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1. Full Text Benchmarking of RNA-sequencing analysis workflows using wholetranscriptome RT-qPCR expression data
by Everaert, C and Luypaert, M and Maag, JLV and Cheng, QX and Dinger, ME and Hellemans, J and Mestdagh, P
SCIENTIFIC REPORTS, ISSN 2045-2322, 05/2017, Volume 7
RNA-sequencing has become the gold standard for whole-transcriptome gene expression quantification. Multiple algorithms have been developed to derive gene... 
TOPHAT | GENE | QUANTIFICATION | MULTIDISCIPLINARY SCIENCES
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2. Full Text HISAT: A fast spliced aligner with low memory requirements
by Kim, Daehwan and Langmead, Ben and Salzberg, Steven L
Nature Methods, ISSN 1548-7091, 03/2015, Volume 12, Issue 4, pp. 357 - 360
HISAT (hierarchical indexing for spliced alignment of transcripts) is a highly efficient system for aligning reads from RNA sequencing experiments. HISAT uses... 
TRANSCRIPTOMES | TOPHAT | ALIGNMENT | GENE | ANNOTATION | BIOCHEMICAL RESEARCH METHODS | RNA-SEQ EXPERIMENTS | READS | Sequence Alignment - methods | Sequence Analysis, DNA - instrumentation | Limit of Detection | Pseudogenes - genetics | Sequence Analysis, RNA | Humans | RNA sequencing | Genetic research | Research | Genomics | Innovations | Ribonucleic acid--RNA | Genomes
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3. Full Text Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts
by Sun, Liang and Luo, Haitao and Bu, Dechao and Zhao, Guoguang and Yu, Kuntao and Zhang, Changhai and Liu, Yuanning and Chen, Runsheng and Zhao, Yi
Nucleic Acids Research, ISSN 0305-1048, 09/2013, Volume 41, Issue 17, pp. e166 - e166
It is a challenge to classify protein-coding or non-coding transcripts, especially those re-constructed from high-throughput sequencing data of poorly... 
EVOLUTION | TOPHAT | INTEGRATIVE ANNOTATION | GENE | RNA-SEQ | BIOCHEMISTRY & MOLECULAR BIOLOGY | REGIONS | EXPRESSION | GENOME | PREDICTION | REVEALS | Proteins - genetics | Sequence Analysis, RNA - methods | Animals | RNA, Long Noncoding - chemistry | Humans | Gene Expression Profiling | Mice | Software | RNA, Long Noncoding - classification | Pongo - genetics | Methods Online
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4. Full Text EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments
by Leng, Ning and Dawson, John A and Thomson, James A and Ruotti, Victor and Rissman, Anna I and Smits, Bart M. G and Haag, Jill D and Gould, Michael N and Stewart, Ron M and Kendziorski, Christina
Bioinformatics, ISSN 1367-4803, 04/2013, Volume 29, Issue 8, pp. 1035 - 1043
Motivation: Messenger RNA expression is important in normal development and differentiation, as well as in manifestation of disease. RNA-seq experiments allow... 
TOPHAT | MEMORY | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | QUANTIFICATION | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | GENE-EXPRESSION | SEQUENCE COUNT DATA | NORMALIZATION | DIFFERENTIAL EXPRESSION ANALYSIS | GENOME | Sequence Analysis, RNA - methods | Cell Line | Embryonic Stem Cells - metabolism | RNA Isoforms - metabolism | Bayes Theorem | Gene Expression Profiling - methods | Software | Models, Statistical | Genome | RNA, Messenger - metabolism | Uncertainty | Genes | Estimating | Inference | Statistical methods | Bayesian analysis | Bioinformatics | Empirical analysis | Original Papers
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5. Full Text How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?
by Schurch, Nicholas J and Schofield, Pietá and Gierliński, Marek and Cole, Christian and Sherstnev, Alexander and Singh, Vijender and Wrobel, Nicola and Gharbi, Karim and Simpson, Gordon G and Owen-Hughes, Tom and Blaxter, Mark and Barton, Geoffrey J
RNA, ISSN 1355-8382, 06/2016, Volume 22, Issue 6, pp. 839 - 851
RNA-seq is now the technology of choice for genome-wide differential gene expression experiments, but it is not clear how many biological replicates are needed... 
