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1. Full Text Genome-wide allele-specific expression analysis using Massively Parallel Signature Sequencing (MPSS™) Reveals cis- and trans-effects on gene expression in maize hybrid meristem tissue
by Guo, Mei and Yang, Sean and Rupe, Mary and Hu, Bin and Bickel, David R and Arthur, Lane and Smith, Oscar
Plant Molecular Biology, ISSN 0167-4412, 3/2008, Volume 66, Issue 5, pp. 551 - 563
Allelic differences in expression are important genetic factors contributing to quantitative trait variation in various organisms. However, the extent of... 
Life Sciences | Plant Pathology | Biochemistry, general | MPSS | Cis - and trans -regulation | Plant Sciences | Allele-specific expression | Heterosis | Zea mays L | Cis- and trans-regulation | ARABIDOPSIS-THALIANA | REGULATORY MUTATIONS | allele-specific expression | cis- and trans-regulation | INBRED LINES | YIELD | BIOCHEMISTRY & MOLECULAR BIOLOGY | PATTERNS | F-1 HYBRID | PLANT SCIENCES | EVOLUTION | heterosis | SELECTION | Zea mays - genetics | Genome, Plant - genetics | Meristem - genetics | Plants, Genetically Modified | RNA, Messenger - genetics | Alleles | Gene Expression Regulation, Plant - genetics | Gene Expression Profiling | Software | Zea mays - growth & development | Genetic research | Corn | Gene expression | Multiprocessing | Analysis | Hybridization | Transgenic plants | Genomics | Index Medicus
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2. Full Text AlleleSeq: analysis of allele‐specific expression and binding in a network framework
by Rozowsky, Joel and Abyzov, Alexej and Wang, Jing and Alves, Pedro and Raha, Debasish and Harmanci, Arif and Leng, Jing and Bjornson, Robert and Kong, Yong and Kitabayashi, Naoki and Bhardwaj, Nitin and Rubin, Mark and Snyder, Michael and Gerstein, Mark
Molecular Systems Biology, ISSN 1744-4292, 2011, Volume 7, Issue 1, pp. 522 - n/a
To study allele‐specific expression (ASE) and binding (ASB), that is, differences between the maternally and paternally derived alleles, we have developed a... 
allele‐specific | networks | RNA‐Seq | ChIP‐Seq | ChIP-Seq | RNA-Seq | allele-specific | MOUSE-BRAIN | POPULATION | TRANSCRIPTION FACTOR-BINDING | X-CHROMOSOME | PROTEIN-DNA INTERACTIONS | BIOCHEMISTRY & MOLECULAR BIOLOGY | RESOLUTION | HUMANS | IDENTIFICATION | HUMAN GENOME | ASSOCIATION | Cell Line | Chromosomes, Human, X - genetics | Oligonucleotide Array Sequence Analysis | Humans | Molecular Sequence Annotation | Gene Expression Regulation | Databases, Genetic | Chromosome Mapping | Transcription Factors - genetics | DNA-Binding Proteins - genetics | Gene Regulatory Networks | Chromosomes, Human, Y - genetics | DNA-Binding Proteins - metabolism | Transcription Factors - metabolism | Sequence Analysis, RNA | Alleles | Polymorphism, Single Nucleotide | Genome, Human | Binding | Construction | Transcription factors | Deactivation | Nucleotide sequence | Pipelines | Data processing | Genomes | Single-nucleotide polymorphism | Inactivation | Gene expression | Ribonucleic acid--RNA | Annotations | Computation | Correlation analysis | Data sets | Computer applications | Gene mapping | Index Medicus
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3. Full Text Bulk segregant RNA-seq reveals expression and positional candidate genes and allele-specific expression for disease resistance against enteric septicemia of catfish
by Wang, Ruijia and Sun, Luyang and Bao, Lisui and Zhang, Jiaren and Jiang, Yanliang and Yao, Jun and Song, Lin and Feng, Jianbin and Liu, Shikai and Liu, Zhanjiang
BMC Genomics, ISSN 1471-2164, 12/2013, Volume 14, Issue 1, pp. 929 - 929
Background: The application of RNA-seq has accelerated gene expression profiling and identification of gene-associated SNPs in many species. However, the... 
