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1. Full Text Make outbreak research open access
by Yozwiak, NL and Schaffner, SF and Sabeti, PC
NATURE, ISSN 0028-0836, 02/2015, Volume 518, Issue 7540, pp. 477 - 479
  In an increasingly connected world, rapid sequencing, combined with new ways to collect clinical and epidemiological data, could transform our response to... 
MULTIDISCIPLINARY SCIENCES | Studies | Datasets | Epidemics | Genomics | Genomes | Epidemiology | Open access
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2. Full Text Data sharing: Make outbreak research open access
by Yozwiak, Nathan L and Schaffner, Stephen F and Sabeti, Pardis C
Nature, ISSN 0028-0836, 02/2015, Volume 518, Issue 7540, pp. 477 - 479
Biomedical Research - ethics | Guidelines as Topic | Sierra Leone - epidemiology | Humans | Biomedical Research - organization & administration | Disease Outbreaks - statistics & numerical data | Ebolavirus - genetics | Hemorrhagic Fever, Ebola - therapy | Research Personnel - organization & administration | Hemorrhagic Fever, Ebola - diagnosis | Publishing | Coronavirus Infections - epidemiology | Time Factors | Genomics - organization & administration | Hemorrhagic Fever, Ebola - virology | Influenza, Human - virology | Genomics - methods | Information Dissemination - ethics | Information Dissemination - methods | Cooperative Behavior | Influenza, Human - epidemiology | International Cooperation | Virology - organization & administration | Guinea - epidemiology | Hemorrhagic Fever, Ebola - epidemiology | Access to Information - ethics | Coronavirus Infections - virology | Disease Outbreaks - prevention & control | Internet | Databases, Nucleic Acid
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3. Full Text Detecting Natural Selection in Genomic Data
by Vitti, Joseph J and Grossman, Sharon R and Sabeti, Pardis C
Annual Review of Genetics, ISSN 0066-4197, 11/2013, Volume 47, Issue 1, pp. 97 - 120
The past fifty years have seen the development and application of numerous statistical methods to identify genomic regions that appear to be shaped by natural... 
population genetics | adaptation | evolutionary genomics | selective sweeps | genome scans | Evolutionary genomics | Genome scans | Population genetics | Adaptation | Selective sweeps | SOFT SWEEPS | MOLECULAR POPULATION-GENETICS | ADAPTIVE PROTEIN EVOLUTION | KRAKAUER TEST | PLASMODIUM-VIVAX | HIGH-ALTITUDE ADAPTATION | RECENT POSITIVE SELECTION | ASCERTAINMENT BIASES | GENETICS & HEREDITY | STATISTICAL TESTS | STRUCTURAL VARIATION | Multifactorial Inheritance - genetics | Gene Frequency | Genomics | Humans | Mutation Rate | Genotyping Techniques | Forecasting | Sequence Analysis, DNA | Linkage Disequilibrium | Selection, Genetic - genetics | Phenotype | Animals | Genetics, Population - methods | Adaptation, Physiological - genetics | Alleles | Models, Genetic | Mutation | Amino Acid Substitution | Evolution, Molecular | Statistical methods | Research | Natural selection | Evolution
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4. Full Text Natural selection and infectious disease in human populations
by Karlsson, Elinor K and Kwiatkowski, Dominic P and Sabeti, Pardis C
Nature Reviews Genetics, ISSN 1471-0056, 2014, Volume 15, Issue 6, pp. 379 - 393
The ancient biological 'arms race' between microbial pathogens and humans has shaped genetic variation in modern populations, and this has important... 
HUMAN GENETIC SUSCEPTIBILITY | CHRONIC HEPATITIS-B | HUMAN-CELLS | RECENT POSITIVE SELECTION | GENETICS & HEREDITY | MAJOR HISTOCOMPATIBILITY COMPLEX | AFRICAN-AMERICANS | PLASMODIUM-VIVAX | VIBRIO-CHOLERAE | GENOME-WIDE ASSOCIATION | DUFFY-BLOOD-GROUP | Communicable Diseases, Emerging - genetics | Communicable Diseases, Emerging - epidemiology | Humans | Selection, Genetic | Communicable Diseases, Emerging - metabolism | Genetic susceptibility | Genetic variation | Communicable diseases | Genotype | Genetic aspects | Risk factors | Natural selection
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5. Full Text Make outbreak research open access: establish principles for rapid and responsible data sharing in epidemics.(Viewpoint essay)
by Yozwiak, Nathan L and Schaffner, Stephen F and Sabeti, Pardis C
Nature, ISSN 0028-0836, 02/2015, Volume 518, Issue 7540, p. 477
Epidemics | Medical research | Genetic research | Medicine, Experimental | Ebola virus infections | Genetic aspects | Research | Methods
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6. Full Text Detecting Novel Associations in Large Data Sets
by David N. Reshef and Yakir A. Reshef and Hilary K. Finucane and Sharon R. Grossman and Gilean McVean and Peter J. Turnbaugh and Eric S. Lander and Michael Mitzenmacher and Pardis C. Sabeti
Science, ISSN 0036-8075, 12/2011, Volume 334, Issue 6062, pp. 1518 - 1524
Identifying interesting relationships between pairs of variables in large data sets is increasingly important. Here, we present a measure of dependence for... 