Yeast | RNA-seq | Experimental design | Benchmarking | Replication | Differential expression | Statistical power | replication | STATISTICAL-METHODS | DESIGN | benchmarking | BIOCHEMISTRY & MOLECULAR BIOLOGY | differential expression | MODEL | yeast | FALSE DISCOVERY RATE | TOPHAT | SEQUENCE | statistical power | GENE-EXPRESSION | experimental design | R-PACKAGE | NORMALIZATION | Sequence Analysis, RNA - methods | Reproducibility of Results | Gene Expression Profiling | RNA, Fungal - genetics | Saccharomyces cerevisiae - genetics
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6. Full Text Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing
by Wang, Bo and Tseng, Elizabeth and Regulski, Michael and Clark, Tyson A and Hon, Ting and Jiao, Yinping and Lu, Zhenyuan and Olson, Andrew and Stein, Joshua C and Ware, Doreen
Nature Communications, ISSN 2041-1723, 06/2016, Volume 7, Issue 1, p. 11708
Zea mays is an important genetic model for elucidating transcriptional networks. Uncertainties about the complete structure of mRNA transcripts limit the... 
NETWORK | TOPHAT | MESSENGER-RNA | ENDOSPERM | EMBRYO | NONCODING RNAS | LANDSCAPE | MULTIDISCIPLINARY SCIENCES | GENE-EXPRESSION | GENOME | INSIGHTS | Sequence Analysis, RNA - methods | Plant Proteins - genetics | Zea mays - genetics | Gene Expression Regulation, Plant | Polymerase Chain Reaction | Gene Expression Profiling - methods | Plant Proteins - metabolism | Transcriptome - genetics
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7. Full Text Identification and characterization of ERV transcripts in goat embryos
by Deng, Ruizhi and Han, Chengquan and Zhao, Lu and Zhang, Qing and Yan, Beifen and Cheng, Rui and Wei, Biao and Meng, Peng and Mao, Tingchao and Zhang, Yong and Liu, Jun
Reproduction, ISSN 1470-1626, 2019, Volume 157, Issue 1, pp. 111 - 122
Endogenous retroviruses (ERVs), which are abundant in mammalian genomes, can modulate the expression of nearby genes, and their expression is dynamic and... 
ACTIVATION | REPRODUCTIVE BIOLOGY | EXPRESSION ANALYSIS | PROTEIN | TOPHAT | GENE | DATABASE | TRANSPOSABLE ELEMENTS | DEVELOPMENTAL BIOLOGY
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8. Full Text PennDiff: detecting differential alternative splicing and transcription by RNA sequencing
by Hu, Yu and Lin, Jennie and Hu, Jian and Hu, Gang and Wang, Kui and Zhang, Hanrui and Reilly, Muredach P and Li, Mingyao
Bioinformatics, ISSN 1367-4803, 07/2018, Volume 34, Issue 14, pp. 2384 - 2391
Abstract Motivation Alternative splicing and alternative transcription are a major mechanism for generating transcriptome diversity. Differential alternative... 
TOPHAT | GENE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | SEQ EXPERIMENTS | EXPRESSION | Original Papers
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9. Full Text Analysis of RNA-seq data using TopHat and cufflinks
by Ghosh, Sreya and Chan, Chon-Kit Kenneth
Methods in Molecular Biology, ISSN 1064-3745, 2016, Volume 1374, pp. 339 - 361
The recent advances in high throughput RNA sequencing (RNA-Seq) have generated huge amounts of data in a very short span of time for a single sample. These... 
TopHat | Transcriptome assembly | RNA-seq | Bowtie | Cuffdiff | Differential gene expression | Cufflinks | CummeRbund | Cuffmerge | Cuffcompare | Sequence Analysis, RNA - methods | Gene Expression Profiling - methods | Computational Biology - methods | Software | Genomics - methods | Transcriptome
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10. Full Text MiRGator v3.0: A microRNA portal for deep sequencing, expression profiling and mRNA targeting
by Cho, Sooyoung and Jang, Insu and Jun, Yukyung and Yoon, Suhyeon and Ko, Minjeong and Kwon, Yeajee and Choi, Ikjung and Chang, Hyeshik and Ryu, Daeun and Lee, Byungwook and Kim, V. Narry and Kim, Wankyu and Lee, Sanghyuk
Nucleic Acids Research, ISSN 0305-1048, 01/2013, Volume 41, Issue 1, pp. D252 - D257
Biogenesis and molecular function are two key subjects in the field of microRNA (miRNA) research. Deep sequencing has become the principal technique in... 
