Regenerate paper list with Georg's papers

papers/_posts/2007-07-20-clark-common-sequence-polymorphisms.md

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+---
+layout: paper
+title: "Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana"
+nickname: 2007-07-20-clark-common-sequence-polymorphisms
+authors: "Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G, Shinn P, Warthmann N, Hu TT, Fu G, Hinds DA, Chen H, Frazer KA, Huson DH, Scholkopf B, Nordborg M, Ratsch G, Ecker JR, Weigel D"
+year: "2007"
+journal: "Science"
+volume: 317
+issue: 5836
+pages: 338-42
+is_published: true
+image: /assets/images/papers/science.png
+projects:
+tags: []
+
+# Text
+fulltext:
+pdf:
+pdflink:
+pmcid: 
+preprint:
+supplement:
+
+# Links
+doi: "10.1126/science.1138632"
+pmid: 17641193
+
+# Data and code
+github:
+neurovault:
+openneuro:
+figshare:
+figshare_names:
+osf:
+---
+{% include JB/setup %}
+
+# Abstract
+
+The genomes of individuals from the same species vary in sequence as a result of different evolutionary processes. To examine the patterns of, and the forces shaping, sequence variation in Arabidopsis thaliana, we performed high-density array resequencing of 20 diverse strains (accessions). More than 1 million nonredundant single-nucleotide polymorphisms (SNPs) were identified at moderate false discovery rates (FDRs), and approximately 4% of the genome was identified as being highly dissimilar or deleted relative to the reference genome sequence. Patterns of polymorphism are highly nonrandom among gene families, with genes mediating interaction with the biotic environment having exceptional polymorphism levels. At the chromosomal scale, regional variation in polymorphism was readily apparent. A scan for recent selective sweeps revealed several candidate regions, including a notable example in which almost all variation was removed in a 500-kilobase window. Analyzing the polymorphisms we describe in larger sets of accessions will enable a detailed understanding of forces shaping population-wide sequence variation in A. thaliana.

papers/_posts/2008-01-22-laubinger-attax-a-whole.md

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+---
+layout: paper
+title: "At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana"
+nickname: 2008-01-22-laubinger-attax-a-whole
+authors: "Laubinger S, Zeller G, Henz SR, Sachsenberg T, Widmer CK, Naouar N, Vuylsteke M, Scholkopf B, Ratsch G, Weigel D"
+year: "2008"
+journal: "Genome Biol"
+volume: 9
+issue: 7
+pages: R112
+is_published: true
+image: /assets/images/papers/genome-biol.png
+projects:
+tags: []
+
+# Text
+fulltext:
+pdf:
+pdflink:
+pmcid: PMC2530869
+preprint:
+supplement:
+
+# Links
+doi: "10.1186/gb-2008-9-7-r112"
+pmid: 18613972
+
+# Data and code
+github:
+neurovault:
+openneuro:
+figshare:
+figshare_names:
+osf:
+---
+{% include JB/setup %}
+
+# Abstract
+
+Gene expression maps for model organisms, including Arabidopsis thaliana, have typically been created using gene-centric expression arrays. Here, we describe a comprehensive expression atlas, Arabidopsis thaliana Tiling Array Express (At-TAX), which is based on whole-genome tiling arrays. We demonstrate that tiling arrays are accurate tools for gene expression analysis and identified more than 1,000 unannotated transcribed regions. Visualizations of gene expression estimates, transcribed regions, and tiling probe measurements are accessible online at the At-TAX homepage.

papers/_posts/2008-01-22-zeller-transcript-normalization-and.md

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+---
+layout: paper
+title: "Transcript normalization and segmentation of tiling array data"
+nickname: 2008-01-22-zeller-transcript-normalization-and
+authors: "Zeller G, Henz SR, Laubinger S, Weigel D, Ratsch G"
+year: "2008"
+journal: "Pac Symp Biocomput"
+volume: 
+issue: 
+pages: 527-38
+is_published: true
+image: /assets/images/papers/pac-symp-biocomput.png
+projects:
+tags: []
+
+# Text
+fulltext:
+pdf:
+pdflink:
+pmcid: 
+preprint:
+supplement:
+
+# Links
+doi: ""
+pmid: 18229713
+
+# Data and code
+github:
+neurovault:
+openneuro:
+figshare:
+figshare_names:
+osf:
+---
+{% include JB/setup %}
+
+# Abstract
+
+For the analysis of transcriptional tiling arrays we have developed two methods based on state-of-the-art machine learning algorithms. First, we present a novel transcript normalization technique to alleviate the effect of oligonucleotide probe sequences on hybridization intensity. It is specifically designed to decrease the variability observed for individual probes complementary to the same transcript. Applying this normalization technique to Arabidopsis tiling arrays, we are able to reduce sequence biases and also significantly improve separation in signal intensity between exonic and intronic/intergenic probes. Our second contribution is a method for transcript mapping. It extends an algorithm proposed for yeast tiling arrays to the more challenging task of spliced transcript identification. When evaluated on raw versus normalized intensities our method achieves highest prediction accuracy when segmentation is performed on transcript-normalized tiling array data.

