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topicstudenttitleurlifounditrating(1-10) csvcommentsadditional links for this topic
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Everyone: assigned reading for all studentsHandouts: instructor will provide offline.say "yes" if you found the paper yourselfrate the paper you picked
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RNA-Seq / Next-gen Sequencing
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EveryoneA survey of sequence alignment algorithms for next-generation sequencinghttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943993/
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EveryoneBWA from bioinformatics.Polanski.2007.pdfHandouts
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nobodyFast and accurate short read alignment with Burrows–Wheeler transformhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705234/
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List your own paper that makes use of RNA-seq to study a disease or biological phenomena. Do not pick a metagenomic (using Next-gen sequencing to study a population of species) study for this topic.
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Bobby LinkNext-Generation mRNA Sequencing Reveals Pyroptosis-Induced CD4+ T Cell Death in Early Simian Immunodeficiency Virus-Infected Lymphoid Tissues.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702687/yes
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genome assemblyhttp://gage.cbcb.umd.edu/data/index.html
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EveryoneAssembly Algorithms for Next-Generation Sequencing Datahttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874646/
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Comparing De Novo Genome Assembly: The Long and Short of Ithttp://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019175
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Haiyue LuA De Novo Genome Assembly Algorithm for Repeats and Nonrepeatshttp://www.hindawi.com/journals/bmri/2014/736473/
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Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assemblyhttp://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062856
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De Novo Genome Assembly Shows Genome Wide Similarity between Trypanosoma brucei brucei and Trypanosoma brucei rhodesiensehttp://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147660
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Whole genome shotgun sequencing guided by bioinformatics pipelines—an optimized approach for an established techniquehttp://www.sciencedirect.com.ezproxy2.library.drexel.edu/science/article/pii/S0168165603002293
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Anna LuMinimus: a fast, lightweight genome assemblerhttp://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-64-
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The fragment assembly string pathhttp://bioinformatics.oxfordjournals.org/content/21/suppl_2/ii79.full.pdfselect this paper only if no one has selected "Exploring single-sample..."
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Exploring single-sample SNP and INDEL calling with whole-genome de novo assemblyhttp://bioinformatics.oxfordjournals.org/content/28/14/1838.fullselect this paper only if no one has selected "The fragment assembly..."
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Celsim paper: A Dataset Generator for Whole Genome Shotgun Sequencinghttps://publications.mpi-cbg.de/Myers_1999_6357.pdf
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microbiome
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everyoneEric P. DluhyThe human microbiome project: exploring the microbial part of ourselves in a changing worldhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3709439/
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Gut Microbiota in Health and Diseasehttp://physrev.physiology.org/content/90/3/859.long
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David GoodmanExperimental and analytical tools for studying the human microbiomehttp://www.nature.com/nrg/journal/v13/n1/full/nrg3129.html
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Advanced computational algorithms for microbial community analysis using massive 16S rRNA sequence datahttp://nar.oxfordjournals.org.ezproxy2.library.drexel.edu/content/38/22/e205.full.pdf#page=1&view=FitH
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Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomeshttps://dnaresearch.oxfordjournals.org/content/14/4/169.full
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Comparative metagenomic analysis of human gut microbiome composition using two different bioinformatics pipelineshttp://www.hindawi.com/journals/bmri/2014/325340/abs/
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Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approachhttp://gut.bmj.com/content/55/2/205.abstract
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Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarrayhttp://onlinelibrary.wiley.com/doi/10.1002/ibd.21319/abstract?userIsAuthenticated=false&deniedAccessCustomisedMessage=
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Greg RisserIntegrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's diseasehttp://journals.plos.org/plosone/article?id=10.1371/journal.pone.0049138