Disease resistance | Catfish | RNA-seq | Bulk segregant analysis | Allele-specific expression | LINKAGE MAP | CHANNEL CATFISH | SNP DISCOVERY | ICTALURUS-PUNCTATUS | IDENTIFICATION | GENOME | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | EPIGENETIC REGULATIONS | IMMUNE-RESPONSES | SEQUENCE | GENETICS & HEREDITY | INFECTION | Fish Diseases - microbiology | Enterobacteriaceae Infections - veterinary | Gene Expression Profiling | Fish Diseases - genetics | Edwardsiella ictaluri | Sepsis - genetics | Animals | Sequence Analysis, RNA | Enterobacteriaceae Infections - genetics | Sepsis - veterinary | Catfishes - genetics | Polymorphism, Single Nucleotide | Disease Resistance - genetics | Sepsis - microbiology | RNA sequencing | Allelomorphism | Genetic susceptibility | Septicemia | Catfishes | Physiological aspects | Genetic aspects | Gene expression | Identification and classification | Methods | Medical research | Genetic research | Medicine, Experimental | Single nucleotide polymorphisms | Studies | Genomics | Epigenetics | Fish | Genomes | Bioinformatics | Aquaculture | Index Medicus
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4. Full Text Cis–trans controls and regulatory novelty accompanying allopolyploidization
by Hu, Guanjing and Wendel, Jonathan F
New Phytologist, ISSN 0028-646X, 03/2019, Volume 221, Issue 4, pp. 1691 - 1700
Allopolyploidy is a prevalent process in plants, having important physiological, ecological and evolutionary consequences. Transcriptomic responses to genomic... 
homoeolog expression bias | nonadditive expression | expression‐level dominance | and | allopolyploidy | cis | allele‐specific expression (ASE) | trans | cis and trans | allele-specific expression (ASE) | expression-level dominance | TRANSCRIPTOME | ALLELE-SPECIFIC EXPRESSION | PLANT SCIENCES | DNA | EXPRESSION LEVEL DOMINANCE | GENE-EXPRESSION | EVOLUTIONARY SIGNIFICANCE | POLYPLOIDY | DIVERGENCE | COFFEA-ARABICA | HYBRID | Genetic research | Epigenetic inheritance | Gene expression | Analysis | Fractionation | Hybrids | Polyploidy | Genes | Dominance | Genomes | Allopolyploidy | Alleles | Gene duplication | Interactions | Framework | Novelty
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5. Full Text Critical evaluation of imprinted gene expression by RNA-seq: A new perspective
by DeVeale, Brian and van der Kooy, Derek and Babak, Tomas
PLoS Genetics, ISSN 1553-7390, 03/2012, Volume 8, Issue 3, pp. e1002600 - e1002600
In contrast to existing estimates of approximately 200 murine imprinted genes, recent work based on transcriptome sequencing uncovered parent-of-origin allelic... 
MOUSE-BRAIN | AMPLIFICATION-FREE | DIFFERENTIAL EXPRESSION | PROTEIN | WIDE IDENTIFICATION | ANNOTATION | ALLELE-SPECIFIC EXPRESSION | RESOLUTION | GENETICS & HEREDITY | IMBALANCE | GENOME | Genomic Imprinting | Gene Expression | Mice, Inbred C57BL | Embryonic Development - genetics | Male | Transcriptome - genetics | Brain - metabolism | Animals | Base Sequence | Alleles | Female | Mice | Polymorphism, Single Nucleotide | RNA sequencing | Brain | Physiological aspects | Genetic aspects | Genetic transcription | Research | Gene expression | Medical research | Ontology | Bias | Statistical methods | Standard deviation | Genomes | Experiments | Estimates | Index Medicus
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6. Full Text Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle
by Khansefid, Majid and Pryce, Jennie E and Bolormaa, Sunduimijid and Chen, Yizhou and Millen, Catriona A and Chamberlain, Amanda J and Vander Jagt, Christy J and Goddard, Michael E
BMC Genomics, ISSN 1471-2164, 11/2018, Volume 19, Issue 1, pp. 793 - 793
Background: The mutations changing the expression level of a gene, or expression quantitative trait loci (eQTL), can be identified by testing the association... 
