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1. Full Text Use of the MS2 aptamer and coat protein for RNA localization in yeast: A response to "MS2 coat proteins bound to yeast mRNAs block 5′ to 3′ degradation and trap mRNA decay products: Implications for the localization of mRNAs by MS2-MCP system"
by Haimovich, Gal and Zabezhinsky, Dmitry and Haas, Brian and Slobodin, Boris and Purushothaman, Pravinkumar and Fan, Lin and Levin, Joshua Z and Nusbaum, Chad and Gerst, Jeffrey E
RNA, ISSN 1355-8382, 05/2016, Volume 22, Issue 5, pp. 660 - 666
The MS2 system has been extensively used to visualize single mRNA molecules in live cells and follow their localization and behavior. In their Letter to the... 
mRNA localization | P-bodies | MS2 aptamer | MS2 coat protein | mRNA decay | TRANSCRIPTS | BIOCHEMISTRY & MOLECULAR BIOLOGY | GENE-EXPRESSION | AFFINITY PURIFICATION TECHNIQUE | IDENTIFICATION | TRANSLATION | Protein Binding | Aptamers, Nucleotide - metabolism | RNA, Messenger - metabolism | Fungal Proteins - metabolism
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2. Full Text Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics
by Shekhar, Karthik and Lapan, Sylvain W and Whitney, Irene E and Tran, Nicholas M and Macosko, Evan Z and Kowalczyk, Monika and Adiconis, Xian and Levin, Joshua Z and Nemesh, James and Goldman, Melissa and McCarroll, Steven A and Cepko, Constance L and Regev, Aviv and Sanes, Joshua R
Cell, ISSN 0092-8674, 08/2016, Volume 166, Issue 5, pp. 1308 - 1323.e30
Patterns of gene expression can be used to characterize and classify neuronal types. It is challenging, however, to generate taxonomies that fulfill the... 
PATHWAYS | GANGLION | AMACRINE CELLS | PROTEIN | RNA-SEQ | BIOCHEMISTRY & MOLECULAR BIOLOGY | GENE-EXPRESSION | MOUSE RETINA | DIFFERENTIATION | CEREBRAL-CORTEX | PARALLEL | CELL BIOLOGY | Retinal Bipolar Cells - cytology | Retinal Bipolar Cells - metabolism | Transcriptome | Amacrine Cells - cytology | Male | Mice, Transgenic | Genetic Markers | Mice, Inbred Strains | Animals | Sequence Analysis, RNA | Retinal Bipolar Cells - classification | Single-Cell Analysis - methods | Female | Transcription, Genetic | Mice | Cluster Analysis | Medical colleges | RNA | Multiprocessing | Neurons | Analysis | Genes | Research institutes | Ophthalmology | Gene expression | Population genetics
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3. Full Text Full-length transcriptome assembly from RNA-Seq data without a reference genome
by Fan, Lin and Nusbaum, Chad and Haas, Brian J and Chen, Zehua and Lindblad-Toh, Kerstin and Raychowdhury, Raktima and Birren, Bruce W and Adiconis, Xian and Gnirke, Andreas and Amit, Ido and Yassour, Moran and Friedman, Nir and Zeng, Qiandong and Hacohen, Nir and Grabherr, Manfred G and Regev, Aviv and Mauceli, Evan and Rhind, Nicholas and Thompson, Dawn A and di Palma, Federica and Levin, Joshua Z and Medicinska fakulteten and Science for Life Laboratory, SciLifeLab and Medicinska och farmaceutiska vetenskapsområdet and Institutionen för medicinsk biokemi och mikrobiologi and Uppsala universitet
Nature Biotechnology, ISSN 1087-0156, 07/2011, Volume 29, Issue 7, pp. 644 - 652
Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data... 
YEAST | EUKARYOTIC TRANSCRIPTOME | PROTEIN | MESSENGER-RNA | ALIGNMENT | GENE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | SCHIZOSACCHAROMYCES-POMBE | RESOURCE | REVEALS | TOOL | Sequence Analysis, RNA - methods | Algorithms | Base Sequence | Transcriptome | Molecular Sequence Data | Gene Expression Profiling - methods | Reference Values | Sequence Analysis, RNA - standards | RNA - chemistry | RNA - genetics | Physiological aspects | Genomes | Aleyrodidae | Genetic aspects | Research | Multiprocessing | Yeast | Insects | Ribonucleic acid--RNA | Gene expression | Genomics | Rodents | Basic Medicine | Medical and Health Sciences | Microbiology in the medical area | Mikrobiologi inom det medicinska området | Medicin och hälsovetenskap | Medicinska och farmaceutiska grundvetenskaper
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4. Full Text Correction to “Chemoproteomic Discovery of Cysteine-Containing Human Short Open Reading Frames
by Schwaid, Adam G and Shannon, D. Alexander and Ma, Jiao and Slavoff, Sarah A and Levin, Joshua Z and Weerapana, Eranthie and Saghatlian, Alan
Journal of the American Chemical Society, ISSN 0002-7863, 01/2014, Volume 136, Issue 2, pp. 820 - 820
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5. Full Text Comprehensive comparative analysis of strand-specific RNA sequencing methods
by Nusbaum, Chad and Regev, Aviv and Adiconis, Xian and Thompson, Dawn Anne and Yassour, Moran and Gnirke, Andreas and Levin, Joshua Z and Friedman, Nir
Nature Methods, ISSN 1548-7091, 09/2010, Volume 7, Issue 9, pp. 709 - 715
Strand-specific, massively parallel cDNA sequencing (RNA-seq) is a powerful tool for transcript discovery, genome annotation and expression profiling. There... 