TOPHAT | DATABASE | GENE | BIOCHEMISTRY & MOLECULAR BIOLOGY | RESOURCE | Sequence Analysis, RNA | Transcriptome | MicroRNAs - metabolism | RNA, Messenger - chemistry | High-Throughput Nucleotide Sequencing | Internet | RNA, Messenger - metabolism | Databases, Nucleic Acid | MicroRNAs - chemistry
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11. Full Text The distinctive mutational spectra of polyomavirus-negative merkel cell carcinoma
by Harms, Paul William and Vats, Pankaj and Verhaegen, Monique Elise and Robinson, Dan R and Wu, Yi-Mi and Dhanasekaran, Saravana Mohan and Palanisamy, Nallasivam and Siddiqui, Javed and Cao, Xuhong and Su, Fengyun and Wang, Rui and Xiao, Hong and Kunju, Lakshmi P and Mehra, Rohit and Tomlins, Scott A and Fullen, Douglas Randall and Bichakjian, Christopher Keram and Johnson, Timothy M and Dlugosz, Andrzej Antoni and Chinnaiyan, Arul M
Cancer Research, ISSN 0008-5472, 09/2015, Volume 75, Issue 18, pp. 3720 - 3727
Merkel cell carcinoma (MCC) is a rare but highly aggressive cutaneous neuroendocrine tumor. Merkel cell polyomavirus (MCPyV) may contribute to tumorigenesis in... 
BREAST-CANCER | MELANOMA | TOPHAT | GENE | ONCOLOGY | SOMATIC MUTATION | OF-FUNCTION MUTATIONS | EXPRESSION | DISCOVERY | Cell Transformation, Neoplastic - radiation effects | Humans | Middle Aged | Male | Receptors, Notch - genetics | Gene Expression Profiling | DNA Mutational Analysis - methods | Merkel cell polyomavirus | Neoplasms, Radiation-Induced - genetics | Cell Transformation, Neoplastic - genetics | Neoplasm Proteins - genetics | Oncogenes | Membrane Proteins - genetics | Carcinoma, Merkel Cell - genetics | Parotid Neoplasms - secondary | Nerve Tissue Proteins - genetics | Ultraviolet Rays - adverse effects | Carrier Proteins - genetics | Point Mutation | Exome - genetics | Oncogene Proteins, Fusion - genetics | Skin Neoplasms - genetics | Aged | DNA, Neoplasm - genetics | Mutation | Carcinoma, Merkel Cell - secondary | Parotid Neoplasms - genetics
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12. Full Text Impaired terpenoid backbone biosynthesis reduces saponin accumulation in Panax notoginseng under Cd stress
by Liao, Peiran and Shi, Yue and Li, Ziwei and Chen, Qi and Xu, Tian-Rui and Cui, Xiuming and Guan, Huilin and Guo, Lanping and Yang, Ye
Functional Plant Biology, ISSN 1445-4408, 2019, Volume 46, Issue 1, pp. 56 - 68
Panax notoginseng saponins (PNS) are major secondary metabolite of Panax notoginseng (Burk.) F. H. Chen. Previous studies identified that P. notoginseng... 
Saponins | Terpenoid backbone biosynthesis | Transcriptome | terpenoid backbone biosynthesis | transcriptome | L | PLANT SCIENCES | SE | TOPHAT | CADMIUM | GENE | ANTIOXIDANT | GROWTH | ROOTS | GINSENOSIDE BIOSYNTHESIS | saponins
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13. Full Text Full‐length transcriptome sequences and splice variants obtained by a combination of sequencing platforms applied to different root tissues of Salvia miltiorrhiza and tanshinone biosynthesis
by Xu, Zhichao and Peters, Reuben J and Weirather, Jason and Luo, Hongmei and Liao, Baosheng and Zhang, Xin and Zhu, Yingjie and Ji, Aijia and Zhang, Bing and Hu, Songnian and Au, Kin Fai and Song, Jingyuan and Chen, Shilin
The Plant Journal, ISSN 0960-7412, 06/2015, Volume 82, Issue 6, pp. 951 - 961
Danshen, Salvia miltiorrhiza Bunge, is one of the most widely used herbs in traditional Chinese medicine, wherein its rhizome/roots are particularly valued.... 
