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1. Full Text Abstract B1-15: Identification of evolutionarily conserved hypoxia-induced genomic pathways responsible for aggressive neuroblastoma phenotypes
by Aplebaum, Mark A and Jha, Aashish R and Chlenski, Alexandre and Hernandez, Kyle and Mariani, Christopher J and Stranger, Barbara E and Cohn, Susan L
Cancer Research, ISSN 0008-5472, 11/2015, Volume 75, Issue 22 Supplement 2, pp. B1 - B1-15
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2. Full Text Abstract A2-55: Identification of evolutionarily conserved hypoxia-induced genomic pathways responsible for aggressive neuroblastoma phenotypes
by Applebaum, Mark A and Jha, Aashish R and Chlenski, Alexandre and Hernandez, Kyle and Mariani, Christopher J and Stranger, Barbara E and Cohn, Susan L
Cancer Research, ISSN 0008-5472, 11/2015, Volume 75, Issue 22 Supplement 1, pp. A2 - A2-55
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3. Full Text Erratum: MiR-9a Minimizes the phenotypic impact of genomic diversity by buffering a transcription factor (Cell (2013) 155 (1556-1567))
by Cassidy, Justin J and Jha, Aashish R and Posadas, Diana M and Giri, Ritika and Venken, Koen J.T and Ji, Jingran and Jiang, Hongmei and Bellen, Hugo J and White, Kevin P and Carthew, Richard W
Cell, ISSN 0092-8674, 04/2014, Volume 157, Issue 3, p. 753
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4. Full Text Ancient human genomes suggest three ancestral populations for present-day Europeans
by Lazaridis, Iosif and Lazaridis, Iosif and Patterson, Nick and Patterson, Nick and Mittnik, Alissa and Mittnik, Alissa and Renaud, Gabriel and Renaud, Gabriel and Mallick, Swapan and Mallick, Swapan and Kirsanow, Karola and Kirsanow, Karola and Sudmant, Peter H and Sudmant, Peter H and Schraiber, Joshua G and Schraiber, Joshua G and Castellano, Sergi and Castellano, Sergi and Lipson, Mark and Lipson, Mark and Berger, Bonnie and Berger, Bonnie and Economou, Christos and Economou, Christos and Bollongino, Ruth and Bollongino, Ruth and Fu, Qiaomei and Fu, Qiaomei and Bos, Kirsten I and Bos, Kirsten I and Nordenfelt, Susanne and Nordenfelt, Susanne and Li, Heng and Li, Heng and de Filippo, Cesare and De Filippo, Cesare and Prüfer, Kay and Prüfer, Kay and Sawyer, Susanna and Sawyer, Susanna and Posth, Cosimo and Posth, Cosimo and Haak, Wolfgang and Haak, Wolfgang and Hallgren, Fredrik and Hallgren, Fredrik and Fornander, Elin and Fornander, Elin and Rohland, Nadin and Rohland, Nadin and Delsate, Dominique and Delsate, Dominique and Francken, Michael and Francken, Michael and Guinet, Jean-Michel and Guinet, Jean-Michel and Wahl, Joachim and Wahl, Joachim and Ayodo, George and Ayodo, George and Babiker, Hamza A and Babiker, Hamza A and Bailliet, Graciela and Bailliet, Graciela and Balanovska, Elena and Balanovska, Elena and Balanovsky, Oleg and Balanovsky, Oleg and Barrantes, Ramiro and Barrantes, Ramiro and Bedoya, Gabriel and Bedoya, Gabriel and Ben-Ami, Haim and Ben-Ami, Haim and Bene, Judit and Bene, Judit and Berrada, Fouad and Berrada, Fouad and Bravi, Claudio M and Bravi, Claudio M and Brisighelli, Francesca and Brisighelli, Francesca and Busby, George B J and Busby, George B.J and Cali, Francesco and Cali, Francesco and Churnosov, Mikhail and Churnosov, Mikhail and Cole, David E C and Cole, David E.C and Corach, Daniel and Corach, Daniel and Damba, Larissa and Damba, Larissa and Van Driem, George and van Driem, George and Dryomov, Stanislav and Dryomov, Stanislav and Dugoujon, Jean-Michel and Dugoujon, Jean-Michel and ... and Humanistiska fakulteten and Stockholms universitet and Institutionen för arkeologi och antikens kultur and Arkeologiska forskningslaboratoriet
Nature, ISSN 0028-0836, 2014, Volume 513, Issue 7518, pp. 409 - 413
We sequenced the genomes of a similar to 7,000-year-old farmer from Germany and eight similar to 8,000-year-old hunter-gatherers from Luxembourg and Sweden. We... 
