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RSS订阅原创 Paper intensive reading (十九)：Batch effects in a multiyear sequencing study
论文题目：Batch effects in a multiyear sequencing study: False biological trends due to changes in read lengthsscholar 引用：9页数：11发表时间：1 March 2018发表刊物：Mol Ecol Resour.作者：D. M. Leigh1,2,3 | H. E. ...
2020-02-05 10:54:42
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原创 Paper intensive reading (十八)：the Analysis of Mass Spectrometry Data for Omics Studies
论文题目：Transformation, Normalization, and Batch Effect in the Analysis of Mass Spectrometry Data for Omics Studiesscholar 引用：8页数：294 来自book：Statistical Analysis of Proteomics, Metabolomics, and Li...
2020-02-05 08:41:43
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原创 Paper intensive reading (十七)：Methods that remove batch effects may lead to exaggerated confidence
论文题目：Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analysesscholar 引用：100页数：11发表时间：August 13, 2015发表刊物：Biostatistics作者：...
2020-02-04 21:31:41
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原创 Paper intensive reading (十六)：Deep learning enables accurate clustering and batch effect removal
论文题目：Deep learning enables accurate clustering and batch effect removal in single-cell RNA-seq analysisscholar 引用：0页数：14发表时间：2019.1.25发表刊物：preprint作者：Xiangjie Li1,2, Yafei Lyu1, Jihwan Park3...
2020-02-04 18:16:28
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原创 Paper intensive reading (十五)：Mitigating the adverse impact of batch effects in sample detection
论文题目：Mitigating the adverse impact of batch effects in sample pattern detectionscholar 引用：6页数：8发表时间：1 March 2018发表刊物：Bioinformatics作者：Teng Fei1, Tengjiao Zhang2, Weiyang Shi3,* and Tianwei ...
2020-02-04 16:55:19
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原创 Paper intensive reading (十四)：Batch effects in single-cell RNA-sequencing data are corrected
论文题目：Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighborsscholar 引用：262页数：12发表时间：2 April 2018发表刊物：nature biotechnology作者：Laleh Haghverdi1,2, Aa...
2020-02-03 16:38:33
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原创 Paper intensive reading (十三)：Removing batch effects in analysis of expression microarray data
论文题目：Removing batch effects in analysis of expression microarray data: an evaluation of six batch adjustment methodsscholar 引用：258页数：10发表时间：February 28, 2011发表刊物：PLOS ONE作者：Chao Chen1,2, Kay...
2020-02-03 11:31:17
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原创 Paper intensive reading (十二)：Batch Effect Correction of RNA-seq Data
论文题目：Batch Effect Correction of RNA-seq Data through Sample 2 Distance Matrix Adjustmentscholar 引用：0页数：25发表时间：June 2019发表刊物：preprint作者：Teng Feiand Tianwei YuEmory University摘要：Batch e...
2020-02-01 20:31:48
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原创 chapter10-batch effects
chapter10-batch effects1.Introduction to batch effects [Rmd]batch effects 产生的原因：measurements are affected by laboratory conditions, reagent lots 试剂批号, and personnel differences. 本章中将介绍：how to de...
2020-01-31 21:42:00
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原创 Paper intensive reading (十一)：Nuclear localization of Zika virus NS5 contributes to suppression
论文题目：Nuclear localization of Zika virus NS5 contributes to suppression of type I interferon production and responsescholar 引用：0页数：10发表时间：20 December 2019发表刊物：JOURNAL OF GENERAL VIROLOGY，IF 2.8...
2020-01-15 23:19:21
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原创 Paper intensive reading (十)：Zika virus infection reprograms global transcription of host cells
论文题目：Zika virus infection reprograms global transcription of host cells to allow sustained infectionscholar 引用：100页数：11发表时间：15 Jan 2019发表刊物：Emerging Microbes & Infections作者：Shashi Kant T...
2020-01-10 13:20:44
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原创 Paper intensive reading (九)：Toll-Like Receptor 7 Agonist GS-9620 Induces Prolonged Inhibition of HBV
论文题目：Toll-Like Receptor 7 Agonist GS-9620 Induces Prolonged Inhibition of HBV via a Type I Interferon-Dependent Mechanismscholar 引用：3页数：11发表时间：13 December 2017发表刊物：Journal of Hepatology作者：Co...
2020-01-10 10:42:35
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原创 Paper intensive reading (八)：rna sequencing of Murine norovirus-infected cells
论文题目：rna sequencing of Murine norovirus-infected cells reveals Transcriptional alteration of genes important to Viral recognition and antigen Presentationscholar 引用：6页数：15发表时间：11 August 2017发表...
