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C14H8orf33 gene 1

Manihot esculenta 1

Annotation 1

Chinese Holstein 1

GWAS 1

Gcov 1

Gradual refinement 1

MPSoC 1

Native simulation 1

Performance estimation 1

Profiling 1

association study 1

automatic annotation configuration 1

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genetic heterogeneity 1

genome-wide association study 1

homologous recombination repair deficiency 1

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Profiling and annotation combined method formultimedia application specificMPSoCperformance estimation

Kai HUANG,Xiao-xu ZHANG,Si-wen XIU,Dan-dan ZHENG,Min YU,De MA,Kai HUANG,Gang CHEN,Xiao-lang YAN

Frontiers of Information Technology & Electronic Engineering 2015, Volume 16, Issue 2,   Pages 135-151 doi: 10.1631/FITEE.1400239

Abstract: Accurate and fast performance estimation is necessary to drive design space exploration and thus support important design decisions. Current techniques are either time consuming or not accurate enough. In this paper, we solve these problems by presenting a hybrid method for multimedia multiprocessor system-on-chip (MPSoC) performance estimation. A general coverage analysis tool GNU gcov is employed to profile the execution statistics during the native simulation. To tackle the complexity and keep the analysis and simulation manageable, the orthogonalization of communication and computation parts is adopted. The estimation result of the computation part is annotated to a transaction accurate model for further analysis, by which a gradual refinement of MPSoC performance estimation is supported. The implementation and its experimental results prove the feasibility and efficiency of the proposed method.

Keywords： MPSoC     Gradual refinement     Native simulation     Performance estimation     Profiling     Annotation     Gcov    

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Annotation and validation of genes involved in photosynthesis and starch synthesis from a

Yang ZHANG,Xin CHEN,Haiyan WANG,Zhiqiang XIA,Peng LING,Wenquan WANG

Frontiers of Agricultural Science and Engineering 2016, Volume 3, Issue 4,   Pages 308-320 doi: 10.15302/J-FASE-2016113

Abstract: resource is the first EST collection from wild cassava and should be of value for gene discovery, genome annotation

Keywords： Manihot esculenta     expressed sequence tag     unigene     pathway     expression pattern    

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The algorithm and realization of linear feature automatic label placement

Yin Yong,Li Chengming,Ding Shengtao

Strategic Study of CAE 2013, Volume 15, Issue 5,   Pages 30-36

Abstract:

This paper discussed several key problems in the automatic annotationof linear elements,proposed to calculate the positioning line of a linear element using reference annotationline and to achieve dynamic segmentation of reference annotation line using reverse Douglas algorithm, using the segmentation result to choose smooth parts of linear elements as candidate annotation positionsrepresentation of linear element annotations was solved and the integrity and aesthetics of automatic annotation

Keywords： linear elements     automatic annotation configuration     reference line     reverse Douglas algorithm    

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Comprehensive functional annotation of susceptibility variants identifies genetic heterogeneity between

Na Qin, Yuancheng Li, Cheng Wang, Meng Zhu, Juncheng Dai, Tongtong Hong, Demetrius Albanes, Stephen Lam, Adonina Tardon, Chu Chen, Gary Goodman, Stig E. Bojesen, Maria Teresa Landi, Mattias Johansson, Angela Risch, H-Erich Wichmann, Heike Bickeboller, Gadi Rennert, Susanne Arnold, Paul Brennan, John K. Field, Sanjay Shete, Loic Le Marchand, Olle Melander, Hans Brunnstrom, Geoffrey Liu, Rayjean J. Hung, Angeline Andrew, Lambertus A. Kiemeney, Shan Zienolddiny, Kjell Grankvist, Mikael Johansson, Neil Caporaso, Penella Woll, Philip Lazarus, Matthew B. Schabath, Melinda C. Aldrich, Victoria L. Stevens, Guangfu Jin, David C. Christiani, Zhibin Hu, Christopher I. Amos, Hongxia Ma, Hongbing Shen

Frontiers of Medicine 2021, Volume 15, Issue 2,   Pages 275-291 doi: 10.1007/s11684-020-0779-4

