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1. Full Text RNA sequencing: advances, challenges and opportunities
by Milos, Patrice M and Ozsolak, Fatih
Nature Reviews Genetics, ISSN 1471-0056, 02/2011, Volume 12, Issue 2, pp. 87 - 98
In the few years since its initial application, massively parallel cDNA sequencing, or RNA-seq, has allowed many advances in the characterization and... 
REGULATORY ROLES | SINGLE-CELL | AMPLIFICATION-FREE | SMALL SAMPLES | MESSENGER-RNA | NUCLEOTIDE RESOLUTION | CELL TRANSCRIPTOME | GENETICS & HEREDITY | GENOME-WIDE ANALYSIS | GENE-EXPRESSION | CDNA SYNTHESIS | Animals | Sequence Analysis, RNA | Alternative Splicing | RNA - analysis | Humans | Transcription, Genetic | RNA - genetics | Physiological aspects | Usage | Nucleotide sequencing | Research | Genetic transcription | RNA
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2. Full Text Quantitative polyadenylation site mapping with single-molecule direct RNA sequencing
by Ozsolak, Fatih and Ozsolak, Fatih
Methods in molecular biology (Clifton, N.J.), ISSN 1064-3745, 2014, Volume 1125, pp. 145 - 155
The known regulatory role of 3' untranslated regions (3'UTRs) and poly(A) tails in RNA localization, stability, and translation, and polyadenylation regulation... 
Direct RNA sequencing | Alternative polyadenylation | Single-molecule sequencing | Next-generation sequencing | Polyadenylation site mapping | Sequence Analysis, RNA - methods | 3' Untranslated Regions - genetics | Humans | Polyadenylation - physiology
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3. Full Text Attomole-level genomics with single-molecule direct DNA, cDNA and RNA sequencing technologies
by Ozsolak, Fatih
Current Issues in Molecular Biology, ISSN 1467-3037, 07/2016, Volume 18, Issue 1, pp. 43 - 48
With the introduction of next-generation sequencing (NGS) technologies in 2005, the domination of microarrays in genomics quickly came to an end due to NGS's... 
BIOCHEMISTRY & MOLECULAR BIOLOGY
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4. Full Text The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA
by Kapranov, Philipp and St Laurent, Georges and Raz, Tal and Ozsolak, Fatih and Reynolds, C Patrick and Sorensen, Poul H.B and Reaman, Gregory and Milos, Patrice and Arceci, Robert J and Thompson, John F and Triche, Timothy J
BMC Biology, ISSN 1741-7007, 12/2010, Volume 8, Issue 1, pp. 149 - 149
Background: Discovery that the transcriptional output of the human genome is far more complex than predicted by the current set of protein-coding annotations... 
AMPLIFICATION | NONCODING RNAS | SARCOMA | BIOLOGY | TILING ARRAYS | MAMMALIAN TRANSCRIPTOME | FUNCTIONAL ANNOTATION | IDENTIFICATION | EXPRESSION | GENOME | FAMILY | Knowledge Bases | Molecular Sequence Annotation - standards | Sarcoma, Ewing - metabolism | Humans | Liver - metabolism | Sarcoma, Ewing - pathology | Molecular Sequence Annotation - trends | Bone Neoplasms - pathology | RNA, Ribosomal - genetics | Genome, Human - genetics | Bone Neoplasms - metabolism | RNA - genetics | Brain - metabolism | RNA, Nuclear - metabolism | Neoplasm Metastasis - genetics | Animals | Adolescent | K562 Cells | Bone Neoplasms - genetics | Genome, Insect | Sequence Analysis, RNA - standards | RNA, Nuclear - genetics | Sarcoma, Ewing - genetics | Drosophila - genetics | RNA sequencing | Methods | Medical research | Pediatrics | Health sciences | Dark matter | Oncology | Genomes | Biology | Life sciences | Manuscripts | Cancer | Tumors
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5. Attomole-level Genomics with Single-molecule Direct DNA, cDNA and RNA Sequencing Technologies
by Ozsolak, Fatih
Current issues in molecular biology, 2016, Volume 18, p. 43
With the introduction of next-generation sequencing (NGS) technologies in 2005, the domination of microarrays in genomics quickly came to an end due to NGS's... 