2020-01-09 21:20:06
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原创 Paper intensive reading (七)：Dengue virus and the host innate immune response
论文题目：Dengue virus and the host innate immune responsescholar 引用：13页数：12发表时间：10 Oct 2018发表刊物：Emerging Microbes & Infections作者：Naoko Uno & Ted M. Ross摘要：Dengue virus (DENV, 登革热病毒) ...
2020-01-09 18:41:21
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原创 NCBI SRA数据库使用详解----学习笔记
SRA(Sequence ReadArchive)数据库是用于存储二代测序的原始数据，包括454，Illumina,SOLiD,lonTorrent, Helicos和CompleteGenomics。除了原始序列数据外，SRA现在也存在raw reads在参考基因的比对信息。 根据SRA数据产生的特点，将SRA数据分为四类：studies--研究课题 experiments--实验设计 ...
2019-12-25 15:58:47
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原创 Paper intensive reading (六)：Altered Interactions between the GM and Colonic Mucosa Precede Polyposis
论文题目：Altered Interactions between the Gut Microbiome and Colonic Mucosa Precede Polyposis in Micelink：https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127985Google citation: 26...
2019-12-06 16:22:04
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原创 BMS8110复习（十三）：Lecture 13 - Precision Medicine
ContentsHistorical Perspective Introduction of Precision Medicine Precision Medicine-related Projects Cancer Genomics & Precision Medicine Challenges to Precision Medicine Case StudyWhich ...
2019-12-04 17:30:53
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原创 BMS8110复习（十二）：Lecture 12 - Single Cell Sequencing
ContentsIntroduction Single-cell RNA-seq data analysis Single-cell sequencing in cancer research Lineage tracing(谱系追踪)Why Single Cell Studies?Challenges for single-cell data analysisGene d...
2019-12-04 16:41:48
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原创 BMS8110复习（十一）：Lecture 11 - DNA Methylation
ContentsEpigenetics DNA Methylation Measuring DNA Methylation Methylation arrays Methylation sequencing Case StudyWhat is epigenetics?Epigenetics refers to stable heritable traits not explai...
2019-12-04 15:59:04
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原创 BMS8110复习（十）：Lecture 10 - ChIP-seq Histone Modifications
ContentsHistone Modifications 组蛋白修饰 Chromatin states 染色质状态 ChromHMM: learning 'hidden' chromatin states Super-enhancers Bivalent promoters 二价启动子Larger DNA structures mediate more compaction....
2019-12-04 15:06:09
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原创 BMS8110复习（九）：Lecture 9 - Network Analysis
OutlineNetwork and System Biology Network Basics Network Inference Network Visualization Case StudiesSystems Biology, What is it?Systems biology is based on the understanding that the whole i...
2019-12-04 11:21:15
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原创 BMS8110复习（八）：Lecture 8- Epigenetics and Epigenomics
OutlineIntroduction to the concept of epigenetics and epigenomics Tissue specific transcriptional regulation Chromatin accessibility Histone Modifications 组蛋白修饰 DNA Methylation Chromatin thr...
2019-12-04 10:28:41
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原创 BMS8110复习（七）：Lecture 7- ChIP Sequencing (transcription factor)
OutlineIntroduction to transcription factor ChIP-seq Experimental Procedure Data Analysis Case StudyTranscription FactorGeneral transcription factor and sequence specific transcription factor...
2019-12-03 17:32:16
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原创 BMS8110复习（六）：Lecture 6 - Molecular Phylogeny and evolution
OutlineIntroduction to molecular evolution Principles of molecular phylogeny and evolution 分子系统发育与进化原理 Goals;historical background; molecular clock hypothesis positive and negative selection; n...
2019-12-03 16:47:05
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原创 BMS8110复习（五）：Lecture 5 - RNA-seq Data Analysis
RNA-seq ApplicationsDifferential expression Gene fusion Alternative splicing Novel transcribed regions Allele-specific(等位基因特异性) expression RNA editing Transcriptome for non-model organisms生...
2019-12-03 15:20:26
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原创 BMS8110复习（四）：Lecture 4 -Gene Expression Microarrays
Lecture 4 -Gene Expression Microarrays基因表达微阵列Outline:Introduction Experimental Design Microarray Data Preprocessing Quality Control of Experiments Differential Gene Expression Analysis Case...
2019-12-02 22:17:29
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原创 BMS8110复习（三）：Lecture 3 - Introduction to Genomics
What is Genome?A genome is the genetic material of an organism. It consists of DNA (or RNA in RNA viruses). The genome includes both the genes (the coding regions) and the non-coding DNA, as well a...