YEAST | EUKARYOTIC TRANSCRIPTOME | SINGLE | NUCLEOTIDE RESOLUTION | PROMOTERS | GENOMES | QUANTIFICATION | CONSTRUCTION | BIOCHEMICAL RESEARCH METHODS | SEQ | REVEALS | Sequence Analysis, RNA - methods | Substrate Specificity | Gene Expression Profiling - methods | Gene Library | Computational Biology | DNA, Complementary - genetics | Methods | Nucleotide sequencing | Research | Scientific method | Ribonucleic acid--RNA | Comparative analysis | Genomics
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6. Full Text Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
by Shalek, Alex K and Satija, Rahul and Adiconis, Xian and Gertner, Rona S and Gaublomme, Jellert T and Raychowdhury, Raktima and Schwartz, Schraga and Yosef, Nir and Malboeuf, Christine and Lu, Diana and Trombetta, John J and Gennert, Dave and Gnirke, Andreas and Goren, Alon and Hacohen, Nir and Levin, Joshua Z and Park, Hongkun and Regev, Aviv
Nature, ISSN 0028-0836, 2013, Volume 498, Issue 7453, pp. 236 - 240
Recent molecular studies have shown that, even when derived from a seemingly homogenous population, individual cells can exhibit substantial differences in... 
LEVEL | MESSENGER-RNA-SEQ | PATHWAY | MULTIDISCIPLINARY SCIENCES | STAT2 Transcription Factor | Reproducibility of Results | Bone Marrow Cells - cytology | Gene Expression Regulation - immunology | Dendritic Cells - immunology | RNA, Messenger - genetics | RNA, Messenger - analysis | In Situ Hybridization, Fluorescence | Viruses - immunology | Gene Expression Profiling | Transcriptome - genetics | Interferons - immunology | Lipopolysaccharides - immunology | Mice, Knockout | Animals | Sequence Analysis, RNA | Interferon Regulatory Factor-7 | Bone Marrow Cells - immunology | RNA Splicing - immunology | Dendritic Cells - cytology | Mice | Single-Cell Analysis | Dendritic Cells - metabolism | Protein Isoforms - genetics | RNA sequencing | Phenotype | Cellular control mechanisms | Research | Gene expression | Observations | Testing | Proteins | Noise | Cell cycle
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7. Full Text Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
by Gnirke, Andreas and Rinn, John L and Regev, Aviv and Adiconis, Xian and Levin, Joshua Z and Robinson, James and Lander, Eric S and Nusbaum, Chad and Fan, Lin and Koziol, Magdalena J and Garber, Manuel and Guttman, Mitchell and Donaghey, Julie
Nature Biotechnology, ISSN 1087-0156, 05/2010, Volume 28, Issue 5, pp. 503 - 510
Massively parallel cDNA sequencing (RNA-Seq) provides an unbiased way to study a transcriptome, including both coding and noncoding genes. Until now, most... 
X-CHROMOSOME | GENE | MAPS | SEQUENCES | NONCODING RNAS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | STEM-CELL | GENOME | SEQ | Sequence Analysis, RNA - methods | Cell Line | Computational Biology - methods | Animals | Gene Library | RNA, Messenger - genetics | Gene Expression Profiling - methods | Transcription, Genetic | Mice | Models, Genetic | Embryonic Stem Cells | DNA, Intergenic - genetics | Physiological aspects | Antisense RNA | Genetic aspects | Research | Embryonic stem cells | Mammals | Proteins | Biotechnology | Gene expression | Research methodology | Deoxyribonucleic acid--DNA
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8. Full Text Erratum: Chemoproteomic discovery of cysteine-containing human short open reading frames (Journal of the American Chemical Society (2013) 135 (16750-16753) DOI:10.1021/ja406606j)
by Schwaid, Adam G and Shannon, D. Alexander and Ma, Jiao and Slavoff, Sarah A and Levin, Joshua Z and Weerapana, Eranthie and Saghatlian, Alan
Journal of the American Chemical Society, ISSN 0002-7863, 01/2014, Volume 136, Issue 2, p. 820
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9. Full Text Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells
by Gnirke, Andreas and Nusbaum, Chad and Fan, Lin and Friedman, Nir and Adiconis, Xian and Regev, Aviv and Levin, Joshua Z and Raychowdhury, Raktima and Amit, Ido and Garber, Manuel and Hacohen, Nir and Rabani, Michal
Nature Biotechnology, ISSN 1087-0156, 05/2011, Volume 29, Issue 5, pp. 436 - 442
Cellular RNA levels are determined by the interplay of RNA production, processing and degradation. However, because most studies of RNA regulation do not... 
YEAST | ACTIVATION | NETWORK | DECAY | DATABASE | TRISTETRAPROLIN | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | STABILITY | SEQUENCE | GENE-EXPRESSION | MICROARRAY ANALYSIS | Up-Regulation | Genetic Association Studies | Down-Regulation | Mice, Inbred C57BL | RNA, Messenger - genetics | Cells, Cultured | Computational Biology | Lipopolysaccharides - metabolism | Models, Molecular | RNA Polymerase II - metabolism | Transcription Factors - genetics | RNA - genetics | Sequence Analysis, RNA - methods | Transcription Factors - metabolism | RNA, Messenger - biosynthesis | Animals | Female | Transcription, Genetic | Biotinylation - methods | Mice | Dendritic Cells - metabolism | RNA - metabolism | Physiological aspects | Research | RNA | Gene expression | Proteolysis | Cellular biology | Ribonucleic acid--RNA | Genomics | Immune system
Journal Article