papers/_posts/2008-06-22-zeller-detecting-polymorphic-regions.md

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+---
+layout: paper
+title: "Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays"
+nickname: 2008-06-22-zeller-detecting-polymorphic-regions
+authors: "Zeller G, Clark RM, Schneeberger K, Bohlen A, Weigel D, Ratsch G"
+year: "2008"
+journal: "Genome Res"
+volume: 18
+issue: 6
+pages: 918-29
+is_published: true
+image: /assets/images/papers/genome-res.png
+projects:
+tags: []
+
+# Text
+fulltext:
+pdf:
+pdflink:
+pmcid: PMC2413159
+preprint:
+supplement:
+
+# Links
+doi: "10.1101/gr.070169.107"
+pmid: 18323538
+
+# Data and code
+github:
+neurovault:
+openneuro:
+figshare:
+figshare_names:
+osf:
+---
+{% include JB/setup %}
+
+# Abstract
+
+Whole-genome oligonucleotide resequencing arrays have allowed the comprehensive discovery of single nucleotide polymorphisms (SNPs) in eukaryotic genomes of moderate to large size. With this technology, the detection rate for isolated SNPs is typically high. However, it is greatly reduced when other polymorphisms are located near a SNP as multiple mismatches inhibit hybridization to arrayed oligonucleotides. Contiguous tracts of suppressed hybridization therefore typify polymorphic regions (PRs) such as clusters of SNPs or deletions. We developed a machine learning method, designated margin-based prediction of polymorphic regions (mPPR), to predict PRs from resequencing array data. Conceptually similar to hidden Markov models, the method is trained with discriminative learning techniques related to support vector machines, and accurately identifies even very short polymorphic tracts (<10 bp). We applied this method to resequencing array data previously generated for the euchromatic genomes of 20 strains (accessions) of the best-characterized plant, Arabidopsis thaliana. Nonredundantly, 27% of the genome was included within the boundaries of PRs predicted at high specificity ( approximately 97%). The resulting data set provides a fine-scale view of polymorphic sequences in A. thaliana; patterns of polymorphism not apparent in SNP data were readily detected, especially for noncoding regions. Our predictions provide a valuable resource for evolutionary genetic and functional studies in A. thaliana, and our method is applicable to similar data sets in other species. More broadly, our computational approach can be applied to other segmentation tasks related to the analysis of genomic variation.

papers/_posts/2008-06-24-laubinger-dual-roles-of.md

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+---
+layout: paper
+title: "Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana"
+nickname: 2008-06-24-laubinger-dual-roles-of
+authors: "Laubinger S, Sachsenberg T, Zeller G, Busch W, Lohmann JU, Ratsch G, Weigel D"
+year: "2008"
+journal: "Proc Natl Acad Sci U S A"
+volume: 105
+issue: 25
+pages: 8795-800
+is_published: true
+image: /assets/images/papers/proc-natl-acad-sci-u-s-a.png
+projects:
+tags: []
+
+# Text
+fulltext:
+pdf:
+pdflink:
+pmcid: PMC2426964
+preprint:
+supplement:
+
+# Links
+doi: "10.1073/pnas.0802493105"
+pmid: 18550839
+
+# Data and code
+github:
+neurovault:
+openneuro:
+figshare:
+figshare_names:
+osf:
+---
+{% include JB/setup %}
+
+# Abstract
+
+The processing of Arabidopsis thaliana microRNAs (miRNAs) from longer primary transcripts (pri-miRNAs) requires the activity of several proteins, including DICER-LIKE1 (DCL1), the double-stranded RNA-binding protein HYPONASTIC LEAVES1 (HYL1), and the zinc finger protein SERRATE (SE). It has been noted before that the morphological appearance of weak se mutants is reminiscent of plants with mutations in ABH1/CBP80 and CBP20, which encode the two subunits of the nuclear cap-binding complex. We report that, like SE, the cap-binding complex is necessary for proper processing of pri-miRNAs. Inactivation of either ABH1/CBP80 or CBP20 results in decreased levels of mature miRNAs accompanied by apparent stabilization of pri-miRNAs. Whole-genome tiling array analyses reveal that se, abh1/cbp80, and cbp20 mutants also share similar splicing defects, leading to the accumulation of many partially spliced transcripts. This is unlikely to be an indirect consequence of improper miRNA processing or other mRNA turnover pathways, because introns retained in se, abh1/cbp80, and cbp20 mutants are not affected by mutations in other genes required for miRNA processing or for nonsense-mediated mRNA decay. Taken together, our results uncover dual roles in splicing and miRNA processing that distinguish SE and the cap-binding complex from specialized miRNA processing factors such as DCL1 and HYL1.

