_name
Biomed Res Intjournal_title
BioMed research internationalauthors
Alioto T,Picardi E,Guigó R,Pesole Gdoi
10.1155/2013/502827subject
Has Abstractpub_date
2013-01-01 00:00:00pages
502827eissn
2314-6133issn
2314-6141journal_volume
2013pub_type
杂志文章abstract::TAL effectors (TALEs) contain a modular DNA-binding domain that is composed of tandem repeats. In all naturally occurring TALEs, the end of tandem repeats is invariantly a truncated half repeat. To investigate the potential role of the last half repeat in TALEs, we performed comparative molecular dynamics simulations ...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2016/8036450
更新日期:2016-01-01 00:00:00
abstract::This study investigates the mechanism underlying the improving effect of zinc on fertility in obese rats using proteomics. The effects of three different doses of ZnSO4 on spermatogenesis and hormone levels were studied. Testicular spermatogenesis was observed by HE staining. Serum estrogen and testosterone levels wer...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2020/9876363
更新日期:2020-05-04 00:00:00
abstract::The repair of bone defects is a big challenge in reconstructive surgery. Periosteal distraction osteogenesis (PDO), as a promising technique used for bone regeneration, forms a space between the periosteum and bone cortex to regenerate the new bone merely by distracting the periosteum. In order to investigate the infl...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2020/7381391
更新日期:2020-04-23 00:00:00
abstract::The aim of the present study was to determine if the Ki-67 labelling index reflects invasiveness of pituitary adenoma and to evaluate IL-17A concentration in blood serum of pituitary adenoma patients. The study was conducted in the Hospital of Lithuanian University of Health Sciences. All pituitary adenomas were analy...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2018/7490585
更新日期:2018-05-31 00:00:00
abstract:Purpose of Review:Transversus abdominis plane (TAP) block is a regional technique for analgesia of the anterolateral abdominal wall. This review highlights the nomenclature system and recent advances in TAP block techniques and proposes directions for future research. Recent Findings:Ultrasound guidance is now conside...
journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2017/8284363
更新日期:2017-01-01 00:00:00
abstract::Pinelliae Rhizoma Praeparatum Cum Alumine (PRPCA) is useful for eliminating dampness and phlegm in clinical settings, targeting the main mechanisms of insomnia as defined in traditional Chinese medicine. However, little is known regarding the sedative and hypnotic effects of PRPCA. In the present study, we examined th...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2019/6198067
更新日期:2019-04-28 00:00:00
abstract::Liquid and solid samples from two wastewater treatment plants (WWTPs) on Gran Canaria Island (Spain) have been tested for the presence of compounds with endocrine-disrupting properties. The selected degradation stages were sampled bimonthly from each WWTP over the 12-month period from July 2010 to July 2011. The analy...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2013/790570
更新日期:2013-01-01 00:00:00
abstract:Aim:To address the impact of noncavity-distorting intramural fibroids on the efficacy of in vitro fertilization-embryo transfer (IVF-ET) outcomes. Methods:The PubMed, Web of Science, Embase, Cochrane Library, and China National Knowledge Infrastructure were searched systematically. A meta-analysis was performed based ...
journal_title:BioMed research international
pub_type: 杂志文章,meta分析
doi:10.1155/2018/8924703
更新日期:2018-09-04 00:00:00
abstract:OBJECTIVE:This study investigates the safety and efficacy of a multimodality approach combining staged endovascular embolizations with subsequent SRS for the management of larger AVMs. METHODS:Ninety-five patients with larger AVMs were treated with staged endovascular embolization followed by SRS between 1996 and 2011...
journal_title:BioMed research international
pub_type: 临床试验,杂志文章
doi:10.1155/2014/306518
更新日期:2014-01-01 00:00:00
abstract:Background:Although both nonfunctional paraganglioma of the bladder (NPB) and urothelial carcinoma of the bladder (UCB) are subtypes of bladder tumors, they are entirely different entities with distinct tissue origins and anatomical locations. However, NPB is frequently misdiagnosed as UCB chiefly due to the similariti...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2019/1097149
更新日期:2019-11-06 00:00:00
abstract::Effects of ketamine and lidocaine on electroencephalographic (EEG) changes were evaluated in minimally anaesthetized dogs, subjected to electric stimulus. Six dogs were subjected to six treatments in a crossover design with a washout period of one week. Dogs were subjected to intravenous boluses of lidocaine 2 mg/kg, ...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/305367
更新日期:2015-01-01 00:00:00
abstract::As the fifth most common cancer in men and the eighth most common cancer in women, hepatocellular carcinoma (HCC) is the leading cause of cancer-related deaths worldwide, with standard chemotherapy and radiation being minimally effective in prolonging survival. Virus hepatitis, particularly HBV and HCV infection is th...
journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2014/735672
更新日期:2014-01-01 00:00:00
abstract::Exposure to engineered nanoparticles (NPs) and to ambient particles (PM) has increased significantly. During the last decades the application of nano-objects to daily-life goods and the emissions produced in highly urbanized cities have considerably augmented. As a consequence, the understanding of the possible effect...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2013/801214
更新日期:2013-01-01 00:00:00
abstract::Gold nanoparticles (AuNPs) have several potential biological applications as well as excellent biocompatibility. AuNPs with surface modification using polyethylene glycol (PEG-AuNPs) can facilitate easy conjugation with various biological molecules of interest. To examine the anticancer bioactivity of PEG-AuNPs, we in...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/182353
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Cost sharing between beneficiaries and government is critical to attain universal health coverage. The government of Ethiopia introduced social health insurance to improve access to quality health services. Hence, HCP are the ultimate frontline service provider; their WTP for health insurance could influence...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2020/8412957
更新日期:2020-04-14 00:00:00
abstract:Objective:ANGPTL7 is a member of the angiogenin-like protein family. Compared to other members, ANGPTL7 is the least known. Recent studies have explored the relationship between ANGPTL7 and multiple pathological processes and diseases. However, there is no research about ANGPTL7 in neonates. This study was designed to ...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2020/1892458
更新日期:2020-11-27 00:00:00
abstract::Graphene is the first 2-dimensional material and possesses a plethora of original properties. Graphene and its derivatives have exhibited a great potential in a number of fields, both medical and nonmedical. The aim of this review is to set the theoretical basis for further research in developing graphene-based endova...
journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2016/3180954
更新日期:2016-01-01 00:00:00
abstract::Diethylnitrosamine (DEN) induces hepatocarcinogenesis, increasing mitotic hepatocytes and leading to chronic inflammation. In addition, type 1 diabetes mellitus (T1DM) is also characterized by a proinflammatory state and by requiring insulin exogenous treatment. Given the association of diabetes, insulin treatment, an...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2018/9472939
更新日期:2018-04-23 00:00:00
abstract::The role of non-steroidal anti-inflammatory drugs in inflammatory bowel disease is controversial, as they have been implicated in disease aggravation. Different from other cyclooxygenase inhibitors, acetylsalicylic acid (ASA) enhances the formation of anti-inflammatory and proresolution lipoxins derived from arachidon...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2013/748160
更新日期:2013-01-01 00:00:00
abstract::Purpose. We examined the role of miR-20b in development of thymoma-associated myasthenia gravis, especially in T cell proliferation and activation. Materials and Methods. Using qRT-PCR, we assessed expression levels of miR-20b and its target genes in cultured cells and patient samples and examined the proliferation of...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2016/9595718
更新日期:2016-01-01 00:00:00
abstract:BACKGROUND:Histones play important roles in both host defenses and inflammation related to microbial infection. A peptide mimotope (SSV) was identified from a novel histone H1 monoclonal antibody (16G9 mAb) that was shown to inhibit the mixed lymphocyte reaction. In the present study, an anti-SSV producing hybridoma wa...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/491649
更新日期:2015-01-01 00:00:00
abstract::Multiparametric MRI of the prostate combines high-resolution anatomic imaging with functional imaging of alterations in normal tissue caused by neoplastic transformation for the identification and characterization of in situ prostate cancer. Lesion detection relies on a systematic approach to the analysis of both anat...
journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2014/684127
更新日期:2014-01-01 00:00:00
abstract::Recent progress in microscopy technologies, biological markers, and automated processing methods is making possible the development of gene expression atlases at cellular-level resolution over whole embryos. Raw data on gene expression is usually very noisy. This noise comes from both experimental (technical/methodolo...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2015/986436
更新日期:2015-01-01 00:00:00
abstract:Purpose:In this study, we examined whether the associations between working hours, job satisfaction, and work-life balance are mediated by occupational stress. In addition, we tested whether perceived time control helps moderate the effects of working hours and occupational stress. Methodology:Questionnaires were admi...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2019/5046934
更新日期:2019-06-23 00:00:00
abstract::Flash-lamp pulsed-dye laser (FPDL) is a nonablative technology, typically used in vascular malformation therapy due to its specificity for hemoglobin. FPDL treatments were performed in a large group of patients with persistent and/or recalcitrant different dermatological lesions with cutaneous microvessel involvement....
journal_title:BioMed research international
pub_type: 临床试验,杂志文章
doi:10.1155/2016/7981640
更新日期:2016-01-01 00:00:00
abstract::In this study, we prepared PTX-loaded mesoporous hollow SnO2 nanofibers conjugated with folic acid (SFNFP) for liver cancer therapy. According to SEM and TEM characterization, SFNF showed a mesoporous hollow structure. The average outer diameter was 200 nm, and the wall thickness was 50 nm. The DSC and XRD study showe...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2018/8526190
更新日期:2018-11-25 00:00:00
abstract:UNLABELLED:H. pylori is related to various gastrointestinal diseases. β₂ Microglobulin (β 2M) is an intrinsic element of major histocompatibility complex (MHC I). Serum β₂M level may increase in inflammatory states. The aim of current study is to evaluate the relationship between β₂M and H. pylori bearing CagA strains....
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/615089
更新日期:2014-01-01 00:00:00
abstract:Background:Ankylosing spondylitis (AS) is a chronic inflammatory disease characterized by sacroiliitis and spinal rigidity of the axial joints. The role of oxidative stress and increased proinflammatory cytokines is well documented in AS pathogenesis. Punicalagin (2,3-hexahydroxydiphenoyl-gallagyl-D-glucose), an ellagi...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2020/4918239
更新日期:2020-09-23 00:00:00
abstract::Long-term application and extensive use of synthetic insecticides have resulted in accumulating their residues in food, milk, water, and soil and cause adverse health effects to human and ecosystems. Therefore, application of natural insecticides in agriculture and public health sectors has been increased as alternati...
journal_title:BioMed research international
pub_type: 杂志文章,评审
doi:10.1155/2018/4308054
更新日期:2018-10-16 00:00:00
abstract::In this paper, differences between multichannel EEG signals of artists and nonartists were analyzed during visual perception and mental imagery of some paintings and at resting condition using approximate entropy (ApEn). It was found that ApEn is significantly higher for artists during the visual perception and the me...
journal_title:BioMed research international
pub_type: 杂志文章
doi:10.1155/2014/764382
更新日期:2014-01-01 00:00:00