Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea

[1]  J. Rink.  Stem cell systems and regeneration in planaria , 2012, Development Genes and Evolution.

[2]  Gary D Bader,et al.  A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals , 2012, Stem cells.

[3]  S. Lapan,et al.  Transcriptome analysis of the planarian eye identifies ovo as a specific regulator of eye regeneration. , 2012, Cell reports.

[4]  G. Bell,et al.  A molecular wound response program associated with regeneration initiation in planarians. , 2012, Genes & development.

[5]  Jordi Solana,et al.  Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNA-seq, RNA interference and irradiation approach , 2012, Genome Biology.

[6]  M. Galloni,et al.  Global irradiation effects, stem cell genes and rare transcripts in the planarian transcriptome. , 2012, The International journal of developmental biology.

[7]  Alejandro González-Sastre,et al.  Inhibitory Smads and bone morphogenetic protein (BMP) modulate anterior photoreceptor cell number during planarian eye regeneration. , 2012, The International journal of developmental biology.

[8]  L. Gentile,et al.  Heterogeneity of planarian stem cells in the S/G2/M phase. , 2012, The International journal of developmental biology.

[9]  Simon J. Morley,et al.  SMG-1 and mTORC1 Act Antagonistically to Regulate Response to Injury and Growth in Planarians , 2012, PLoS genetics.

[10]  J. Baguñá.  The planarian neoblast: the rambling history of its origin and some current black boxes. , 2012, The International journal of developmental biology.

[11]  M. Yamaguchi,et al.  Transcription factor NF-Y is involved in differentiation of R7 photoreceptor cell in Drosophila , 2011, Biology Open.

[12]  A. Aboobaker,et al.  Early planarian brain regeneration is independent of blastema polarity mediated by the Wnt/β-catenin pathway. , 2011, Developmental biology.

[13]  Michael Boutros,et al.  The head-regeneration transcriptome of the planarian Schmidtea mediterranea , 2011, Genome Biology.

[14]  G. Barsh,et al.  Digital gene expression for non-model organisms. , 2011, Genome research.

[15]  J. de Lorgeril,et al.  Whole Transcriptome Profiling of Successful Immune Response to Vibrio Infections in the Oyster Crassostrea gigas by Digital Gene Expression Analysis , 2011, PloS one.

[16]  Christoph Dieterich,et al.  De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. , 2011, Genome research.

[17]  F. Cebrià,et al.  EGFR signaling regulates cell proliferation, differentiation and morphogenesis during planarian regeneration and homeostasis. , 2011, Developmental biology.

[18]  S. Letovsky,et al.  Protocol Dependence of Sequencing-Based Gene Expression Measurements , 2011, PloS one.

[19]  Peter W. Reddien,et al.  Polarized notum Activation at Wounds Inhibits Wnt Function to Promote Planarian Head Regeneration , 2011, Science.

[20]  A. Weisz,et al.  Specific inhibition of NF-Y subunits triggers different cell proliferation defects , 2011, Nucleic acids research.

[21]  M. Mann,et al.  System-Wide Temporal Characterization of the Proteome and Phosphoproteome of Human Embryonic Stem Cell Differentiation , 2011, Science Signaling.

[22]  J. Abril,et al.  A proteomics approach to decipher the molecular nature of planarian stem cells , 2011, BMC Genomics.

[23]  Joanna Rowsell,et al.  A Dual Platform Approach to Transcript Discovery for the Planarian Schmidtea Mediterranea to Establish RNAseq for Stem Cell and Regeneration Biology , 2010, PloS one.

[24]  Sean M. Grimmond,et al.  The uniqueome: a mappability resource for short-tag sequencing , 2010, Bioinform..

[25]  P. Newmark,et al.  A functional genomic screen in planarians identifies novel regulators of germ cell development. , 2010, Genes & development.

[26]  Joshua D. Meisel,et al.  The Mi-2-like Smed-CHD4 gene is required for stem cell differentiation in the planarian Schmidtea mediterranea , 2010, Development.

[27]  H. Schöler,et al.  Smed-SmB, a member of the LSm protein superfamily, is essential for chromatoid body organization and planarian stem cell proliferation , 2010, Development.

[28]  A. Aboobaker,et al.  The TALE Class Homeobox Gene Smed-prep Defines the Anterior Compartment for Head Regeneration , 2010, PLoS genetics.

