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science & technology (23) 23
humans (18) 18
life sciences & biomedicine (15) 15
chromatin (11) 11
gene expression (10) 10
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accessibility (5) 5
amyotrophic lateral sclerosis (5) 5
cells (5) 5
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genetic aspects (5) 5
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genotype (5) 5
single-cell analysis - methods (5) 5
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gene expression profiling (4) 4
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1. Full Text Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
by Darren A. Cusanovich and Riza Daza and Andrew Adey and Hannah A. Pliner and Lena Christiansen and Kevin L. Gunderson and Frank J. Steemers and Cole Trapnell and Jay Shendure
Science (American Association for the Advancement of Science), ISSN 0036-8075, 5/2015, Volume 348, Issue 6237, pp. 910 - 914
REPORTS | Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | HL-60 Cells | Chromatin - metabolism | Single-Cell Analysis - methods | Epigenesis, Genetic | Humans | HEK293 Cells | Chromatin | Research | Analysis | Cells | Indexing | Cellular biology | Tissues | Index Medicus | Multiplexing | Cellular | Landscapes | Accessibility | Strategy | Culture | Combinatorial analysis
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2. Full Text Reversed graph embedding resolves complex single-cell trajectories
by Qiu, Xiaojie and Mao, Qi and Tang, Ying and Wang, Li and Chawla, Raghav and Pliner, Hannah A and Trapnell, Cole
Nature methods, ISSN 1548-7091, 10/2017, Volume 14, Issue 10, pp. 979 - 982
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biochemical Research Methods | Science & Technology | Transcription Factors - metabolism | Algorithms | Animals | Models, Biological | Computer Simulation | Mutation | Transcription Factors - genetics | Transcriptome - physiology | Cell Differentiation - physiology | Gene Expression Regulation, Developmental - physiology | Usage | Research | Genes | Transcription factors | Cell fate | Gene regulation | Computer applications | Decisions | Embedding | Trajectories | Gene expression | Index Medicus
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3. Full Text Supervised classification enables rapid annotation of cell atlases
by Pliner, Hannah A and Shendure, Jay and Trapnell, Cole
Nature methods, ISSN 1548-7091, 10/2019, Volume 16, Issue 10, pp. 983 - 986
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Biochemical Research Methods | Science & Technology | Sequence Analysis, RNA - methods | Algorithms | Animals | Datasets as Topic | Atlases as Topic | Single-Cell Analysis - methods | Humans | Transcription, Genetic | Gene Expression Profiling | RNA sequencing | Genetic transcription | Identification and classification | Analysis | Molecular diagnostic techniques | Chromatin | Annotations | Profiling | Transcription | Data sets | Atlases | Index Medicus
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4. Full Text The cis-regulatory dynamics of embryonic development at single-cell resolution
by Cusanovich, Darren A and Reddington, James P and Garfield, David A and Daza, Riza M and Aghamirzaie, Delasa and Marco-Ferreres, Raquel and Pliner, Hannah A and Christiansen, Lena and Qiu, Xiaojie and Steemers, Frank J and Trapnell, Cole and Shendure, Jay and Furlong, Eileen E. M
Nature (London), ISSN 0028-0836, 03/2018, Volume 555, Issue 7697, pp. 538 - 542
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | Genetic research | Embryonic development | Unicellular organisms | Genetic aspects | Research | Genetic regulation | Ectoderm | Chromatin | Accessibility | Transgenic | Mesoderm | Genomes | Regulatory sequences | Nuclei | Embryogenesis | Cell fate | Egg laying | Blastoderm | Bioinformatics | Endoderm | Mesendoderm | Discriminant analysis | Gastrulation | Gene expression | Transposase | Embryos | Embryonic growth stage | Enhancers | Dynamic tests | Insects | Spatial heterogeneity | Nuclei (cytology) | Combinatorial analysis | Index Medicus | regulatory landscape | single cell | single cell epigenetics | embryonic development | open chromatin | developmental enhancers | cell fate decisions | ATAC-seq
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5. Full Text Joint profiling of chromatin accessibility and gene expression in thousands of single cells
by Cao, Junyue and Cusanovich, Darren A and Ramani, Vijay and Aghamirzaie, Delasa and Pliner, Hannah A and Hill, Andrew J and Daza, Riza M and McFaline-Figueroa, Jose L and Packer, Jonathan S and Christiansen, Lena and Steemers, Frank J and Adey, Andrew C and Trapnell, Cole and Shendure, Jay