RNA-sequencing | Allele specific expression | ASE analysis | Genome-wide association study | eQTL mapping | Genetic variation of complex traits | TRANSCRIPTOME | ANGUS CATTLE | REGULATORY VARIATION | BEEF-CATTLE | GENOMIC BREEDING VALUES | RNA-SEQ | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | RESIDUAL FEED-INTAKE | GENETICS & HEREDITY | QUALITY TRAITS | MU-CALPAIN | CALPASTATIN | Gene Expression | Genome-Wide Association Study | Reproducibility of Results | Quantitative Trait, Heritable | Chromosome Mapping | Multifactorial Inheritance | Genetic Variation | Animals | Sequence Analysis, RNA | Cattle | Alleles | Polymorphism, Single Nucleotide | Quantitative Trait Loci | Quantitative trait loci | Genetic aspects | Research | Gene expression | Genes | Genomics | Genomes | Single-nucleotide polymorphism | Tissues | Ribonucleic acid--RNA | Loci | Gene sequencing | Genetic variance | Mutation | Feeds | Gene mapping | Variation | Bioinformatics | Chromosomes | Polymorphism | Index Medicus
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7. Full Text From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing
by Marinov, Georgi K and Williams, Brian A and McCue, Ken and Schroth, Gary P and Gertz, Jason and Myers, Richard M and Wold, Barbara J
Genome Research, ISSN 1088-9051, 2014, Volume 24, Issue 3, pp. 496 - 510
Single-cell RNA-seq mammalian transcriptome studies are at an early stage in uncovering cell-to-cell variation in gene expression, transcript processing and... 
LANDSCAPE | BIOCHEMISTRY & MOLECULAR BIOLOGY | ALLELE-SPECIFIC EXPRESSION | TUMOR-CELLS | NOISE | MONOALLELIC EXPRESSION | NETWORK ANALYSIS | HUMAN GENOME | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | CONSEQUENCES | SEQ | REVEALS | RNA Splicing | Reproducibility of Results | Sequence Analysis, RNA | RNA - analysis | Genes | Humans | Transcriptome | Cell Line, Tumor | Gene Expression Profiling - methods | Genome, Human | RNA - genetics | Research | Genetic transcription | Gene expression | RNA splicing | Index Medicus | Method
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8. Full Text Autosomal monoallelic expression in the mouse
by Zwemer, Lillian M and Zak, Alexander and Thompson, Benjamin R and Kirby, Andrew and Daly, Mark J and Chess, Andrew and Gimelbrant, Alexander A
Genome Biology, ISSN 1474-7596, 02/2012, Volume 13, Issue 2, pp. R10 - R10
Background: Random monoallelic expression defines an unusual class of genes displaying random choice for expression between the maternal and paternal alleles.... 
INACTIVATION | INTERLEUKIN-2 | X-CHROMOSOME | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | ALLELE-SPECIFIC EXPRESSION | GENETICS & HEREDITY | GENE-EXPRESSION | CD4(+) T-CELLS | GENOME | Allelic Imbalance - genetics | Genetic Association Studies | Oligonucleotide Array Sequence Analysis | Gene Expression - genetics | Humans | Genotype | Animals | Chromosomes - genetics | Alleles | Mice | Polymorphism, Single Nucleotide | Genome | X Chromosome - genetics | Index Medicus | Research
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9. Full Text Discovering single nucleotide polymorphisms regulating human gene expression using allele specific expression from RNA-seq data
by Kang, Eun Yong and Martin, Lisa J and Mangul, Serghei and Isvilanonda, Warin and Zou, Jennifer and Ben-David, Eyal and Han, Buhm and Lusis, Aldons J and Shifman, Sagiv and Eskin, Eleazar
Genetics, ISSN 0016-6731, 11/2016, Volume 204, Issue 3, pp. 1057 - 1064
The study of the genetics of gene expression is of considerable importance to understanding the nature of common, complex diseases. The most widely applied... 
Expression quantitative trait loci | Causal variants | Allele specific expression | expression quantitative trait loci | CELLS | TRANSCRIPTOME | GENETICS & HEREDITY | IMBALANCE | TRAIT | FUNCTIONAL VARIATION | causal variants | GENOME | Promoter Regions, Genetic | European Continental Ancestry Group - genetics | HapMap Project | Immune System Diseases - genetics | Europe | Humans | Transcriptome | Algorithms | Alleles | Cell Line, Tumor | Polymorphism, Single Nucleotide | Genome-Wide Association Study - methods | Quantitative Trait Loci | Allelomorphism | RNA sequencing | Usage | Research | Gene expression | Genetic variation | Studies | Haplotypes | Genomes | Bias | Quality | Index Medicus | Investigations
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10. Full Text Evidence for weak selective constraint on human gene expression
by Glassberg, Emily C and Gao, Ziyue and Harpak, Arbel and Lan, Xun and Lan, Xun and Pritchard, Jonathan K and Pritchard, Jonathan K
Genetics, ISSN 0016-6731, 02/2019, Volume 211, Issue 2, pp. 757 - 772
Gene expression variation is a major contributor to phenotypic variation in human complex traits. Selection on complex traits may therefore be reflected in... 