single‐molecule real‐time sequencing | tanshinone biosynthesis | Salvia miltiorrhiza | alternative splicing | next‐generation sequencing | single-molecule real-time sequencing | next-generation sequencing | LANDSCAPE | TRADITIONAL MEDICINE | VIEW | DISCOVERY | PLANT SCIENCES | EVOLUTION | TOPHAT | RNA-SEQ | COMPLEXITY | BIOLOGY | SUPERFAMILY | Plant Roots - metabolism | Alternative Splicing | Diterpenes, Abietane - metabolism | Transcriptome | Plant Roots - genetics | Gene Expression Profiling - methods | Diterpenes, Abietane - biosynthesis | Plant Proteins - genetics | Salvia miltiorrhiza - metabolism | Gene Expression Regulation, Plant | Salvia miltiorrhiza - genetics | Plant Proteins - metabolism | High-Throughput Nucleotide Sequencing - methods | Sequence Analysis, DNA - methods | Genomics | Herbal medicine | Chinese medicine | Biosynthesis | Botany
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14. Full Text Characterization of long non-coding RNA and messenger RNA profiles in follicular fluid from mature and immature ovarian follicles of healthy women and women with polycystic ovary syndrome
by Jiao, Jiao and Shi, Bei and Wang, Tianren and Fang, Yuanyuan and Cao, Tiefeng and Zhou, Yiming and Wang, Xiuxia and Li, Da
Human Reproduction, ISSN 0268-1161, 09/2018, Volume 33, Issue 9, pp. 1735 - 1748
Abstract STUDY QUESTION Do long non-coding RNA (lncRNA) and messenger RNA (mRNA) profiles in follicular fluid from mature and immature ovarian follicles differ... 
RNA sequencing | Polycystic ovary syndrome | LncRNAs | MRNAs | Immature follicles | Follicular fluid | Mature follicles | lncRNAs | STEROIDOGENESIS | IDENTIFICATION | polycystic ovary syndrome | follicular fluid | OBSTETRICS & GYNECOLOGY | TRANSCRIPTS | mature follicles | REPRODUCTIVE BIOLOGY | TOPHAT | GENE | immature follicles | mRNAs | EXPRESSION | REVEALS
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15. Full Text The papain-like cysteine protease CEP1 is involved in programmed cell death and secondary wall thickening during xylem development in Arabidopsis
by Han, Jingyi and Li, Hui and Yin, Bin and Zhang, Yongzhuo and Liu, Yadi and Cheng, Ziyi and Liu, Di and Lu, Hai
Journal of Experimental Botany, ISSN 0022-0957, 01/2019, Volume 70, Issue 1, pp. 205 - 215
The papain-like cysteine protease CEP1 is involved in clearing cellular contents during programmed cell death and regulating secondary wall thickening during... 
MECHANISM | WOOD | MODEL | PLANT SCIENCES | secondary wall | VACUOLE | TOPHAT | Cysteine protease | GENE | xylem development | BIOSYNTHESIS | AUTOLYSIS | DEGRADATION | TRACHEARY ELEMENT DIFFERENTIATION | programmed cell death | Research Papers
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16. Coronary vessel extraction algorithm for block detection in angiograms
by Sambath, M and Johnaravindhar, D and Nayar, Pradeep G
International Journal of Pharmaceutical Research, 04/2019, Volume 11, Issue 2, pp. 38 - 44
X-ray angiograghy | DICOM | Tophat transform | Coronary vessels
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17. Full Text Transcriptome comparison between prenatal and postnatal Large White livers identifies differences in the expression level of genes related to metabolism and postnatal growth
by Liu, Honglin and Liu, Jingge and Ning, Caibo and Li, Rongyang and Li, Bojiang and Wu, Wangjun
Gene, ISSN 0378-1119, 02/2019, Volume 686, pp. 92 - 103
The current study examined the liver transcriptomic profiles of the Large White different in developmental periods. It was performed on pigs of two... 
RNA sequencing | miR-18b | miR-130b-3p | Insulin-like growth factor 1 | Hepatic transcriptome | SYSTEM | PROFILES | TISSUE | PROLIFERATION | CANCER | INSULIN | TOPHAT | FATTY-ACID OXIDATION | GENETICS & HEREDITY | EFFICIENCY
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