Paradigm shifts in genomics through the FANTOM projects

[1]  Piero Carninci,et al.  Engineering mammalian cell factories with SINEUP noncoding RNAs to improve translation of secreted proteins. , 2015, Gene.

[2]  Piero Carninci,et al.  Paradigm shifts in genomics through the FANTOM projects , 2015, Mammalian Genome.

[3]  Piero Carninci,et al.  SINEUPs are modular antisense long non-coding RNAs that increase synthesis of target proteins in cells , 2015, Front. Cell. Neurosci..

[4]  Thomas J. Ha,et al.  Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells , 2015, Science.

[5]  S. Dhanasekaran,et al.  The landscape of long noncoding RNAs in the human transcriptome , 2015, Nature Genetics.

[6]  Lukasz Huminiecki,et al.  A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators , 2014, Genome Biology.

[7]  A. Sandelin,et al.  Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance , 2014, Nature Genetics.

[8]  Piotr J. Balwierz,et al.  PHAGOCYTES, GRANULOCYTES, AND MYELOPOIESIS Transcription and enhancer pro fi ling in human monocyte subsets , 2022 .

[9]  Piero Carninci,et al.  Redefinition of the human mast cell transcriptome by deep-CAGE sequencing. , 2014, Blood.

[10]  A. Sandelin,et al.  Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation. , 2014, Blood.

[11]  Piero Carninci,et al.  Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing , 2014, Genome research.

[12]  Hai Fang,et al.  The Evolution of Human Cells in Terms of Protein Innovation , 2014, Molecular biology and evolution.

[13]  Piero Carninci,et al.  Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation , 2014, Proceedings of the National Academy of Sciences.

[14]  Cesare Furlanello,et al.  A promoter-level mammalian expression atlas , 2015 .

[15]  T. Meehan,et al.  An atlas of active enhancers across human cell types and tissues , 2014, Nature.

[16]  Yoshihide Hayashizaki,et al.  Interactive visualization and analysis of large-scale sequencing datasets using ZENBU , 2014, Nature Biotechnology.

[17]  Philipp Kapranov,et al.  VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer , 2013, Genome Biology.

[18]  David R. Kelley,et al.  Transposable elements reveal a stem cell-specific class of long noncoding RNAs , 2012, Genome Biology.

[19]  Piero Carninci,et al.  Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat , 2012, Nature.

[20]  Nadav S. Bar,et al.  Landscape of transcription in human cells , 2012, Nature.

[21]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

[22]  Jay W. Shin,et al.  Establishment of single-cell screening system for the rapid identification of transcriptional modulators involved in direct cell reprogramming , 2012, Nucleic acids research.

[23]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[24]  Jay W. Shin,et al.  Reconstruction of Monocyte Transcriptional Regulatory Network Accompanies Monocytic Functions in Human Fibroblasts , 2012, PloS one.

[25]  A. Sandelin,et al.  Metazoan promoters: emerging characteristics and insights into transcriptional regulation , 2012, Nature Reviews Genetics.

[26]  Piero Carninci,et al.  5′ end–centered expression profiling using cap-analysis gene expression and next-generation sequencing , 2012, Nature Protocols.

[27]  Mikhail Pachkov,et al.  MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences , 2012, Bioinform..

[28]  Piero Carninci,et al.  Automated Workflow for Preparation of cDNA for Cap Analysis of Gene Expression on a Single Molecule Sequencer , 2012, PloS one.

[29]  Howard Y. Chang,et al.  Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. , 2011, Molecular cell.

[30]  Howard Y. Chang,et al.  Molecular mechanisms of long noncoding RNAs. , 2011, Molecular cell.

[31]  Howard Y. Chang,et al.  Genome-wide measurement of RNA secondary structure in yeast , 2010, Nature.

[32]  I. Amit,et al.  Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome , 2009, Science.

[33]  Martin S. Taylor,et al.  The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line , 2009, Nature Genetics.

[34]  J. Kawai,et al.  Tiny RNAs associated with transcription start sites in animals , 2009, Nature Genetics.

[35]  J. Kawai,et al.  The regulated retrotransposon transcriptome of mammalian cells , 2009, Nature Genetics.

[36]  R. Sachidanandam,et al.  Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs , 2009, Nature.

[37]  Howard Y. Chang,et al.  Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs , 2007, Cell.

