Reddien PW. Specialized progenitors and regeneration. Development. 2013; 140(5):951–7.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rink J. Stem cell systems and regeneration in planaria. Dev Genes Evol. 2013; 223(1-2):67–84.
Article
PubMed Central
PubMed
Google Scholar
Elliott S, Sánchez Alvarado A. The history and enduring contributions of planarians to the study of animal regeneration. Rev Dev Biol. 2013; 2(3):301–26.
CAS
Google Scholar
Baguñà J. The planarian neoblast: the rambling history of its origin and some current black boxes. Int J Dev Biol. 2012; 56(1-3):19–37.
Article
PubMed
Google Scholar
Sánchez Alvarado A, Newmark PA. Double-stranded RNA specifically disrupts gene expression during planarian regeneration. Proc Natl Acad Sci USA. 1999; 96(9):5049–54.
Article
PubMed Central
PubMed
Google Scholar
Reddien PW, Bermange AL, Murfitt KJ, Jennings JR, Sánchez Alvarado A. Identification of genes needed for regeneration, stem cell function, and tissue homeostasis by systematic gene perturbation in planaria. Dev Cell. 2005; 8(5):635–49.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rossi L, Salvetti A, Marincola FM, Lena A, Deri P, Mannini L, et al. Deciphering the molecular machinery of stem cells: a look at the neoblast gene expression profile. Genome Biol. 2007; 8(4):62.
Fernández-Taboada E, Rodríguez-Esteban G, Saló E, Abril JF. A proteomics approach to decipher the molecular nature of planarian stem cells. BMC Genomics. 2011; 12:133.
Böser A, Drexler HC, Reuter H, Schmitz H, Wu G, Schöler HR, et al. SILAC proteomics of planarians identifies ncoa5 as a conserved component of pluripotent stem cells. Cell Reports. 2013; 5(4):1142–55.
Article
PubMed
Google Scholar
Abril JF, Cebrià F, Rodríguez-Esteban G, Horn T, Fraguas S, Calvo B, et al. Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea. BMC Genomics. 2010; 11(1):731.
Blythe MJ, Kao D, Malla S, Rowsell J, Wilson R, Evans D, et al. A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology. PLoS One. 2010; 5(12):15617.
Adamidi C, Wang Y, Gruen D, Mastrobuoni G, You X, Tolle D, et al. De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics. Genome Res. 2011; 21(7):1193–200.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sandmann T, Vogg MC, Owlarn S, Boutros M, Bartscherer K. The head-regeneration transcriptome of the planarian Schmidtea mediterranea. Genome Biol. 2011; 12(8):76.
Labbé RM, Irimia M, Currie KW, Lin A, Zhu SJ, Brown DD, et al. A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals. Stem Cells. 2012; 30(8):1734–45.
Article
PubMed Central
PubMed
Google Scholar
Resch AM, Palakodeti D, Lu YC, Horowitz M, Graveley BR. Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea. PLoS One. 2012; 7(4):34447.
Rouhana L, Vieira AP, Roberts-Galbraith RH, Newmark PA. PRMT5 and the role of symmetrical dimethylarginine in chromatoid bodies of planarian stem cells. Development. 2012; 139(6):1083–94.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kao D, Felix D, Aboobaker A. The planarian regeneration transcriptome reveals a shared but temporally shifted regulatory program between opposing head and tail scenarios. BMC Genomics. 2013; 16(14):797.
Solana J, Kao D, Mihaylova Y, Jaber-Hijazi F, Malla S, Wilson R, et al. Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNAseq, RNA interference and irradiation approach. Genome Biol. 2012; 13(3):19.
Scimone M, Kravarik K, Lapan S, Reddien P. Neoblast specialization in regeneration of the planarian Schmidtea mediterranea. Stem Cell R. 2014; 3(2):339–52.
Article
CAS
Google Scholar
Oshlack A, Wakefield MJ. Transcript length bias in RNA-seq data confounds systems biology. Biol Direct. 2009; 4:14.
Raz T, Kapranov P, Lipson D, Letovsky S, Milos PM, Thompson JF. Protocol dependence of sequencing-based gene expression measurements. PLoS One. 2011; 6(5):19287.