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Comparison of the fecal microbiota profiles between ulcerative colitis and Crohn's disease using terminal restriction fragment length polymorphism analysishttp://link.springer.com/article/10.1007/s00535-010-0368-4
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Remediation of C. difficile infection: Lawley et al., PLoS Pathogens (2012)
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Analysis of membrane proteins in the GOS dataset: Patel et al.,Genome Res (2010)
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Metagenomic / metatranscriptomic AMD analysis - Hua et al., ISME J (2015)
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Metabolites and microbes in bacterial vaginosis: Srinivasan et al.,Genome Res (2010)
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Impact of low-dose penicillin on mouse development – Cox et al., Cell (2014)
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microarray
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everyoneAnalysis of microarray experiments of gene expression profilinghttp://vortex.cs.wayne.edu/papers/Analysis.of.microarray.experiments.tarca.pdf
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Mengxi YangComputational genetics: Computational analysis of microarray datahttp://www.nature.com/nrg/journal/v2/n6/full/nrg0601_418a.html
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David GoodmanMicroarray data normalization and transformationhttp://www.nature.com/ng/journal/v32/n4s/pdf/ng1032.pdf
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Analysis of microarray gene expression datahttps://www.ebi.ac.uk/huber/docs/hvhv.pdfDon't select this paper
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Reliable detection of beta-thalassemia and G6PD mutations by a DNA microarray.http://www.clinchem.org/content/48/11/2051.long
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Brinda KamaliaBeta-Globin mutation detection by tagged single-base extension and hybridization to universal glass and flow-through microarrayshttp://www.nature.com/ejhg/journal/v12/n7/abs/5201192a.html
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Simultaneous detection of alpha-thalassemia and beta-thalassemia by oligonucleotide microarray.http://www.haematologica.org/content/89/8/1012
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Anna LuGene selection and classification of microarray data using random foresthttp://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-3.
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Bobby LinkLinear Models and Empirical Bayes Methods for
Assessing Differential Expression in Microarray
Experiments
http://www.statsci.org/smyth/pubs/ebayes.pdftechnical/statistical
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Comprehensive literature review and statistical considerations for microarray meta-analysishttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351145/
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Spectral Biclustering of Microarray Data: Coclustering Genes and Conditionshttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC430175/
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Biclustering microarray data by Gibbs samplinghttp://bioinformatics.oxfordjournals.org/content/19/suppl_2/ii196.short
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Jessica EagerAn integrated tool for microarray data clustering and cluster validity assessmenthttp://bioinformatics.oxfordjournals.org/content/21/4/451.full.pdfnotagoodpaper
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Comparisons and validation of statistical clustering techniques for microarray gene expression datahttp://bioinformatics.oxfordjournals.org/content/19/4/459.short
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Genesis: cluster analysis of microarray datahttp://bioinformatics.oxfordjournals.org/content/18/1/207.abstract
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Heba Abid Microarray analysis reveals genetic pathways modulated by tipifarnib in acute myeloid leukemiahttp://bmccancer.biomedcentral.com/articles/10.1186/1471-2407-4-56
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Nick O'GradyDNA microarrays for comparison of gene expression profiles between diagnosis and relapse in precursor-B acute lymphoblastic leukemiahttp://www.nature.com/leu/journal/v17/n7/full/2402974a.html
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DNA Microarray Assay Helps to Identify Functional Genes Specific for Leukemia Stem Cellshttp://www.hindawi.com/journals/dpis/2013/520285/
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Vivian WuIdentification and Validation of Commonly Overexpressed Genes in Solid Tumors by Comparison of Microarray Datahttp://ac.els-cdn.com/S147655860480006X/1-s2.0-S147655860480006X-main.pdf?_tid=69a1f716-108f-11e6-ac51-00000aacb362&acdnat=1462212062_2bbbc2d366aeda26d91087e6638d1373
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DONOTSELECTFeature Selection Strategoieshttp://math.usask.ca/~miket/S344D..pdf
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drugrepositioning
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The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Diseasehttp://science.sciencemag.org/content/313/5795/1929.fullhttps://portals.broadinstitute.org/cmap/
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Vivian WuHuman Disease Networkhttp://www.pnas.org/content/104/21/8685.full
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Nick O'GradyTranscriptional data: a new gateway to drug repositioning?http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3625109/