[29]  A. Lena,et al.  An RbAp48-like gene regulates adult stem cells in planarians , 2010, Journal of Cell Science.

[30]  A. MacLeod,et al.  Digital gene expression analysis of two life cycle stages of the human-infective parasite, Trypanosoma brucei gambiense reveals differentially expressed clusters of co-regulated genes , 2010, BMC Genomics.

[31]  Bret J. Pearson,et al.  A planarian p53 homolog regulates proliferation and self-renewal in adult stem cell lineages , 2010, Development.

[32]  Colin N. Dewey,et al.  RNA-Seq gene expression estimation with read mapping uncertainty , 2009, Bioinform..

[33]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[34]  David I. Smith,et al.  3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer , 2009, BMC Genomics.

[35]  P. Meinicke.  UFO: a web server for ultra-fast functional profiling of whole genome protein sequences , 2009, BMC Genomics.

[36]  David J. Forsthoefel,et al.  Emerging patterns in planarian regeneration. , 2009, Current opinion in genetics & development.

[37]  Wendy S. Beane,et al.  Regeneration: The origin of cancer or a possible cure? , 2009, Seminars in cell & developmental biology.

[38]  A. Oshlack,et al.  Transcript length bias in RNA-seq data confounds systems biology , 2009, Biology Direct.

[39]  A. S. Knight,et al.  A Lin-9 complex is recruited by B-Myb to activate transcription of G2/M genes in undifferentiated embryonal carcinoma cells , 2009, Oncogene.

[40]  L. Tang,et al.  Gene expression profile analysis of human hepatocellular carcinoma using SAGE and LongSAGE , 2009, BMC Medical Genomics.

[41]  Enrique Blanco,et al.  Coordinate control of synaptic-layer specificity and rhodopsins in photoreceptor neurons , 2008, Nature.

[42]  P. Reddien,et al.  Gene nomenclature guidelines for the planarian Schmidtea mediterranea , 2008, Developmental dynamics : an official publication of the American Association of Anatomists.

[43]  R. Vossen,et al.  Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms , 2008, Nucleic acids research.

[44]  Wing Hung Wong,et al.  SeqMap: mapping massive amount of oligonucleotides to the genome , 2008, Bioinform..

[45]  A. Sánchez Alvarado,et al.  Molecular analysis of stem cells and their descendants during cell turnover and regeneration in the planarian Schmidtea mediterranea. , 2008, Cell stem cell.

[46]  Jeong Hoon Kim,et al.  CCAR1, a key regulator of mediator complex recruitment to nuclear receptor transcription complexes. , 2008, Molecular cell.

[47]  N. Kreshchenko.  Functions of Flatworm Neuropeptides NPF, GYIRF and FMRF in Course of Pharyngeal Regeneration of Anterior Body Fragments of Planarian, Girardia tigrina , 2008, Acta biologica Hungarica.

[48]  M. Robles,et al.  University of Birmingham High throughput functional annotation and data mining with the Blast2GO suite , 2022 .

[49]  Teresa Adell,et al.  Silencing of Smed-βcatenin1 generates radial-like hypercephalized planarians , 2008, Development.

[50]  P. Reddien,et al.  Smed-βcatenin-1 Is Required for Anteroposterior Blastema Polarity in Planarian Regeneration , 2008, Science.

[51]  Jochen C. Rink,et al.  β-Catenin Defines Head Versus Tail Identity During Planarian Regeneration and Homeostasis , 2008, Science.

[52]  Sofia M. C. Robb,et al.  MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. , 2007, Genome research.

[53]  F. Cebrià.  Regenerating the central nervous system: how easy for planarians! , 2007, Development Genes and Evolution.

[54]  E. Saló,et al.  The BMP pathway is essential for re-specification and maintenance of the dorsoventral axis in regenerating and intact planarians. , 2007, Developmental biology.

[55]  S. Rowland-Jones,et al.  Deep analysis of cellular transcriptomes – LongSAGE versus classic MPSS , 2007, BMC Genomics.

[56]  Sofia M. C. Robb,et al.  SmedGD: the Schmidtea mediterranea genome database , 2007, Nucleic Acids Res..