Science (American Association for the Advancement of Science), ISSN 0036-8075, 09/2018, Volume 361, Issue 6409, pp. 1380 - 1385
Science & Technology - Other Topics | Multidisciplinary Sciences | Science & Technology | A549 Cells | Chromatin - metabolism | NIH 3T3 Cells | Transcription, Genetic - drug effects | Kidney - drug effects | Humans | Regulatory Elements, Transcriptional - drug effects | Gene Expression Profiling - methods | Kidney - cytology | Gene Expression Regulation - drug effects | Animals | Dexamethasone - pharmacology | Single-Cell Analysis - methods | HEK293 Cells | Mice | Genomics - methods | RNA sequencing | Chromatin | Genetic research | Genetic aspects | Research | Gene expression | Cells | Methods | Adenocarcinoma | Dexamethasone | Kidneys | Accessibility | Genomes | Biology | Ribonucleic acid--RNA | Subgroups | Covariance | Lungs | DNA methylation | Methylation | Molecular biology | Combinatorial analysis | Index Medicus
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6. Full Text Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease
by Nalls, Mike A and Pankratz, Nathan and Lill, Christina M and Do, Chuong B and Hernandez, Dena G and Saad, Mohamad and DeStefano, Anita L and Kara, Eleanna and Bras, Jose and Sharma, Manu and Schulte, Claudia and Keller, Margaux F and Arepalli, Sampath and Letson, Christopher and Edsall, Connor and Stefansson, Hreinn and Liu, Xinmin and Pliner, Hannah and Lee, Joseph H and Cheng, Rong and Ikram, M. Arfan and Ioannidis, John P. A and Hadjigeorgiou, Georgios M and Bis, Joshua C and Martinez, Maria and Perlmutter, Joel S and Goate, Alison and Marder, Karen and Fiske, Brian and Sutherland, Margaret and Xiromerisiou, Georgia and Myers, Richard H and Clark, Lorraine N and Stefansson, Kari and Hardy, John A and Heutink, Peter and Chen, Honglei and Wood, Nicholas W and Houlden, Henry and Payami, Haydeh and Brice, Alexis and Scott, William K and Gasser, Thomas and Bertram, Lars and Eriksson, Nicholas and Foroud, Tatiana and Singleton, Anew B and GenePD and IPDG and Ashkenazi Jewish Dataset Investiga and 23AndMe and NABEC and HIHG and Greek Parkinson's Dis Consortium and GParkinson's Study Grp PSG Parkins and NGRC and Alzheimer Genetic Analysis Gr and CHARGE and UKBEC and Parkinson's Study Group (PSG) Parkinson's Research: The Organized GENetics Initiative (PROGENI) and Hussman Institute of Human Genomics (HIHG) and 23andMe and Greek Parkinson's Disease Consortium and International Parkinson's Disease Genomics Consortium (IPDGC) and Cohorts for Health and Aging Research in Genetic Epidemiology (CHARGE) and United Kingdom Brain Expression Consortium (UKBEC) and NeuroGenetics Research Consortium (NGRC) and Ashkenazi Jewish Dataset Investigator and North American Brain Expression Consortium (NABEC) and Alzheimer Genetic Analysis Group and The Ashkenazi Jewish Dataset Investigator
Nature genetics, ISSN 1061-4036, 2014, Volume 46, Issue 9, pp. 989 - +
Life Sciences & Biomedicine | Genetics & Heredity | Science & Technology | Genetic Predisposition to Disease | Humans | Risk Factors | Genotype | Polymorphism, Single Nucleotide | Genetic Loci | Parkinson Disease - genetics | Genome-Wide Association Study - methods | Case-Control Studies | Genome-wide association studies | Parkinson's disease | Genetic aspects | Single nucleotide polymorphisms | Identification and classification | Methods | Risk factors | Studies | Genealogy | Parkinsons disease | Quality control | DNA methylation | Statistical methods | Genomes | Health risk assessment | Meta-analysis | Index Medicus
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7. Full Text Mutations in the Matrin 3 gene cause familial amyotrophic lateral sclerosis
by Johnson, Janel O and Pioro, Erik P and Boehringer, Ashley and Chia, Ruth and Feit, Howard and Renton, Alan E and Pliner, Hannah A and Abramzon, Yevgeniya and Marangi, Giuseppe and Winborn, Brett J and Gibbs, J. Raphael and Nalls, Michael A and Morgan, Sarah and Shoai, Maryam and Hardy, John and Pittman, Alan and Orrell, Richard W and Malaspina, Andrea and Sidle, Katie C and Fratta, Pietro and Harms, Matthew B and Baloh, Robert H and Pestronk, Alan and Weihl, Conrad C and Rogaeva, Ekaterina and Zinman, Lorne and Drory, Vivian E and Borghero, Giuseppe and Mora, Gabriele and Calvo, Andrea and Rothstein, Jeffrey D and Drepper, Carsten and Sendtner, Michael and Singleton, Andrew B and Taylor, J Paul and Cookson, Mark R and Restagno, Gabriella and Sabatelli, Mario and Bowser, Robert and Chio`, Adriano and Traynor, Bryan J and Moglia, Cristina and Cammarosano, Stefania and Canosa, Antonio and Gallo, Sara and Brunetti, Maura and Ossola, Irene and