Hong LZ, Li J, Schmidt-Kuntzel A, Warren WC, Barsh GS. Digital gene expression for non-model organisms. Genome Res. 2012; 21(11):1905–15.
Article
Google Scholar
Hanriot L, Keime C, Gay N, Faure C, Dossat C, Wincker P, et al. A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome. BMC Genomics. 2008; 16(9):418.
Veitch NJ, Johnson PC, Trivedi U, Terry S, Wildridge D, MacLeod A. 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. BMC Genomics. 2010; 11(1):124.
’t Hoen PAC, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RHAM, de Menezes RX, et al. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res. 2008; 36(21):141.
Asmann YW, Klee EW, Thompson EA, Perez EA, Middha S, Oberg AL, et al. 3’ tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer. BMC Genomics. 2009; 10(1):531.
de Lorgeril J, Zenagui R, Rosa RD, Piquemal D, Bachère E. Whole transcriptome profiling of successful immune response to vibrio infections in the oyster Crassostrea gigas by digital gene expression analysis. PLoS ONE. 2011; 6(8):23142.
Philippe N, Bou Samra E, Boureux A, Mancheron A, Ruffle F, Bai Q, et al. Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome. Nucleic Acids Res. 2014; 42(5):2820–32.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dong H, Ge X, Shen Y, Chen L, Kong Y, Zhang H, et al. Gene expression profile analysis of human hepatocellular carcinoma using SAGE and LongSAGE. BMC Med Genomics. 2009; 2(1):5.
Hayashi T, Asami M, Higuchi S, Shibata N, Agata K. Isolation of planarian X-ray-sensitive stem cells by fluorescence-activated cell sorting. Dev Growth Differ. 2006; 48(6):371–80.
Article
PubMed
Google Scholar
Moritz S, Stöckle F, Ortmeier C, Schmitz H, Rodríguez-Esteban G, Key G, et al. Heterogeneity of planarian stem cells in the S/G2/M phase. Int J Dev Biol. 2012; 56(1-3):117–25.
Article
CAS
PubMed
Google Scholar
Mukherjee K, Bürglin TR. Comprehensive analysis of animal TALE homeobox genes: new conserved motifs and cases of accelerated evolution. J Mol Evol. 2007; 65(2):137–53.
Article
CAS
PubMed
Google Scholar
Bhattacharya A, Deng J, Zhang Z, Behringer R, de Crombrugghe B, Maity S. The B subunit of the CCAAT box binding transcription factor complex (CBF/NF-Y) is essential for early mouse development and cell proliferation. Cancer Res. 2003; 63(23):8167–72.
CAS
PubMed
Google Scholar
Zhang X, Hao L, Meng L, Liu M, Zhao L, Hu F, et al. Digital Gene Expression tag profiling analysis of the gene expression patterns regulating the early stage of mouse spermatogenesis. PLoS ONE. 2013; 8(3):58680.
Gowda M, Jantasuriyarat C, Dean RA, Wang GL. Robust-LongSAGE (RL-SAGE): a substantially improved LongSAGE method for gene discovery and transcriptome analysis. Plant Physiol. 2004; 134(3):890–7.
Article
PubMed Central
CAS
PubMed
Google Scholar
Galloni M. Global irradiation effects, stem cell genes and rare transcripts in the planarian transcriptome. Int J Dev Biol. 2012; 56(1-3):103–16.
Article
CAS
PubMed
Google Scholar
Taft A, Vermeire J, Bernier J, Birkeland S, Cipriano M, Papa A, et al. Transcriptome analysis of Schistosoma mansoni larval development using serial analysis of gene expression (SAGE). Parasitology. 2009; 136(05):469.
Pelechano V, Steinmetz L. Gene regulation by antisense transcription. Nat Rev Genet. 2013; 14(12):880–93.
Article
CAS
PubMed
Google Scholar
Boguski MS, Lowe TMJ, Tolstoshev CM. dbEST - database for “expressed sequence tags”. Nat Genet. 1993; 4(4):332–3.
Article
CAS
PubMed
Google Scholar
Sánchez Alvarado A, Newmark PA, Robb SM, Juste R. The Schmidtea mediterranea database as a molecular resource for studying platyhelminthes, stem cells and regeneration. Development. 2002; 129(24):5659–65.