2019-12-02 09:59:14
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原创 Paper intensive reading (五)：A Review on Role of Microbiome in Obesity and Antiobesity Properties
论文题目：A Review on Role of Microbiome in Obesity and Antiobesity Properties of Probiotic SupplementsPublished 9 May 2019Bhagavathi Sundaram Sivamaruthi, Periyanaina Kesika, Natarajan Suganthy, and C...
2019-12-01 16:35:19
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原创 Paper intensive reading (四)：Establishing What Constitutes a Healthy Human Gut Microbiome
论文题目：Establishing What Constitutes a Healthy Human Gut Microbiome: State of the Science, Regulatory Considerations, and Future DirectionsPublished: 02 August 2019McBurney, ..., Jens Latulippe, Mar...
2019-11-30 23:13:37
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原创 Paper intensive reading (三)：Interactions Between Food and Gut Microbiota: Impact on Human Health
论文题目：Interactions Between Food and Gut Microbiota: Impact on Human HealthVolume publication date March 2019YanbeiWu, JiaweiWan,..., Thomas T.Y.WangPublished in Annual Review of Food Science and ...
2019-11-29 09:58:43
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原创 Paper intensive reading (二)：Role of the gut microbiota in nutrition and health
论文题目：Role of the gut microbiota in nutrition and healthPublished 13 June 2018Ana M Valdes, associate professor12, Jens Walter, CAIP chair for nutrition, microbes, and gastrointestinal health3,...
2019-11-27 22:06:45
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原创 Paper intensive reading (一)：Your microbiome is what you eat
论文题目：Your microbiome is what you eat论文简介：这篇论文是2019年10月17日发表在Nature Reviews Microbiology上的一篇综述。three recent studies highlight how the gut microbiome responds to dietary change, with potential conse...
2019-11-27 16:42:41
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原创 BMS8110复习（二）：Lecture 2 - Programming in R
R is free and powerful programming language for statistical computing and data visualization.1. R can be used to compute a large variety of classical statistic tests including:Student's t-test: co...
2019-11-27 09:25:18
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原创 BMS8110复习（一）：Lecture 1-Introduction to Bioinformatics
Wiki definition:Bioinformatics is an interdisciplinary field that develpes methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics com...
2019-11-26 15:44:40
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原创 Paper reading (一百)：Effects of oral supplementation with probiotics or synbiotics in obese adults
论文题目：Effects of oral supplementation with probiotics or synbiotics in overweight and obese adults: a systematic review and meta-analyses of randomized trialsscholar 引用：1页数：21发表时间：28 March 2019...
2019-11-21 17:03:50
190
原创 Paper reading (九十九)：Effects of probiotics in subjects with overweight or obesity
论文题目：Effects of probiotics on body weight, body mass index, fat mass and fat percentage in subjects with overweight or obesity: a systematic review and meta‐analysis of randomized controlled trialss...
2019-11-21 13:29:23
196
原创 Paper reading (九十八)：Endothelial dysfunction: what is the role of the microbiota?
论文题目：Endothelial dysfunction: what is the role of the microbiota?scholar 引用：3页数：3发表时间：08January 2018发表刊物：Gut作者：Erwin G Zoetendal, Hauke Smidt作者单位：Wageningen University & Research摘要：...
2019-11-21 11:25:16
296
原创 Paper reading (九十七)：Modulating the microbiome to improve therapeutic response in cancer
论文题目：Modulating the microbiome to improve therapeutic response in cancerscholar 引用：20页数：16发表时间：1 February 2019发表刊物：The Lancet Oncology作者：Jennifer L McQuade, Carrie R Daniel, Beth A Helmink, ...
2019-11-21 09:41:32
277
原创 Paper reading (九十六)：Safety of Lactobacillus Reuteri DSM 17938 in Healthy Children 2–5 Years of Age
论文题目：Safety of Lactobacillus Reuteri DSM 17938 in Healthy Children 2–5 Years of Agescholar 引用：0页数：11发表时间：1August 2019发表刊物：The Pediatric Infectious Disease Journal作者：Kosek,Margaret N. MD,......
2019-11-20 20:14:09
401
原创 Paper reading (九十五)：Effect of prebiotic and probiotic supplementation on major depressive disorder
论文题目：Effect of prebiotic and probiotic supplementation on circulating pro-inflammatory cytokines and urinary cortisol levels in patients with major depressive disorder: A double-blind, placebo-control...
2019-11-20 18:45:05
268
百度的何中军在《神经网络机器翻译技术及应用》中提到的5篇论文
2019-03-21
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