Marinou, Kalliopi and Papetti, Laura and Pisano, Fabrizio and Pinter, Giuseppe Lauria and Conte, Amelia and Luigetti, Marco and Zollino, Marcella and Lattante, Serena and Marangi, Giuseppe and la Bella, Vincenzo and Spataro, Rossella and Colletti, Tiziana and Battistini, Stefania and Ricci, Claudia and Caponnetto, Claudia and Mancardi, Gianluigi and Mandich, Paola and Salvi, Fabrizio and Bartolomei, Ilaria and Mandrioli, Jessica and Sola, Patrizia and Lunetta, Christian and Penco, Silvana and Monsurrò, Maria Rosaria and Conforti, Francesca Luisa and Tedeschi, Gioacchino and Gambardella, Antonio and Quattrone, Aldo and Volanti, Paolo and Floris, Gianluca and Cannas, Antonino and Piras, Valeria and Marrosu, Francesco and Marrosu, Maria Giovanna and Murru, Maria Rita and Pugliatti, Maura and Parish, Leslie D and Sotgiu, Alessandra and Solinas, Giuliana and Ulgheri, Lucia and Ticca, Anna and Simone, Isabella and Logroscino, Giancarlo and Pirisi, Angelo and ITALSGEN
Nature neuroscience, ISSN 1097-6256, 2014, Volume 17, Issue 5, pp. 664 - 666
Neurosciences | Neurosciences & Neurology | Life Sciences & Biomedicine | Science & Technology | RNA-Binding Proteins - genetics | Genetic Predisposition to Disease - genetics | Spinal Cord - metabolism | Amyotrophic Lateral Sclerosis - genetics | Humans | Middle Aged | Computational Biology | Nuclear Matrix-Associated Proteins - metabolism | Family Health | Genotype | Male | Muscle, Skeletal - metabolism | Mutation - genetics | DNA-Binding Proteins - metabolism | Amyotrophic Lateral Sclerosis - pathology | Neurologic Examination | Nuclear Matrix-Associated Proteins - genetics | DNA Mutational Analysis | Spinal Cord - pathology | Aged, 80 and over | Female | Aged | Muscle, Skeletal - pathology | RNA-Binding Proteins - metabolism | Gene mutations | Amyotrophic lateral sclerosis | Development and progression | Genetic aspects | Research | Neurological research | Neurophysiology | Index Medicus
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8. Full Text Searching for Grendel: origin and global spread of the C9ORF72 repeat expansion
by Pliner, Hannah A and Mann, David M and Traynor, Bryan J
Acta neuropathologica, ISSN 0001-6322, 3/2014, Volume 127, Issue 3, pp. 391 - 396
Medicine & Public Health | Pathology | Neurosciences | Clinical Neurology | Neurosciences & Neurology | Life Sciences & Biomedicine | Science & Technology | Proteins - genetics | DNA Repeat Expansion | European Continental Ancestry Group - genetics | Time Factors | Internationality | Amyotrophic Lateral Sclerosis - genetics | Humans | C9orf72 Protein | Human Migration | Evolution, Molecular | Amyotrophic lateral sclerosis | Index Medicus
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9. Full Text The accessible chromatin landscape of the murine hippocampus at single-cell resolution
by Sinnamon, John R and Torkenczy, Kristof A and Linhoff, Michael W and Vitak, Sarah A and Mulqueen, Ryan M and Pliner, Hannah A and Trapnell, Cole and Steemers, Frank J and Mandel, Gail and Adey, Andrew C
Genome research, ISSN 1088-9051, 05/2019, Volume 29, Issue 5, pp. 857 - 869
Biochemistry & Molecular Biology | Genetics & Heredity | Life Sciences & Biomedicine | Biotechnology & Applied Microbiology | Science & Technology | Pyramidal Cells - cytology | Chromatin - metabolism | Pyramidal Cells - metabolism | Transposases - metabolism | Cells, Cultured | Sequence Analysis, DNA | Hippocampus - metabolism | Neuronal Plasticity - genetics | Animals | Cell Nucleus - metabolism | Cell Nucleus - genetics | Epigenomics - methods | Single-Cell Analysis - methods | Transposases - genetics | Mice | Chromatin - genetics | Cell Lineage - genetics | Chromatin | Maps | Transposase | Pyramidal cells | Hippocampus | Index Medicus | Resource
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10. Full Text A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility
by Cusanovich, Darren A and Hill, Andrew J and Aghamirzaie, Delasa and Daza, Riza M and Pliner, Hannah A and Berletch, Joel B and Filippova, Galina N and Huang, Xingfan and Christiansen, Lena and DeWitt, William S and Lee, Choli and Regalado, Samuel G and Read, David F and Steemers, Frank J and Disteche, Christine M and Trapnell, Cole and Shendure, Jay
Cell (Cambridge), ISSN 0092-8674, 08/2018, Volume 174, Issue 5, pp. 1309 - 1324.e18
single cell | GWAS | chromatin accessibility | regulatory | epigenomics | chromatin | epigenetics | ATAC-seq | Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Science & Technology | Cell Biology | Epigenetic inheritance | Chromatin | Genetic transcription | Analysis | Genomics | Cells | Index Medicus
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