Article
PubMed
Google Scholar
Zayas RM, Bold TD, Newmark PA. Spliced-leader trans-splicing in freshwater planarians. Mol Biol Evol. 2005; 22(10):2048–54.
Article
CAS
PubMed
Google Scholar
Zayas RM, Hernández A, Habermann B, Wang Y, Stary JM, Newmark PA. The planarian Schmidtea mediterranea as a model for epigenetic germ cell specification: analysis of ESTs from the hermaphroditic strain. Proc Natl Acad Sci U S A. 2005; 102(51):18491–6.
Article
PubMed Central
CAS
PubMed
Google Scholar
The Schmidtea mediterranea Genome Sequencing Project. http://genome.wustl.edu/genomes/detail/schmidtea-mediterranea.
NCBI Genome Database: Schmidtea mediterranea. http://www.ncbi.nlm.nih.gov/genome/232.
Reverter A, McWilliam S, Barris W, Dalrymple B. A rapid method for computationally inferring transcriptome coverage and microarray sensitivity. Bioinformatics. 2004; 21(1):80–9.
Article
PubMed
Google Scholar
Saha S, Sparks A, Rago C, Akmaev V, Wang C, Vogelstein B, et al. Using the transcriptome to annotate the genome. Nat Biotechnol. 2002; 20(5):508–12.
Article
CAS
PubMed
Google Scholar
Chen J, Sun M, Lee S, Zhou G, Rowley J, Wang S. Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc Natl Acad Sci U S A. 2002; 99(19):12257–62.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pleasance E, Marra M, Jones S. Assessment of SAGE in transcript identification. Genome Res. 2003; 13(6):1203–15.
Article
PubMed Central
CAS
PubMed
Google Scholar
Keime C, Sémon M, Mouchiroud D, Duret L, Gandrillon O. Unexpected observations after mapping LongSAGE tags to the human genome. BMC Bioinf. 2007; 8(1):154.
Hene L, Sreenu V, Vuong M, Abidi S, Sutton J, Rowland-Jones S, et al. Deep analysis of cellular transcriptomes-LongSAGE versus classic MPSS. BMC Genomics. 2007; 8(1):333.
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinf. 2009; 10(1):421.
Smed, 454 Contig Browser. https://planarian.bio.ub.edu/datasets/454/planarian_menu.php.
Eisenhoffer G, Kang H, Sánchez Alvarado A. Molecular analysis of stem cells and their descendants during cell turnover and regeneration in the planarian Schmidtea mediterranea. Cell Stem Cell. 2008; 3(3):327–39.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lapan S, Reddien P. Transcriptome analysis of the planarian eye identifies ovo as a specific regulator of eye regeneration. Cell Rep. 2012; 2(2):294–307.
Article
PubMed Central
CAS
PubMed
Google Scholar
González-Estévez C, Felix DA, Smith MD, Paps J, Morley SJ, James V, et al. SMG-1 and mTORC1 act antagonistically to regulate response to injury and growth in planarians. PLoS Genet. 2012; 8(3):1002619.
Wenemoser D, Lapan SW, Wilkinson AW, Bell GW, Reddien PW. A molecular wound response program associated with regeneration initiation in planarians. Genes Dev. 2012; 26(9):988–1002.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wolff E, Dubois F. Sur la migration des cellules de regeneration chez les planaires. Rev Suisse Zool. 1948; 55:218–27.
Google Scholar
Reddien P, Oviedo N, Jennings J, Jenkin J, Sánchez Alvarado A. SMEDWI-2 is a PIWI-Like protein that regulates planarian stem cells. Science. 2005; 310(5752):1327–30.
Article
CAS
PubMed
Google Scholar
Guo T, Peters A, Newmark P. A Bruno-like gene is required for stem cell maintenance in planarians. Dev Cell. 2006; 11(2):159–69.
Article
CAS
PubMed
Google Scholar
Kim JH, Yang CK, Heo K, Roeder RG, An W, Stallcup MR. CCAR1, a key regulator of mediator complex recruitment to nuclear receptor transcription complexes. Mol Cell. 2008; 31(4):510–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ball EE, Rehm EJ, Goodman CS. Cloning of a grasshopper cDNA coding for a protein homologous to the A1, A2/B1 proteins of mammalian hnRNP. Nucleic Acids Res. 1991; 19(2):397.