Heritability | Gene expression | Allele-specific expression | Stabilizing selection | IMPACT | EVOLUTION | VARIANTS | GENETICS & HEREDITY | TRAITS | ASSOCIATION | DISCOVERY | Copy number | Genes | Gene regulation | Genomics | Phenotypic variations | Genomes | Genetic diversity | Consortia | Depletion | Gene frequency | Alleles | Index Medicus | Investigations
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11. Full Text Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast
by McManus, C. Joel and May, Gemma E and Spealman, Pieter and Shteyman, Alan
Genome Research, ISSN 1088-9051, 2014, Volume 24, Issue 3, pp. 422 - 430
Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly... 
REGULATORY CHANGES | DROSOPHILA-MELANOGASTER | BIOCHEMISTRY & MOLECULAR BIOLOGY | ALLELE-SPECIFIC EXPRESSION | TRANSLATION | TRANS | GENOME | EVOLUTION | RNA-SEQ | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | IN-VIVO | GENETICS & HEREDITY | INTERSPECIFIC HYBRIDS | Gene Expression Regulation, Fungal | Species Specificity | RNA, Messenger - genetics | Gene Expression Profiling | Phylogeny | Saccharomyces - genetics | Codon | Genome, Fungal | Ribosomes - genetics | 5' Untranslated Regions | Genes, Fungal | RNA, Fungal - genetics | Saccharomyces - classification | Evolution, Molecular | Genetic aspects | Research | Yeast fungi | Gene expression | Index Medicus
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12. Full Text Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis
by Maroilley, T and Lemonnier, G and Lecardonnel, J and Esquerré, D and Ramayo-Caldas, Y and Mercat, M.J and Rogel-Gaillard, C and Estellé, J
BMC Genomics, ISSN 1471-2164, 12/2017, Volume 18, Issue 1, pp. 967 - 967
Background: Efforts to improve sustainability in livestock production systems have focused on two objectives: investigating the genetic control of immune... 
EQTL | RNA-Seq | Transcriptome | EGWAS | Allele-Specific Expression | Blood | Pig | IMMUNITY | COMPLEX | MEAT QUALITY | CANDIDATE GENES | MOUSE | eQTL | DISCOVERY | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | eGWAS | GENETICS & HEREDITY | QUALITY TRAITS | COEXPRESSION NETWORKS | EQTL-ANALYSIS | Histocompatibility Antigens - genetics | Genome-Wide Association Study | Gene Expression Regulation | Male | Biomarkers - blood | Swine - genetics | Gene Regulatory Networks | Animals | Alleles | Swine - blood | Female | Polymorphism, Single Nucleotide | Histocompatibility Antigens - metabolism | Quantitative Trait Loci | RNA - blood | RNA sequencing | Quantitative genetics | Genetic markers | RNA | Swine | Analysis | Genes | Genomics | Livestock | Genomes | Genetic transcription | Single nucleotide polymorphisms | Index Medicus
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13. Full Text RPASE: Individual‐based allele‐specific expression detection without prior knowledge of haplotype phase
by Wang, Mi and Uebbing, Severin and Pawitan, Yudi and Scofield, Douglas G and Teknisk-naturvetenskapliga vetenskapsområdet and Evolutionsbiologi and Biologiska sektionen and Uppsala universitet and Institutionen för ekologi och genetik
Molecular Ecology Resources, ISSN 1755-098X, 11/2018, Volume 18, Issue 6, pp. 1247 - 1262
Variation in gene expression is believed to make a significant contribution to phenotypic diversity and divergence. The analysis of allele‐specific expression... 
regulatory variation | allele‐specific expression | RNA‐seq | gene expression evolution | allele-specific expression | RNA-seq | BIOCHEMISTRY & MOLECULAR BIOLOGY | REGULATORY EVOLUTION | CIS | DROSOPHILA | EVOLUTIONARY BIOLOGY | CAPSELLA-GRANDIFLORA | GENE-EXPRESSION | FRAMEWORK | ECOLOGY | DIVERGENCE | SEQUENCING DATA | SELECTION | RNA-SEQ DATA | Animals | Sequence Analysis, RNA | Alleles | Biological Variation, Population | Birds | Gene Expression Profiling - methods | Polymorphism, Single Nucleotide | Genetic research | Genetic aspects | Single nucleotide polymorphisms | Gene expression | Analysis | Divergence | Landscape | Single-nucleotide polymorphism | Ribonucleic acid--RNA | Index Medicus | Biological Sciences | Naturvetenskap | Biologiska vetenskaper | Evolutionsbiologi | Natural Sciences | Evolutionary Biology
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