papers/_posts/2009-01-22-naouar-quantitative-rna-expression.md

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+---
+layout: paper
+title: "Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes"
+nickname: 2009-01-22-naouar-quantitative-rna-expression
+authors: "Naouar N, Vandepoele K, Lammens T, Casneuf T, Zeller G, van Hummelen P, Weigel D, Ratsch G, Inze D, Kuiper M, De Veylder L, Vuylsteke M"
+year: "2009"
+journal: "Plant J"
+volume: 57
+issue: 1
+pages: 184-94
+is_published: true
+image: /assets/images/papers/plant-j.png
+projects:
+tags: []
+
+# Text
+fulltext:
+pdf:
+pdflink:
+pmcid: 
+preprint:
+supplement:
+
+# Links
+doi: "10.1111/j.1365-313X.2008.03662.x"
+pmid: 18764924
+
+# Data and code
+github:
+neurovault:
+openneuro:
+figshare:
+figshare_names:
+osf:
+---
+{% include JB/setup %}
+
+# Abstract
+
+The Affymetrix ATH1 array provides a robust standard tool for transcriptome analysis, but unfortunately does not represent all of the transcribed genes in Arabidopsis thaliana. Recently, Affymetrix has introduced its Arabidopsis Tiling 1.0R array, which offers whole-genome coverage of the sequenced Col-0 reference strain. Here, we present an approach to exploit this platform for quantitative mRNA expression analysis, and compare the results with those obtained using ATH1 arrays. We also propose a method for selecting unique tiling probes for each annotated gene or transcript in the most current genome annotation, TAIR7, generating Chip Definition Files for the Tiling 1.0R array. As a test case, we compared the transcriptome of wild-type plants with that of transgenic plants overproducing the heterodimeric E2Fa-DPa transcription factor. We show that with the appropriate data pre-processing, the estimated changes per gene for those with significantly different expression levels is very similar for the two array types. With the tiling arrays we could identify 368 new E2F-regulated genes, with a large fraction including an E2F motif in the promoter. The latter groups increase the number of excellent candidates for new, direct E2F targets by almost twofold, from 181 to 334.

papers/_posts/2009-01-22-plantegenet-comprehensive-analysis-of.md

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+---
+layout: paper
+title: "Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance"
+nickname: 2009-01-22-plantegenet-comprehensive-analysis-of
+authors: "Plantegenet S, Weber J, Goldstein DR, Zeller G, Nussbaumer C, Thomas J, Weigel D, Harshman K, Hardtke CS"
+year: "2009"
+journal: "Mol Syst Biol"
+volume: 5
+issue: 
+pages: 242
+is_published: true
+image: /assets/images/papers/mol-syst-biol.png
+projects:
+tags: []
+
+# Text
+fulltext:
+pdf:
+pdflink:
+pmcid: PMC2657532
+preprint:
+supplement:
+
+# Links
+doi: "10.1038/msb.2008.79"
+pmid: 19225455
+
+# Data and code
+github:
+neurovault:
+openneuro:
+figshare:
+figshare_names:
+osf:
+---
+{% include JB/setup %}
+
+# Abstract
+
+In Arabidopsis thaliana, gene expression level polymorphisms (ELPs) between natural accessions that exhibit simple, single locus inheritance are promising quantitative trait locus (QTL) candidates to explain phenotypic variability. It is assumed that such ELPs overwhelmingly represent regulatory element polymorphisms. However, comprehensive genome-wide analyses linking expression level, regulatory sequence and gene structure variation are missing, preventing definite verification of this assumption. Here, we analyzed ELPs observed between the Eil-0 and Lc-0 accessions. Compared with non-variable controls, 5' regulatory sequence variation in the corresponding genes is indeed increased. However, approximately 42% of all the ELP genes also carry major transcription unit deletions in one parent as revealed by genome tiling arrays, representing a >4-fold enrichment over controls. Within the subset of ELPs with simple inheritance, this proportion is even higher and deletions are generally more severe. Similar results were obtained from analyses of the Bay-0 and Sha accessions, using alternative technical approaches. Collectively, our results suggest that drastic structural changes are a major cause for ELPs with simple inheritance, corroborating experimentally observed indel preponderance in cloned Arabidopsis QTL.