[57]  Krishanu Mukherjee,et al.  Comprehensive Analysis of Animal TALE Homeobox Genes: New Conserved Motifs and Cases of Accelerated Evolution , 2007, Journal of Molecular Evolution.

[58]  Tingxi Guo,et al.  Regeneration and maintenance of the planarian midline is regulated by a slit orthologue. , 2007, Developmental biology.

[59]  K. Agata,et al.  Regeneration‐dependent conditional gene knockdown (Readyknock) in planarian: Demonstration of requirement for Djsnap‐25 expression in the brain for negative phototactic behavior , 2007, Development, growth & differentiation.

[60]  Olivier Gandrillon,et al.  Unexpected observations after mapping LongSAGE tags to the human genome , 2007, BMC Bioinformatics.

[61]  Erik L. L. Sonnhammer,et al.  Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server , 2007, Nucleic Acids Res..

[62]  F. Marincola,et al.  Deciphering the molecular machinery of stem cells: a look at the neoblast gene expression profile , 2007, Genome Biology.

[63]  E. Saló,et al.  The planarian nanos-like gene Smednos is expressed in germline and eye precursor cells during development and regeneration , 2007, Development Genes and Evolution.

[64]  W Brad Barbazuk,et al.  Gene discovery and annotation using LCM-454 transcriptome sequencing. , 2006, Genome research.

[65]  Tetsutaro Hayashi,et al.  Isolation of planarian X‐ray‐sensitive stem cells by fluorescence‐activated cell sorting , 2006, Development, growth & differentiation.

[66]  Antoine H. F. M. Peters,et al.  A Bruno-like gene is required for stem cell maintenance in planarians. , 2006, Developmental cell.

[67]  E. Saló.  The power of regeneration and the stem-cell kingdom: freshwater planarians (Platyhelminthes). , 2006, BioEssays : news and reviews in molecular, cellular and developmental biology.

[68]  B. Habermann,et al.  The planarian Schmidtea mediterranea as a model for epigenetic germ cell specification: analysis of ESTs from the hermaphroditic strain. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[69]  Peter W. Reddien,et al.  SMEDWI-2 Is a PIWI-Like Protein That Regulates Planarian Stem Cells , 2005, Science.

[70]  R. Zayas,et al.  Spliced-leader trans-splicing in freshwater planarians. , 2005, Molecular biology and evolution.

[71]  Jiang Zhu,et al.  NF-Ya activates multiple hematopoietic stem cell (HSC) regulatory genes and promotes HSC self-renewal. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[72]  F. Cebrià,et al.  Planarian homologs of netrin and netrin receptor are required for proper regeneration of the central nervous system and the maintenance of nervous system architecture , 2005, Development.

[73]  W. Gehring,et al.  New perspectives on eye development and the evolution of eyes and photoreceptors. , 2005, The Journal of heredity.

[74]  Adam L. Bermange,et al.  Identification of genes needed for regeneration, stem cell function, and tissue homeostasis by systematic gene perturbation in planaria. , 2005, Developmental cell.

[75]  Ewan Birney,et al.  Automated generation of heuristics for biological sequence comparison , 2005, BMC Bioinformatics.

[76]  Serena J Silver,et al.  Signaling circuitries in development: insights from the retinal determination gene network , 2004, Development.

[77]  P. Reddien,et al.  Fundamentals of planarian regeneration. , 2004, Annual review of cell and developmental biology.

[78]  V. Gremigni,et al.  Erratum to “Djeyes absent (Djeya) controls prototypic planarian eye regeneration by cooperating with the transcription factor Djsix-1” [Dev. Biol. 269 (2004) 346–359] , 2004 .

[79]  V. Gremigni,et al.  Djeyes absent (Djeya) controls prototypic planarian eye regeneration by cooperating with the transcription factor Djsix-1. , 2004, Developmental biology.

[80]  K. Agata,et al.  Morphological and Functional Recovery of the Planarian Photosensing System during Head Regeneration , 2004, Zoological science.

[81]  Guo-Liang Wang,et al.  Robust-LongSAGE (RL-SAGE): A Substantially Improved LongSAGE Method for Gene Discovery and Transcriptome Analysis1[w] , 2004, Plant Physiology.

[82]  R. Guigó,et al.  Reconsidering the evolution of eukaryotic selenoproteins: a novel nonmammalian family with scattered phylogenetic distribution , 2004, EMBO reports.