Sequence Analysis, RNA - methods | Genomics | Humans | High-Throughput Nucleotide Sequencing | Genome, Human | Sequence Analysis, DNA - methods
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6. Full Text Third-generation sequencing techniques and applications to drug discovery
by Ozsolak, Fatih
Expert Opinion on Drug Discovery, ISSN 1746-0441, 03/2012, Volume 7, Issue 3, pp. 231 - 243
Introduction: There is an immediate need for functional and molecular studies to decipher differences between disease and 'normal' settings to identify large... 
genetics | third-generation sequencing | drug discovery | next-generation sequencing | epigenetics | pharmacogenetics | Epigenetics | Genetics | Third-generation sequencing | Pharmacogenetics | Next-generation sequencing | Drug discovery | AMPLIFICATION-FREE | DNA METHYLATION | SINGLE-MOLECULE | GUT MICROBIOTA | CANCER | CHALLENGES | GENOME SEQUENCE | ALPHA-HEMOLYSIN | PHARMACOLOGY & PHARMACY | OUTBREAK | REVEALS | Sequence Analysis, RNA - methods | Pharmacogenetics - methods | Humans | Drug Design | Drug Discovery - methods | Genome, Human | High-Throughput Nucleotide Sequencing - methods | Sequence Analysis, DNA - methods | High-Throughput Screening Assays - methods | Third generation sequencing | Next generation sequencing
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7. Full Text High-throughput mapping of the chromatin structure of human promoters
by Ozsolak, Fatih and Liu, X Shirley and Fisher, David E and Song, Jun S
Nature Biotechnology, ISSN 1087-0156, 02/2007, Volume 25, Issue 2, pp. 244 - 248
Our understanding of how chromatin structure influences cellular processes such as transcription and replication has been limited by a lack of... 
YEAST | CHROMOSOME | MELANOMA | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | DNA | LINEAGE SURVIVAL | GENE-REGULATION | GENOME-WIDE | MITF | TRANSCRIPTIONAL REGULATION | NUCLEOSOME POSITIONS | Algorithms | Oligonucleotide Array Sequence Analysis - methods | Base Sequence | Chromosome Mapping - methods | Humans | Molecular Sequence Data | Nucleosomes - genetics | Promoter Regions, Genetic - genetics | Sequence Analysis, DNA - methods | Genome, Human - genetics | Physiological aspects | Chromatin | Chromosome mapping | Research | Structure | Methods | Cellular biology | Gene expression | Research methodology
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8. Full Text The Lkb1 metabolic sensor maintains haematopoietic stem cell survival
by Gurumurthy, Sushma and Xie, Stephanie Z and Alagesan, Brinda and Kim, Judith and Yusuf, Rushdia Z and Saez, Borja and Tzatsos, Alexandros and Ozsolak, Fatih and Milos, Patrice and Ferrari, Francesco and Park, Peter J and Shirihai, Orian S and Scadden, David T and Bardeesy, Nabeel
Nature, ISSN 0028-0836, 12/2010, Volume 468, Issue 7324, pp. 659 - 663
Haematopoietic stem cells (HSCs) can convert between growth states that have marked differences in bioenergetic needs. Although often quiescent in adults,... 
SYSTEM | APOPTOSIS | GLUCOSE-HOMEOSTASIS | ENERGY | TUMOR SUPPRESSION | PATHWAY | PEUTZ-JEGHERS-SYNDROME | MULTIDISCIPLINARY SCIENCES | IN-VIVO | KINASE | MICE | Protein-Serine-Threonine Kinases - deficiency | AMP-Activated Protein Kinases - metabolism | Cell Proliferation | TOR Serine-Threonine Kinases - metabolism | Multiprotein Complexes | Hematopoietic Stem Cells - pathology | Homeostasis | Male | Autophagy | Mechanistic Target of Rapamycin Complex 1 | Hematopoiesis | Tumor Suppressor Proteins - deficiency | Adenosine Triphosphate - metabolism | Bone Marrow - metabolism | Tumor Suppressor Proteins - genetics | Membrane Potential, Mitochondrial | Female | Protein-Serine-Threonine Kinases - metabolism | Tumor Suppressor Proteins - metabolism | Cell Survival | Mice, Inbred C57BL | Protein-Serine-Threonine Kinases - genetics | Lipid Metabolism | Hematopoietic Stem Cells - metabolism | Mitochondria - metabolism | Mitochondria - pathology | Animals | Proteins - metabolism | Cell Cycle | Energy Metabolism | Bone Marrow - pathology | Hematopoietic Stem Cells - cytology | Mice | Enzyme Activation | Proteins - antagonists & inhibitors | Apoptosis | Oxidative stress | Physiological aspects | Tumor suppressor genes | Genetic aspects | Research | Hematopoietic stem cells | Risk factors | Proteins | Stem cells | Cell cycle | Bone marrow | Kinases | Metabolism | Tumors
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9. Full Text RNA sequencing of pancreatic circulating tumour cells implicates WNT signalling in metastasis
by Yu, Min and Ting, David T and Stott, Shannon L and Wittner, Ben S and Ozsolak, Fatih and Paul, Suchismita and Ciciliano, Jordan C and Smas, Malgorzata E and Winokur, Daniel and Gilman, Anna J and Ulman, Matthew J and Xega, Kristina and Contino, Gianmarco and Alagesan, Brinda and Brannigan, Brian W and Milos, Patrice M and Ryan, David P and Sequist, Lecia V and Bardeesy, Nabeel and Ramaswamy, Sridhar and Toner, Mehmet and Maheswaran, Shyamala and Haber, Daniel A
Nature, ISSN 0028-0836, 07/2012, Volume 487, Issue 7408, pp. 510 - 513
Circulating tumour cells (CTCs) shed into blood from primary cancers include putative precursors that initiate distal metastases(1). Although these cells are... 