Abstract: Functional annotation and gene-based analysis implicated 894 target genes, including 274 specifics for

Keywords： lung cancer     genome-wide association study     function annotation     immune     homologous recombination repair    

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A post-GWAS replication study confirming the association of

Shaohua YANG,Chao QI,Yan XIE,Xiaogang CUI,Yahui GAO,Jianping JIANG,Li JIANG,Shengli ZHANG,Qin ZHANG,Dongxiao SUN

Frontiers of Agricultural Science and Engineering 2014, Volume 1, Issue 4,   Pages 321-330 doi: 10.15302/J-FASE-2014037

Abstract: Genome-wide association studies with an Illumina Bovine50K chip have detected 105 SNPs associated with one or multiple milk production traits in the Chinese Holstein population. Of these, 38 significant SNPs detected with high confidence by both L1-TDT and MMRA methods were selected to further mine potential key genes affecting milk yield and milk composition. By blasting the flanking sequences of these 38 SNPs with the bovine genome sequence combined with comparative genomics analysis, 26 genes were found to contain or be near to such SNPs. Among them, the gene is merely 87 bp away from the significant SNP, Hapmap30383-BTC-005848. Hence, we report herein genotype-phenotype associations to further validate the genetic effects of the gene. By pooled DNA sequencing of 14 unrelated Holstein sires, a total of 18 with seven novel SNPs were identified. Among them, nine SNPs were in the 5′ regulatory region, one in exon 6 and the other in the 3′ UTR and 3′ regulatory region. A total of nine of these identified SNPs were successfully genotyped and analyzed by mass spectrometry for association with five milk production traits in an independent resource population. The results showed that these SNPs were statistically significant for more than two traits [ <(0.0001-0.0267)]. In addition, mRNA expression analyses revealed that was ubiquitous in eight different tissues, with a relatively higher expression level in the mammary gland than in other tissues. These findings, therefore, provide strong evidence for association of variants with milk yield and milk composition traits and may be applied in Chinese Holstein breeding programs.

Keywords： GWAS     functional annotation     Chinese Holstein     milk production traits     C14H8orf33 gene     single nucleotide    

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Title Author Date Type Operation

Profiling and annotation combined method formultimedia application specificMPSoCperformance estimation

Kai HUANG,Xiao-xu ZHANG,Si-wen XIU,Dan-dan ZHENG,Min YU,De MA,Kai HUANG,Gang CHEN,Xiao-lang YAN

Journal Article

Annotation and validation of genes involved in photosynthesis and starch synthesis from a

Yang ZHANG,Xin CHEN,Haiyan WANG,Zhiqiang XIA,Peng LING,Wenquan WANG

Journal Article

The algorithm and realization of linear feature automatic label placement

Yin Yong,Li Chengming,Ding Shengtao

Journal Article

Comprehensive functional annotation of susceptibility variants identifies genetic heterogeneity between

Na Qin, Yuancheng Li, Cheng Wang, Meng Zhu, Juncheng Dai, Tongtong Hong, Demetrius Albanes, Stephen Lam, Adonina Tardon, Chu Chen, Gary Goodman, Stig E. Bojesen, Maria Teresa Landi, Mattias Johansson, Angela Risch, H-Erich Wichmann, Heike Bickeboller, Gadi Rennert, Susanne Arnold, Paul Brennan, John K. Field, Sanjay Shete, Loic Le Marchand, Olle Melander, Hans Brunnstrom, Geoffrey Liu, Rayjean J. Hung, Angeline Andrew, Lambertus A. Kiemeney, Shan Zienolddiny, Kjell Grankvist, Mikael Johansson, Neil Caporaso, Penella Woll, Philip Lazarus, Matthew B. Schabath, Melinda C. Aldrich, Victoria L. Stevens, Guangfu Jin, David C. Christiani, Zhibin Hu, Christopher I. Amos, Hongxia Ma, Hongbing Shen

Journal Article

A post-GWAS replication study confirming the association of

Shaohua YANG,Chao QI,Yan XIE,Xiaogang CUI,Yahui GAO,Jianping JIANG,Li JIANG,Shengli ZHANG,Qin ZHANG,Dongxiao SUN

Journal Article