[38]  P. Stadler,et al.  RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription , 2007, Science.

[39]  Martin S. Taylor,et al.  Genome-wide analysis of mammalian promoter architecture and evolution , 2006, Nature Genetics.

[40]  Jun Kawai,et al.  Clusters of Internally Primed Transcripts Reveal Novel Long Noncoding RNAs , 2006, PLoS genetics.

[41]  Jun Kawai,et al.  Pseudo–Messenger RNA: Phantoms of the Transcriptome , 2006, PLoS genetics.

[42]  Sin Lam Tan,et al.  Complex Loci in Human and Mouse Genomes , 2006, PLoS genetics.

[43]  C. Kai,et al.  CAGE: cap analysis of gene expression , 2006, Nature Methods.

[44]  S. Batalov,et al.  Antisense Transcription in the Mammalian Transcriptome , 2005, Science.

[45]  S. Salzberg,et al.  The Transcriptional Landscape of the Mammalian Genome , 2005, Science.

[46]  G. Helt,et al.  Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution , 2005, Science.

[47]  E. Liu,et al.  5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[48]  Jun Kawai,et al.  Solution structure of a BolA‐like protein from Mus musculus , 2004, Protein science : a publication of the Protein Society.

[49]  J. Kawai,et al.  Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[50]  M. Fagiolini,et al.  Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts. , 2003, BioTechniques.

[51]  M. Tomita,et al.  Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. , 2003, Genome research.

[52]  Yoshihide Hayashizaki,et al.  Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. , 2003, Genome research.

[53]  M. Fagiolini,et al.  Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. , 2003, Genome research.

[54]  David A. Hume,et al.  A Guide to the Mammalian Genome , 2003 .

[55]  Colin N. Dewey,et al.  Initial sequencing and comparative analysis of the mouse genome. , 2002 .

[56]  E. Birney,et al.  Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs , 2002, Nature.

[57]  Piero Carninci,et al.  Extra-long first-strand cDNA synthesis. , 2002, BioTechniques.

[58]  Piero Carninci,et al.  Balanced-size and long-size cloning of full-length, cap-trapped cDNAs into vectors of the novel lambda-FLC family allows enhanced gene discovery rate and functional analysis. , 2001, Genomics.

[59]  Piero Carninci,et al.  Cloning full-length, cap-trapper-selected cDNAs by using the single-strand linker ligation method. , 2001, BioTechniques.

[60]  C. Bult,et al.  Functional annotation of a full-length mouse cDNA collection , 2001, Nature.

[61]  Piero Carninci,et al.  RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer. , 2000, Genome research.

[62]  Piero Carninci,et al.  Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. , 2000, Genome research.

[63]  Stephen M. Mount,et al.  The genome sequence of Drosophila melanogaster. , 2000, Science.

[64]  J. Kawai,et al.  Automated filtration-based high-throughput plasmid preparation system. , 1999, Genome research.

[65]  N Sasaki,et al.  Thermostabilization and thermoactivation of thermolabile enzymes by trehalose and its application for the synthesis of full length cDNA. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[66]  Piero Carninci,et al.  High-efficiency full-length cDNA cloning by biotinylated CAP trapper. , 1996, Genomics.

[67]  Francis S. Collins,et al.  Positional cloning moves from perditional to traditional , 1995, Nature Genetics.

[68]  Man-Hung Eric Tang,et al.  promoters using DeepCAGE Genome-wide detection and analysis of hippocampus core , 2009 .

[69]  A. Sandelin,et al.  Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. , 2009, Genome research.

[70]  Boris Lenhard,et al.  Antisense Transcription in the Mammalian Transcriptome RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group) and the FANTOM Consortium , 2005 .

[71]  Mouse Genome Sequencing Consortium Initial sequencing and comparative analysis of the mouse genome , 2002, Nature.

[72]  The FANTOM Consortium and the RIKEN Genome Exploration Team,et al.  Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs , 2002 .

[73]  International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome , 2001, Nature.

[74]  Piero Carninci,et al.  High efficiency selection of full-length cDNA by improved biotinylated cap trapper. , 1997, DNA research : an international journal for rapid publication of reports on genes and genomes.

[75]  Piero Carninci,et al.  Unamplified Cap Analysis of Gene Expression on a Single-molecule Sequencer , 2022 .