Datasets | Baseball statistics | Microbiota | Sample size | Diet | RESEARCH ARTICLES | Genes | Mathematical functions | Coefficients | Statistics | Estimators | REGRESSION | INFORMATION | MULTIDISCIPLINARY SCIENCES | MICROBIOME | HEALTH | PRINCIPAL CURVES | CYCLE | Obesity | Data Interpretation, Statistical | Gene Expression | Baseball - statistics & numerical data | Saccharomyces cerevisiae - genetics | Humans | Male | Algorithms | Animals | Intestines - microbiology | Female | Genes, Fungal | Mice | Genomics - methods | Metagenome | Physiological aspects | Research | Microbiota (Symbiotic organisms) | Gene expression | Data analysis
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7. Detecting Natural Selection in Genomic Data
by Vitti, Joseph J and Grossman, Sharon R and Sabeti, Pardis C
Annual Review of Genetics, ISSN 0066-4197, 01/2013, Volume 47, pp. 97 - 97
The past fifty years have seen the development and application of numerous statistical methods to identify genomic regions that appear to be shaped by natural... 
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8. Full Text Nucleic acid detection with CRISPR-Cas13a/C2c2
by Gootenberg, Jonathan S and Abudayyeh, Omar O and Lee, Jeong Wook and Essletzbichler, Patrick and Dy, Aaron J and Joung, Julia and Verdine, Vanessa and Donghia, Nina and Daringer, Nichole M and Freije, Catherine A and Myhrvold, Cameron and Bhattacharyya, Roby P and Livny, Jonathan and Regev, Aviv and Koonin, Eugene V and Hung, Deborah T and Sabeti, Pardis C and Collins, James J and Zhang, Feng
Science, ISSN 0036-8075, 04/2017, Volume 356, Issue 6336, pp. 438 - 442
Rapid, inexpensive, and sensitive nucleic acid detection may aid point-of-care pathogen detection, genotyping, and disease monitoring. The RNA-guided,... 
CRISPR-CAS SYSTEMS | AMPLIFICATION | CIRCULATING TUMOR DNA | PROTEINS | MULTIDISCIPLINARY SCIENCES | ZIKA VIRUS | Circulating Tumor DNA - analysis | Zika Virus - genetics | Circulating Tumor DNA - genetics | Ribonucleases - chemistry | Humans | Bacterial Proteins - chemistry | RNA, Viral - analysis | RNA Cleavage | Zika Virus - isolation & purification | Dengue Virus - genetics | Bacteria - isolation & purification | RNA, Viral - genetics | Zika Virus Infection - diagnosis | Neoplasms - genetics | Point-of-Care Systems | Clustered Regularly Interspaced Short Palindromic Repeats | DNA, Bacterial - analysis | Bacteria - pathogenicity | Dengue Virus - isolation & purification | Mutation | Dengue - diagnosis | Methods | Nucleotide sequencing | DNA sequencing | Vector-borne diseases | Pathogens | CRISPR | Target recognition | Nucleotide sequence | Dengue | Viruses | Zika virus | Nucleic acids | Ribonuclease | Recombinase | Ribonucleic acid--RNA | Sensitivity | Genotyping | Reagents | Bacteria | Deoxyribonucleic acid--DNA | Amplification | Ribonucleic acids | Deoxyribonucleic acid
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9. Full Text A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection
by Sharon R. Grossman and Ilya Shylakhter and Elinor K. Karlsson and Elizabeth H. Byrne and Shannon Morales and Gabriel Frieden and Elizabeth Hostetter and Elaine Angelino and Manuel Garber and Or Zuk and Eric S. Lander and Stephen F. Schaffner and Pardis C. Sabeti
Science, ISSN 0036-8075, 2/2010, Volume 327, Issue 5967, pp. 883 - 886
The human genome contains hundreds of regions whose patterns of genetic variation indicate recent positive natural selection, yet for most the underlying gene... 