Rigbolt KTG, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, et al. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. Sci Signal. 2011; 4(164):3.
Rossman T, Wang Z. Expression cloning for arsenite-resistance resulted in isolation of tumor-suppressor fau cdna: possible involvement of the ubiquitin system in arsenic carcinogenesis. Carcinogenesis. 1999; 20(2):311–6.
Article
CAS
PubMed
Google Scholar
Kimura K, Cuvier O, Hirano T. Chromosome condensation by a human condensin complex in Xenopus egg extracts. J Biol Chem. 2001; 276(8):5417–20.
Article
CAS
PubMed
Google Scholar
Allende ML, Amsterdam A, Becker T, Kawakami K, Gaiano N, Hopkins N. Insertional mutagenesis in zebrafish identifies two novel genes, pescadillo and dead eye, essential for embryonic development. Genes Dev. 1996; 10(24):3141–55.
Article
CAS
PubMed
Google Scholar
Knight AS, Notaridou M, Watson RJ. A Lin-9 complex is recruited by B-Myb to activate transcription of G2/M genes in undifferentiated embryonal carcinoma cells. Oncogene. 2009; 28(15):1737–47.
Article
CAS
PubMed
Google Scholar
Zhu SJ, Pearson BJ. The Retinoblastoma pathway regulates stem cell proliferation in freshwater planarians. Dev Biol. 2013; 373(2):442–52.
Article
CAS
PubMed
Google Scholar
Nakamura Y, Tanaka H, Arakawa H, Yamaguchi T, Shiraishi K, Fukuda S, et al. A ribonucleotide reductase gene involved in a p53-dependent cell-cycle checkpoint for DNA damage. Nature. 2000; 404(6773):42–9.
Article
PubMed
Google Scholar
Bertolino E, Reimund B, Wildt-Perinic D, Clerc RG. A novel homeobox protein which recognizes a TGT core and functionally interferes with a retinoid-responsive motif. J Biol Chem. 1995; 270(52):31178–88.
Article
CAS
PubMed
Google Scholar
Felix DA, Aboobaker AA. The TALE class homeobox gene Smed-prep defines the anterior compartment for head regeneration. PLoS Genet. 2010; 6(4):1000915.
Chen CC, Wang IE, Reddien PW. pbx is required for pole and eye regeneration in planarians. Development. 2013; 140(4):719–29.
Article
PubMed Central
CAS
PubMed
Google Scholar
Blassberg RA, Felix DA, Tejada-Romero B, Aboobaker AA. PBX/extradenticle is required to re-establish axial structures and polarity during planarian regeneration. Development. 2013; 140(4):730–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fraguas S, Barberán S, Cebrià F. EGFR signaling regulates cell proliferation, differentiation and morphogenesis during planarian regeneration and homeostasis. Dev Biol. 2011; 354(1):87–101.
Article
CAS
PubMed
Google Scholar
Iglesias M, Almuedo-Castillo M, Aboobaker AA, Saló E. Early planarian brain regeneration is independent of blastema polarity mediated by the Wnt/ β-catenin pathway. Dev Biol. 2011; 358(1):68–78.
Article
CAS
PubMed
Google Scholar
Petersen CP, Reddien PW. Polarized notum activation at wounds inhibits wnt function to promote planarian head regeneration. Science. 2011; 332(6031):852–5.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gurley KA, Rink JC, Sánchez Alvarado A. Beta-catenin defines head versus tail identity during planarian regeneration and homeostasis. Science. 2008; 319(5861):323–7.
Article
PubMed Central
CAS
PubMed
Google Scholar
Petersen C, Reddien P. Smed-betacatenin-1 is required for anteroposterior blastema polarity in planarian regeneration. Science. 2008; 319(5861):327–30.
Article
CAS
PubMed
Google Scholar
Oviedo NJ, Newmark PA, Sánchez Alvarado A. Allometric scaling and proportion regulation in the freshwater planarian Schmidtea mediterranea. Dev Dyn. 2003; 226(2):326–33.
Article
CAS
PubMed
Google Scholar
Fraguas S, Barberán S, Iglesias M, Rodríguez-Esteban G, Cebrià F. egr-4, a target of EGFR signaling, is required for the formation of the brain primordia and head regeneration in planarians. Development. 2014; 141(9):1835–47.