papers/_posts/2009-06-22-zeller-stressinduced-changes-in.md

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+---
+layout: paper
+title: "Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays"
+nickname: 2009-06-22-zeller-stressinduced-changes-in
+authors: "Zeller G, Henz SR, Widmer CK, Sachsenberg T, Ratsch G, Weigel D, Laubinger S"
+year: "2009"
+journal: "Plant J"
+volume: 58
+issue: 6
+pages: 1068-82
+is_published: true
+image: /assets/images/papers/plant-j.png
+projects:
+tags: []
+
+# Text
+fulltext:
+pdf:
+pdflink:
+pmcid: 
+preprint:
+supplement:
+
+# Links
+doi: "10.1111/j.1365-313X.2009.03835.x"
+pmid: 19222804
+
+# Data and code
+github:
+neurovault:
+openneuro:
+figshare:
+figshare_names:
+osf:
+---
+{% include JB/setup %}
+
+# Abstract
+
+The responses of plants to abiotic stresses are accompanied by massive changes in transcriptome composition. To provide a comprehensive view of stress-induced changes in the Arabidopsis thaliana transcriptome, we have used whole-genome tiling arrays to analyze the effects of salt, osmotic, cold and heat stress as well as application of the hormone abscisic acid (ABA), an important mediator of stress responses. Among annotated genes in the reference strain Columbia we have found many stress-responsive genes, including several transcription factor genes as well as pseudogenes and transposons that have been missed in previous analyses with standard expression arrays. In addition, we report hundreds of newly identified, stress-induced transcribed regions. These often overlap with known, annotated genes. The results are accessible through the Arabidopsis thaliana Tiling Array Express (At-TAX) homepage, which provides convenient tools for displaying expression values of annotated genes, as well as visualization of unannotated transcribed regions along each chromosome.

papers/_posts/2009-07-22-schweikert-mgeneweb-a-web.md

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+---
+layout: paper
+title: "mGene.web: a web service for accurate computational gene finding"
+nickname: 2009-07-22-schweikert-mgeneweb-a-web
+authors: "Schweikert G, Behr J, Zien A, Zeller G, Ong CS, Sonnenburg S, Ratsch G"
+year: "2009"
+journal: "Nucleic Acids Res"
+volume: 37
+issue: Web Server issue
+pages: W312-6
+is_published: true
+image: /assets/images/papers/nucleic-acids-res.png
+projects:
+tags: []
+
+# Text
+fulltext:
+pdf:
+pdflink:
+pmcid: PMC2703990
+preprint:
+supplement:
+
+# Links
+doi: "10.1093/nar/gkp479"
+pmid: 19494180
+
+# Data and code
+github:
+neurovault:
+openneuro:
+figshare:
+figshare_names:
+osf:
+---
+{% include JB/setup %}
+
+# Abstract
+
+We describe mGene.web, a web service for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. It offers pre-trained models for the recognition of gene structures including untranslated regions in an increasing number of organisms. With mGene.web, users have the additional possibility to train the system with their own data for other organisms on the push of a button, a functionality that will greatly accelerate the annotation of newly sequenced genomes. The system is built in a highly modular way, such that individual components of the framework, like the promoter prediction tool or the splice site predictor, can be used autonomously. The underlying gene finding system mGene is based on discriminative machine learning techniques and its high accuracy has been demonstrated in an international competition on nematode genomes. mGene.web is available at http://www.mgene.org/web, it is free of charge and can be used for eukaryotic genomes of small to moderate size (several hundred Mbp).