Haplotypes | Datasets | Genes | Positive selection | Humans | Alleles | Genetic loci | Evolution | Reports | Genomes | Genetic mutation | MULTIDISCIPLINARY SCIENCES | Computational Biology - methods | Selection, Genetic | Population Groups - genetics | Genetic Loci | DNA, Intergenic - genetics | Regulatory Sequences, Nucleic Acid - genetics | Polymorphism, Genetic | Genetic Variation | Software | Genome, Human | Evolution, Molecular | Research | Human genome | Genetic variation | Identification and classification | Natural selection | Signal transduction | Genetic diversity | Mutation | Evolutionary biology | Cellular biology | Genomics
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10. Full Text Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak
by Gire, Stephen K and Goba, Augustine and Andersen, Kristian G and Sealfon, Rachel S. G and Park, Daniel J and Kanneh, Lansana and Jalloh, Simbirie and Momoh, Mambu and Fullah, Mohamed and Dudas, Gytis and Wohl, Shirlee and Moses, Lina M and Yozwiak, Nathan L and Winnicki, Sarah and Matranga, Christian B and Malboeuf, Christine M and Qu, James and Gladden, Adrianne D and Schaffner, Stephen F and Yang, Xiao and Jiang, Pan-Pan and Nekoui, Mahan and Colubri, Andres and Ruth Coomber, Moinya and Fonnie, Mbalu and Moigboi, Alex and Gbakie, Michael and Kamara, Fatima K and Tucker, Veronica and Konuwa, Edwin and Saffa, Sidiki and Sellu, Josephine and Azziz Jalloh, Abdul and Kovoma, Alice and Koninga, James and Mustapha, Ibrahim and Kargbo, Kandeh and Foday, Momoh and Yillah, Mohamed and Kanneh, Franklyn and Robert, Willie and Massally, James L. B and Chapman, Sinéad B and Bochicchio, James and Murphy, Cheryl and Nusbaum, Chad and Young, Sarah and Birren, Bruce W and Grant, Donald S and Scheiffelin, John S and Lander, Eric S and Happi, Christian and Gevao, Sahr M and Gnirke, Andreas and Rambaut, Andrew and Garry, Robert F and Humarr Khan, S and Sabeti, Pardis C
Science, ISSN 0036-8075, 09/2014, Volume 345, Issue 6202, pp. 1369 - 1372
In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 Ebola virus genomes from 78... 
POLYMERASE | RNA | PURIFYING SELECTION | HEMORRHAGIC-FEVER | MULTIDISCIPLINARY SCIENCES | Sierra Leone - epidemiology | Genome, Viral - genetics | Humans | Hemorrhagic Fever, Ebola - transmission | Ebolavirus - genetics | Hemorrhagic Fever, Ebola - epidemiology | Sequence Analysis, DNA | Ebolavirus - isolation & purification | Genetic Variation | Epidemiological Monitoring | Disease Outbreaks | Base Sequence | Hemorrhagic Fever, Ebola - virology | Mutation | Genomics - methods | Medical research | Disease transmission | Genomics | Distribution | Medicine, Experimental | Ebola virus infections | Genetic aspects | Research | Sentinel health events | Ebola virus | Epidemics | Origins | Surveillance | Mortality | Viral diseases | Viruses | Outbreaks | Evolution | Central Africa
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11. Full Text Clinical Illness and Outcomes in Patients with Ebola in Sierra Leone
by Schieffelin, John S and Shaffer, Jeffrey G and Goba, Augustine and Gbakie, Michael and Gire, Stephen K and Colubri, Andres and Sealfon, Rachel S.G and Kanneh, Lansana and Kanneh, Franklyn and Moigboi, Alex and Momoh, Mambu and Fullah, Mohammed and Moses, Lina M and Brown, Bethany L and Andersen, Kristian G and Winnicki, Sarah and Schaffner, Stephen F and Park, Daniel J and Yozwiak, Nathan L and Jiang, Pan-Pan and Kargbo, David and Jalloh, Simbirie and Fonnie, Mbalu and Sinnah, Vandi and French, Issa and Kovoma, Alice and Kamara, Fatima K and Tucker, Veronica and Konuwa, Edwin and Sellu, Josephine and Mustapha, Ibrahim and Foday, Momoh and Yillah, Mohamed and Saffa, Sidiki and Massally, James L.B and Boisen, Matt L and Branco, Luis M and Vandi, Mohamed A and Grant, Donald S and Happi, Christian and Gevao, Sahr M and Fletcher, Thomas E and Fowler, Robert A and Bausch, Daniel G and Sabeti, Pardis C and Khan, S. Humarr and Garry, Robert F and Viral Hemorrhagic Fever Consortium and WHO Clinical Response Team and KGH Lassa Fever Program
The New England Journal of Medi