STEM-CELL | TRANSCRIPTOME | PATHWAY | MULTIDISCIPLINARY SCIENCES | Cell Survival | Humans | Pancreatic Neoplasms - pathology | Neoplastic Cells, Circulating - metabolism | RNA, Messenger - analysis | Pancreatic Neoplasms - genetics | Wnt Proteins - metabolism | Wnt2 Protein - genetics | Wnt2 Protein - metabolism | Neoplasm Metastasis - genetics | RNA, Messenger - biosynthesis | Contact Inhibition | Animals | Sequence Analysis, RNA | Wnt Proteins - genetics | Wnt Signaling Pathway - genetics | Mice | MAP Kinase Kinase Kinases - antagonists & inhibitors | Genes, Neoplasm - genetics | Gene Expression Regulation, Neoplastic - genetics | Disease Models, Animal | RNA sequencing | Pancreatic cancer | Physiological aspects | Development and progression | Genetic aspects | Research | Metastasis | Tumors | Cancer | Proteins | Pancreas
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10. Full Text Direct RNA sequencing
by Ozsolak, Fatih and Platt, Adam R and Jones, Dan R and Reifenberger, Jeffrey G and Sass, Lauryn E and McInerney, Peter and Thompson, John F and Bowers, Jayson and Jarosz, Mirna and Milos, Patrice M
Nature, ISSN 0028-0836, 10/2009, Volume 461, Issue 7265, pp. 814 - 818
Our understanding of human biology and disease is ultimately dependent on a complete understanding of the genome and its functions. The recent application of... 
YEAST | MESSENGER-RNA | TRANSCRIPTOME | MULTIDISCIPLINARY SCIENCES | 2ND-STRAND CDNA SYNTHESIS | POLYADENYLATION | TERMINATION | EXPRESSION | DNA-POLYMERASES | GENOME | PCR | RNA, Fungal - analysis | RNA - analysis | Saccharomyces cerevisiae - genetics | DNA, Complementary - genetics | Templates, Genetic | Gene Expression Profiling - methods | RNA - genetics | Sequence Analysis, RNA - methods | RNA - isolation & purification | Polymerase Chain Reaction | RNA, Fungal - genetics | RNA, Fungal - isolation & purification | Oligoribonucleotides - genetics | Usage | DNA microarrays | Nucleotide sequencing | Research | Genetic transcription | Methods | Genetic engineering | Biomedical research | E coli | DNA polymerase | Reaction kinetics
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11. Full Text Chromatin structure analyses identify miRNA promoters
by Ozsolak, Fatih and Poling, Laura L and Wang, Zhengxin and Liu, Hui and Liu, X. Shirley and Roeder, Robert G and Zhang, Xinmin and Song, Jun S and Fisher, David E
Genes and Development, ISSN 0890-9369, 11/2008, Volume 22, Issue 22, pp. 3172 - 3183
Although microRNAs (miRNAs) are key regulators of gene expression in normal human physiology and disease, transcriptional regulation of miRNAs is poorly... 