Article
CAS
PubMed
Google Scholar
Vogg MC, Owlarn S, Pérez Rico YA, Xie J, Suzuki Y, Gentile L, et al. Stem cell-dependent formation of a functional anterior regeneration pole in planarians requires Zic and Forkhead transcription factors. Dev Biol. 2014; 390(2):136–48.
Article
CAS
PubMed
Google Scholar
Vásquez-Doorman C, Petersen CP. zic-1 expression in planarian neoblasts after injury controls anterior pole regeneration. PLoS Genet. 2014; 10(7):1004452.
Scimone ML, Lapan SW, Reddien PW. A forkhead transcription factor is wound-induced at the planarian midline and required for anterior pole regeneration. PLoS Genet. 2014; 10(1):1003999.
González-Sastre A, Molina MD, Saló E. Inhibitory Smads and bone morphogenetic protein (BMP) modulate anterior photoreceptor cell number during planarian eye regeneration. Int J Dev Biol. 2012; 56(1-2-3):155–63.
Article
PubMed
Google Scholar
Dolfini D, Mantovani R. Targeting the Y/CCAAT box in cancer: YB-1 (YBX1) or NF-Y?Cell Death Differ. 2013; 20(5):676–85.
Article
PubMed Central
CAS
PubMed
Google Scholar
Maity S, Golumbek P, Karsenty G, de Crombrugghe B. Selective activation of transcription by a novel CCAAT binding factor. Science. 1988; 241(4865):582–5.
Article
CAS
PubMed
Google Scholar
Hatamochi A, Golumbek P, Van Schaftingen E, de Crombrugghe B. A CCAAT DNA binding factor consisting of two different components that are both required for DNA binding. J Biol Chem. 1988; 263(12):5940–7.
CAS
PubMed
Google Scholar
Hooft van Huijsduijnen R, Bollekens J, Dom A, Benoist C, Mathis D. Properties of a CCAAT box-binding protein. Nucleic Acids Res. 1987; 15(18):7265–82.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kim C, Sheffery M. Physical characterization of the purified CCAAT transcription factor, alpha-CP1. J Biol Chem. 1990; 265(22):13362–9.
CAS
PubMed
Google Scholar
Yoshioka Y, Ly L, Yamaguchi M. Transcription factor NF-Y is involved in differentiation of R7 photoreceptor cell in Drosophila. Biol Open. 2012; 1(1):19–29.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ly L, Yoshida H, Yamaguchi M. Nuclear transcription factor y and its roles in cellular processes related to human disease. Am J Cancer Res. 2013; 3(4):339–46.
PubMed Central
PubMed
Google Scholar
Wang Y, Stary J, Wilhelm J, Newmark P. A functional genomic screen in planarians identifies novel regulators of germ cell development. Genes Dev. 2010; 24(18):2081–92.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhu J, Zhang Y, Joe G, Pompetti R, Emerson S. NF-Ya activates multiple hematopoietic stem cell (HSC) regulatory genes and promotes HSC self-renewal. Proc Natl Acad Sci. 2005; 102(33):11728–33.
Article
PubMed Central
CAS
PubMed
Google Scholar
Benatti P, Dolfini D, Viganò A, Ravo M, Weisz A, Imbriano C. Specific inhibition of NF-Y subunits triggers different cell proliferation defects. Nucleic Acids Res. 2011; 39(13):5356–68.
Article
PubMed Central
CAS
PubMed
Google Scholar
van Wolfswinkel J, Wagner D, Reddien P. Single-cell analysis reveals functionally distinct classes within the planarian stem cell compartment. Cell Stem Cell. 2014; 15(3):326–39.
Article
CAS
PubMed
Google Scholar
Unneberg P, Wennborg A, Larsson M. Transcript identification by analysis of short sequence tags-influence of tag length, restriction site and transcript database. Nucleic Acids Res. 2003; 31(8):2217–26.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li B, Ruotti V, Stewart R, Thomson J, Dewey C. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics. 2009; 26(4):493–500.
Article
PubMed Central
PubMed
Google Scholar
Koehler R, Issac H, Cloonan N, Grimmond SM. The uniqueome: a mappability resource for short-tag sequencing. Bioinformatics. 2010; 27(2):272–4.