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A computational method for drug repositioning using publicly available gene expression datahttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4674855/
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Bobby LinkDrug repositioning for non-small cell lung cancer by using machine learning algorithms and topological graph theory.http://www.ncbi.nlm.nih.gov/pubmed/26817825
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Genes2FANs: connecting genes through functional association networkshttp://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-156
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Heba Abid Drug-target networkhttp://www.nature.com/nbt/journal/v25/n10/full/nbt1338.html
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Predicting new molecular targets for known drugshttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784146/
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Mengxi YangA computational method for drug repositioning using publicly available gene expression datahttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4674855/
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David GoodmanComputational approaches for drug repositioning and combination therapy design.http://www.ncbi.nlm.nih.gov/pubmed/20556864
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Gene Ontology and KEGG Pathway Enrichment Analysis of a Drug Target-Based Classification System.http://www.ncbi.nlm.nih.gov/pubmed/25951454
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Drug repositioning for personalized medicinehttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446277/
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phylogeny
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IgTree©: Creating Immunoglobulin variable region gene lineage trees
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Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestorshttp://arxiv.org/abs/1303.0424
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Reconstructing a B-cell clonal lineage. II. Mutation, selection, and affinity maturationhttps://www.researchgate.net/profile/Christopher_Woods/publication/262055694_Reconstructing_a_B-Cell_Clonal_Lineage._II._Mutation_Selection_and_Affinity_Maturation/links/0a85e53a4708734638000000.pdf
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Jessica EagerSearch and clustering orders of magnitude faster than BLASThttp://www.ncbi.nlm.nih.gov/pubmed/20709691also read & present the algorithm descriptions from the supplementary doc. Additional figures and descriptions available at: http://drive5.com/usearch/manual/algorithms.html
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Tolerating some redundancy significantly speeds up clustering of large protein databases.http://bioinformatics.oxfordjournals.org/content/18/1/77.full.pdf
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Vivian WuParallel creation of non-redundant gene indices from partial mRNA transcriptshttp://www.sandia.gov/~ktpedre/copyrighted-papers/fgcs_18_2002_863_870.pdf
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Haiyue LuA novel hierarchical clustering algorithm for gene sequenceshttp://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-174
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Efficient agglomerative hierarchical clusteringhttp://www.sciencedirect.com/science/article/pii/S0957417414006150/pdfft?md5=363dee86e050fbc152da17ce42311b74&pid=1-s2.0-S0957417414006150-main.pdf
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Optimal implementations of UPGMA and other common clustering algorithmshttps://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&cad=rja&uact=8&ved=0ahUKEwiD7ZHqvaLMAhWI4iYKHYLPBdgQFggpMAE&url=http%3A%2F%2Fwww.cs.technion.ac.il%2F~moran%2Fr%2FPS%2Fupgma.pdf&usg=AFQjCNGX3EQ3YOrVmTplm3XDxeh7Lgh4xw&sig2=6aeT2TzIgjJP5fw_2pNwnA
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Greg RisserThe Diversity and Molecular Evolution of B-Cell Receptors during Infectionhttp://mbe.oxfordjournals.org/content/early/2016/02/29/molbev.msw015.full
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Practical Performance of Tree Comparison Metricshttp://sysbio.oxfordjournals.org/content/64/2/205.long
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Relative Efficiencies of the Fitch-Margoliash, Maximum- Parsimony, Maximum-Likelihood, Minimum-Evolution, and Neighbor-joining Methods of Phylogenetic Tree Construction in Obtaining the Correct Treehttp://chagall.med.cornell.edu/BioinfoCourse/PDFs/Lecture6/saitou1989.pdf
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Optimal algorithms for comparing trees with labeled leaveshttp://link.springer.com/article/10.1007%2FBF01908061
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Comparison of phylogenetic trees through alignment of embedded evolutionary distances
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Eric P. DluhyPractical Performance of Tree Comparison Metricshttps://academic.oup.com/sysbio/article-lookup/doi/10.1093/sysbio/syu085
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miRNAs
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Mengxi YangComputational methods for analysis of cellular functions and pathways collectively targeted by differentially expressed microRNAhttp://www.sciencedirect.com/science/article/pii/S1046202307002010yes
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proteomics
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ptnsurface
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