Promoter | Chromatin | MicroRNA | Transcription | ALPHA-AMANITIN | C-MYC | DEVELOPMENTAL BIOLOGY | chromatin | ANIMAL DEVELOPMENT | CELL BIOLOGY | CAENORHABDITIS-ELEGANS | GENETICS & HEREDITY | GENOME-WIDE ANALYSIS | GENE-EXPRESSION | microRNA | promoter | HISTONE MODIFICATIONS | MICRORNA EXPRESSION | RNA-POLYMERASE-III | RNA, Small Interfering - genetics | Luciferases - metabolism | Humans | Gene Expression Regulation, Neoplastic | Nucleosomes - genetics | Promoter Regions, Genetic - genetics | Recombinant Fusion Proteins - metabolism | Luciferases - genetics | Transfection | Chromatin Immunoprecipitation | RNA Interference | Cloning, Molecular | Cell Line, Tumor | Recombinant Fusion Proteins - genetics | Transcription, Genetic | MicroRNAs - genetics | HeLa Cells | Chromatin - genetics | Promoters (Genetics) | RNA | Analysis | Research | Genetic transcription | Structure | Research Paper
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12. Full Text Transcriptome profiling using single-molecule direct RNA sequencing
by Ozsolak, Fatih and Milos, Patrice M
Methods in molecular biology (Clifton, N.J.), ISSN 1064-3745, 2011, Volume 733, pp. 51 - 61
Methods for in-depth characterization of transcriptomes and quantification of transcript levels have emerged as valuable tools for understanding cellular... 
Sequence Analysis, RNA - methods | Nucleic Acid Hybridization | Animals | RNA, Untranslated - metabolism | Base Sequence | Humans | Polyadenylation | Gene Expression Profiling - methods | Mice | RNA, Untranslated - genetics | RNA - genetics | RNA - metabolism | RNA sequencing | Single-molecule sequencing | Transcriptome profiling | Polyadenylation site mapping
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13. Full Text Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation
by Sherstnev, Alexander and Duc, Céline and Cole, Christian and Zacharaki, Vasiliki and Hornyik, Csaba and Ozsolak, Fatih and Milos, Patrice M and Barton, Geoffrey J and Simpson, Gordon G
Nature Structural and Molecular Biology, ISSN 1545-9993, 08/2012, Volume 19, Issue 8, pp. 845 - 852
It has recently been shown that RNA 3'-end formation plays a more widespread role in controlling gene expression than previously thought. To examine the impact... 
ENDOGENOUS SIRNAS | POLY(A) SIGNALS | REVERSE TRANSCRIPTION | BIOCHEMISTRY & MOLECULAR BIOLOGY | POLYMERASE | NATURAL ANTISENSE TRANSCRIPTS | MECHANISMS | GENOME | CELL BIOLOGY | BIOPHYSICS | ALTERNATIVE POLYADENYLATION | DEGRADATION | TERMINATION | RNA, Untranslated - metabolism | Genes, Plant | RNA, Messenger - genetics | Molecular Sequence Data | Chromosome Mapping | RNA, Plant - genetics | RNA, Messenger - metabolism | RNA, Plant - metabolism | RNA, Untranslated - genetics | RNA, Small Nucleolar - genetics | Arabidopsis - metabolism | Arabidopsis - genetics | RNA, Small Nucleolar - metabolism | Sequence Analysis, RNA | Base Sequence | RNA, Antisense - metabolism | RNA, Plant - chemistry | Gene Expression Regulation, Plant | Polyadenylation | RNA, Untranslated - chemistry | Nucleic Acid Conformation | RNA 3' End Processing | Oligodeoxyribonucleotides - metabolism | RNA, Antisense - genetics | RNA sequencing | RNA | Arabidopsis | Plant genetics | Physiological aspects | Genetic aspects | Research | Insects | Ribonucleic acid--RNA | Gene expression
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14. Full Text Global Analysis of mRNA Isoform Half-Lives Reveals Stabilizing and Destabilizing Elements in Yeast
by Geisberg, Joseph V and Moqtaderi, Zarmik and Fan, Xiaochun and Ozsolak, Fatih and Struhl, Kevin
Cell, ISSN 0092-8674, 02/2014, Volume 156, Issue 4, pp. 812 - 824
We measured half-lives of 21,248 mRNA 3′ isoforms in yeast by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing... 
EXTENSIVE ALTERNATIVE POLYADENYLATION | DECAY | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | POLY(A)-BINDING PROTEIN | GENE-EXPRESSION | TRIPLE-HELIX | GENOME-WIDE MEASUREMENT | 3' ENDS | SACCHAROMYCES-CEREVISIAE | EXOSOME COMPLEX | CELL BIOLOGY | Genome-Wide Association Study | Saccharomyces cerevisiae - genetics | RNA, Fungal - chemistry | Half-Life | RNA Stability | RNA, Messenger - metabolism | RNA, Fungal - metabolism | Saccharomyces cerevisiae - metabolism | Sequence Alignment | Genome, Fungal | Nucleotide Motifs | Base Sequence | RNA, Messenger - chemistry | Analysis | Messenger RNA | Protein binding
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