Article
PubMed Central
PubMed
Google Scholar
Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP. Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet. 2014; 15(2):121–32.
Article
CAS
PubMed
Google Scholar
Morey M, Yee S, Herman T, Nern A, Blanco E, Zipursky SL. Coordinate control of synaptic-layer specificity and rhodopsins in photoreceptor neurons. Nature. 2008; 456(7223):795–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pearson BJ, Sánchez Alvarado A. A planarian p53 homolog regulates proliferation and self-renewal in adult stem cell lineages. Development. 2009; 137(2):213–21.
Article
Google Scholar
Oviedo N, Beane W. Regeneration: the origin of cancer or a possible cure?Semin Cell Dev Biol. 2009; 20(5):557–64.
Article
PubMed Central
PubMed
Google Scholar
Pearson B, Sánchez Alvarado A. Regeneration, stem cells, and the evolution of tumor suppression. Cold Spring Harb Symp Quant Biol. 2008; 73(0):565–72.
Article
CAS
PubMed
Google Scholar
PlanMine. http://planmine.mpi-cbg.de.
Piquemal D, Commes T, Manchon L, Lejeune M, Ferraz C, Pugnère D, et al. Transcriptome analysis of monocytic leukemia cell differentiation. Genomics. 2002; 80(3):361–71.
Article
CAS
PubMed
Google Scholar
Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, et al. NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res. 2013; 41(D1):991–5.
Article
Google Scholar
NCBI Gene Expression Omnibus. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE51681.
The Perl Programming Language. https://www.perl.org.
Jiang H, Wong W. SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics. 2008; 24(20):2395–6.
Article
PubMed Central
CAS
PubMed
Google Scholar
SeqMap - A Tool for Mapping Millions of Short Sequences to the Genome. http://www-personal.umich.edu/~jianghui/seqmap.
Benson D, Clark K, Karsch-Mizrachi I, Lipman D, Ostell J, Sayers E. Genbank. Nucleic Acids Res. 2013; 42(D1):32–7.
Article
Google Scholar
Slater G, Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinf. 2005; 6(1):31.
jQuery jqGrid JavaScript Library. http://plugins.jquery.com/jqGrid.
GBrowse, 2. http://gmod.org/wiki/GBrowse.
Dimmer E, Huntley R, Alam-Faruque Y, Sawford T, O’Donovan C, Martin M, et al. The UniProt-GO Annotation database in 2011. Nucleic Acids Res. 2011; 40(D1):565–70.
Article
Google Scholar
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Res. 2014; 42(D1):222–30.
Article
Google Scholar
Pfam Database of Protein Families. http://pfam.xfam.org.
HMMER: Biosequence Analysis Using Profile Hidden Markov Models. http://hmmer.org.
Reddien PW, Newmark PA, Sánchez Alvarado A. Gene nomenclature guidelines for the planarian Schmidtea mediterranea. Dev Dyn. 2008; 237(11):3099–101.
Article
PubMed
Google Scholar
Gray KA, Daugherty LC, Gordon SM, Seal RL, Wright MW, Bruford EA. Genenames.org: the HGNC resources in 2013. Nucleic Acids Res. 2013; 41(D1):545–52.
Article
Google Scholar
Molina M, Saló E, Cebrià F. The BMP pathway is essential for re-specification and maintenance of the dorsoventral axis in regenerating and intact planarians. Dev Biol. 2007; 311(1):79–94.
Article
CAS
PubMed
Google Scholar
Cebriá F, Guo T, Jopek J, Newmark P. Regeneration and maintenance of the planarian midline is regulated by a slit orthologue. Devel Biol. 2007; 307(2):394–406.
Article
Google Scholar
King R, Newmark P. In situ hybridization protocol for enhanced detection of gene expression in the planarian Schmidtea mediterranea. BMC Dev Biol. 2013; 13(1):8.
Cebrià F, Newmark P. Planarian homologs of netrin and netrin receptor are required for proper regeneration of the central nervous system and the maintenance of nervous system architecture. Development. 2005; 132(16):3691–703.
Article
PubMed
Google Scholar
Cebrià F. Organization of the nervous system in the model planarian Schmidtea mediterranea: an immunocytochemical study. Neurosci Res. 2008; 61(4):375–84.
Article
PubMed
Google Scholar