[83]  J. Deng,et al.  The B subunit of the CCAAT box binding transcription factor complex (CBF/NF-Y) is essential for early mouse development and cell proliferation. , 2003, Cancer research.

[84]  Marco A Marra,et al.  Assessment of SAGE in transcript identification. , 2003, Genome research.

[85]  P. Unneberg,et al.  Transcript identification by analysis of short sequence tags—influence of tag length, restriction site and transcript database , 2002 .

[86]  Y. Saitoh,et al.  Intercalary regeneration in planarians , 2003, Developmental dynamics : an official publication of the American Association of Anatomists.

[87]  Alejandro Sánchez Alvarado,et al.  Allometric scaling and proportion regulation in the freshwater planarian Schmidtea mediterranea , 2003, Developmental dynamics : an official publication of the American Association of Anatomists.

[88]  Phillip A. Newmark,et al.  The Schmidtea mediterranea database as a molecular resource for studying platyhelminthes, stem cells and regeneration , 2002, Development.

[89]  J. Rowley,et al.  Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[90]  L. Manchon,et al.  Transcriptome analysis of monocytic leukemia cell differentiation. , 2002, Genomics.

[91]  J. Baguñá,et al.  Regeneration in planarians and other worms: New findings, new tools, and new perspectives. , 2002, The Journal of experimental zoology.

[92]  A. Sparks,et al.  Using the transcriptome to annotate the genome , 2002, Nature Biotechnology.

[93]  V. Gremigni,et al.  Genetic network of the eye in Platyhelminthes: expression and functional analysis of some players during planarian regeneration. , 2002, Gene.

[94]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[95]  V. Gremigni,et al.  The genetic network of prototypic planarian eye regeneration is Pax6 independent. , 2002, Development.

[96]  Phillip A. Newmark,et al.  Not your father's planarian: a classic model enters the era of functional genomics , 2002, Nature Reviews Genetics.

[97]  J. Baguñá,et al.  Effects of activators and antagonists of the neuropeptides substance P and substance K on cell proliferation in planarians. , 2002, The International journal of developmental biology.

[98]  D. Hatfield,et al.  "Selenium: Its Molecular Biology and Role in Human Health" , 2002 .

[99]  J. Garcia-Fernández,et al.  Hox and ParaHox Genes in Flatworms: Characterization and Expression1 , 2001 .

[100]  T. Nogi,et al.  Position‐specific and non‐colinear expression of the planarian posterior (Abdominal‐B‐like) gene , 2001, Development, growth & differentiation.

[101]  O. Cuvier,et al.  Chromosome Condensation by a Human Condensin Complex inXenopus Egg Extracts* , 2001, The Journal of Biological Chemistry.

[102]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[103]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[104]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[105]  K. Ikeo,et al.  Searching for the prototypic eye genetic network: Sine oculis is essential for eye regeneration in planarians. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[106]  A. Sánchez Alvarado,et al.  Bromodeoxyuridine specifically labels the regenerative stem cells of planarians. , 2000, Developmental biology.

[107]  Yusuke Nakamura,et al.  A ribonucleotide reductase gene involved in a p53-dependent cell-cycle checkpoint for DNA damage , 2000, Nature.

[108]  J. Treisman.  A conserved blueprint for the eye? , 1999, BioEssays : news and reviews in molecular, cellular and developmental biology.

[109]  K Ikeo,et al.  Pax 6: mastering eye morphogenesis and eye evolution. , 1999, Trends in genetics : TIG.

[110]  K. Watanabe,et al.  The planarian HOM/HOX homeobox genes (Plox) expressed along the anteroposterior axis. , 1999, Developmental biology.

[111]  A. Sánchez Alvarado,et al.  Double-stranded RNA specifically disrupts gene expression during planarian regeneration. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[112]  T. Rossman,et al.  Expression cloning for arsenite-resistance resulted in isolation of tumor-suppressor fau cDNA: possible involvement of the ubiquitin system in arsenic carcinogenesis. , 1999, Carcinogenesis.

[113]  J. Bayascas,et al.  Platyhelminthes have a Hox code differentially activated during regeneration, with genes closely related to those of spiralian protostomes , 1998, Development Genes and Evolution.

[114]  J. Hintze,et al.  Violin plots : A box plot-density trace synergism , 1998 .

[115]  A. Amsterdam,et al.  Insertional mutagenesis in zebrafish identifies two novel genes, pescadillo and dead eye, essential for embryonic development. , 1996, Genes & development.

[116]  E. Bertolino,et al.  A Novel Homeobox Protein Which Recognizes a TGT Core and Functionally Interferes with a Retinoid-responsive Motif (*) , 1995, The Journal of Biological Chemistry.

[117]  M. Boguski,et al.  dbEST — database for “expressed sequence tags” , 1993, Nature Genetics.

[118]  J. Garcia-Fernández,et al.  Planarian homeobox genes: cloning, sequence analysis, and expression. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[119]  C. Goodman,et al.  Cloning of a grasshopper cDNA coding for a protein homologous to the A1, A2/B1 proteins of mammalian hnRNP. , 1991, Nucleic acids research.

[120]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[121]  M. Sheffery,et al.  Physical characterization of the purified CCAAT transcription factor, alpha-CP1. , 1990, The Journal of biological chemistry.

[122]  J. Baguñá,et al.  Regeneration and pattern formation in planarians. III. that neoblasts are totipotent stem cells and the cells , 1989 .

[123]  G. Karsenty,et al.  Selective activation of transcription by a novel CCAAT binding factor. , 1988, Science.

[124]  E. Van Schaftingen,et al.  A CCAAT DNA binding factor consisting of two different components that are both required for DNA binding. , 1988, The Journal of biological chemistry.

[125]  C. Benoist,et al.  Properties of a CCAAT box-binding protein. , 1987, Nucleic acids research.

[126]  A. Bautz,et al.  Somatostatin-like peptide and regeneration capacities in planarians. , 1986, General and comparative endocrinology.

[127]  I. Martelly,et al.  Effects of serotonin and catecholamines on RNA synthesis in planarians; in vitro and in vivo studies. , 1981, Cell differentiation.

[128]  Par Raphaël Franquinet.  Rôle de la sérotonine et des catécholamines dans la régénération de la planaire Polycelis tenuis , 1979 .

[129]  J. Hanoune,et al.  The adenylate cyclase system of planaria Polycelis tenuis: activation by serotonin and guanine nucleotides. , 1978, Biochimica et biophysica acta.

[130]  Phillip A. Newmark,et al.  PRMT5 and the role of symmetrical dimethylarginine in chromatoid bodies of planarian stem cells , 2012, Development.

[131]  Robert Fredriksson,et al.  Mapping the human membrane proteome : a majority of the human membrane proteins can be classified according to function and evolutionary origin , 2015 .

[132]  E. Saló,et al.  The planarian eye: a simple and plastic system with great regenerative capacity , 2008 .

[133]  P. Wincker,et al.  A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome , 2008, BMC Genomics.

[134]  Bret J. Pearson,et al.  Regeneration, stem cells, and the evolution of tumor suppression. , 2008, Cold Spring Harbor symposia on quantitative biology.

[135]  Bastien Chevreux.  MIRA: An Automated Genome and EST Assembler , 2007 .

[136]  Mamoun Ahram,et al.  Estimation of Membrane Proteins in the Human Proteome , 2006, Silico Biol..

[137]  Gang Wang,et al.  ConiferEST: an integrated bioinformatics system for data reprocessing and mining of conifer expressed sequence tags (ESTs) , 2007, BMC Genomics.

[138]  J. Baguñá,et al.  Regeneration and pattern formation in planarians III . Evidence that neoblasts are totipotent stem cells and the source of blastema cells , 2005 .

[139]  R. Guigó,et al.  Comparison of splice sites in mammals and chicken. , 2005, Genome research.

[140]  Brian P. Dalrymple,et al.  A rapid method for computationally inferring transcriptome coverage and microarray sensitivity , 2005, Bioinform..

[141]  L. Wagner,et al.  21. UniGene: A Unified View of the Transcriptome , 2003 .

[142]  Shigeki Mitaku,et al.  SOSUI: classification and secondary structure prediction system for membrane proteins , 1998, Bioinform..

[143]  R. Franquinet.  [The role of serotonin and catecholamines in the regeneration of the Planaria Polycelis tenvis]. , 1979, Journal of embryology and experimental morphology.

[144]  F. Dubois,et al.  Sur la migration des cellules de régénération chez les Planaires , 1948 .