GENETIC DIVERSITY | AFRICA | CAVE | FARMERS | MULTIDISCIPLINARY SCIENCES | NEANDERTHAL | WIDE ASSOCIATION | DNA-SEQUENCING DATA | ADMIXTURE | HUNTER-GATHERERS | HISTORY | Europeans | Human genome | Genetic research | Genetic aspects | Research | Population genetics | Natural history | Population | Genomes | Genealogy | Index Medicus | Quantitative Biology - Populations and Evolution | Genètica de poblacions humanes | Genoma humà | Arkeologi | Humanities | Archaeology | Historia och arkeologi | History and Archaeology | Humaniora
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5. Full Text The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
by Mallick, Swapan and Li, Heng and Lipson, Mark and Mathieson, Iain and Gymrek, Melissa and Racimo, Fernando and Zhao, Mengyao and Chennagiri, Niru and Nordenfelt, Susanne and Tandon, Arti and Skoglund, Pontus and Lazaridis, Iosif and Sankararaman, Sriram and Fu, Qiaomei and Rohland, Nadin and Renaud, Gabriel and Erlich, Yaniv and Willems, Thomas and Gallo, Carla and Spence, Jeffrey P and Song, Yun S and Poletti, Giovanni and Balloux, Francois and Van Driem, George and De Knijff, Peter and Romero, Irene Gallego and Jha, Aashish R and Behar, Doron M and Bravi, Claudio M and Capelli, Cristian and Hervig, Tor and Moreno-Estrada, Andres and Posukh, Olga L and Balanovska, Elena and Balanovsky, Oleg and Karachanak-Yankova, Sena and Sahakyan, Hovhannes and Toncheva, Draga and Yepiskoposyan, Levon and Tyler-Smith, Chris and Xue, Yali and Abdullah, M. Syafiq and Ruiz-Linares, Andres and Beall, Cynthia M and Di Rienzo, Anna and Jeong, Choongwon and Starikovskaya, Elena B and Metspalu, Ene and Parik, Jüri and Villems, Richard and Henn, Brenna M and Hodoglugil, Ugur and Mahley, Robert and Sajantila, Antti and Stamatoyannopoulos, George and Wee, Joseph T. S and Khusainova, Rita and Khusnutdinova, Elza and Litvinov, Sergey and Ayodo, George and Comas, David and Hammer, Michael F and Kivisild, Toomas and Klitz, William and Winkler, Cheryl A and Labuda, Damian and Bamshad, Michael and Jorde, Lynn B and Tishkoff, Sarah A and Watkins, W. Scott and Metspalu, Mait and Dryomov, Stanislav and Sukernik, Rem and Singh, Lalji and Thangaraj, Kumarasamy and Paäbo, Svante and Kelso, Janet and Patterson, Nick and Reich, David
Nature, ISSN 0028-0836, 2016, Volume 538, Issue 7624, pp. 201 - 206
Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at... 
DISPERSAL | AFRICA | MUTATION-RATE | MODERN HUMANS | MULTIDISCIPLINARY SCIENCES | SEQUENCE | NEANDERTHAL | ADMIXTURE | INFERENCE | ANCESTRY | HISTORY | Genetics, Population | History, Ancient | Datasets as Topic | Species Specificity | Genomics | Humans | Mutation Rate | Neanderthals - genetics | Continental Population Groups - genetics | Phylogeny | Sequence Analysis, DNA | Genome, Human - genetics | Human Migration - history | New Guinea | Animals | Time Factors | Genetic Variation - genetics | African Continental Ancestry Group - genetics | Australia | Oceanic Ancestry Group - genetics | Genetic research | Genomes | Research | Biological diversity | Datasets | Demography | Population | Genetic diversity | Mutation | Hominids | Index Medicus | Genètica | Filogènia | Genoma humà | Genòmica
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6. Full Text An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia
by Morten Rasmussen and Xiaosen Guo and Yong Wang and Kirk E. Lohmueller and Simon Rasmussen and Anders Albrechtsen and Line Skotte and Stinus Lindgreen and Mait Metspalu and Thibaut Jombart and Toomas Kivisild and Weiwei Zhai and Anders Eriksson and Andrea Manica and Ludovic Orlando and Francisco M. De La Vega and Silvana Tridico and Ene Metspalu and Kasper Nielsen and María C. Ávila-Arcos and J. Víctor Moreno-Mayar and Craig Muller and Joe Dortch and M. Thomas P. Gilbert and Ole Lund and Agata Wesolowska and Monika Karmin and Lucy A. Weinert and Bo Wang and Jun Li and Shuaishuai Tai and Fei Xiao and Tsunehiko Hanihara and George van Driem and Aashish R. Jha and François-Xavier Ricaut and Peter de Knijff and Andrea B Migliano and Irene Gallego Romero and Karsten Kristiansen and David M. Lambert and Søren Brunak and Peter Forster and Bernd Brinkmann and Olaf Nehlich and Michael Bunce and Michael Richards and Ramneek Gupta and Carlos D. Bustamante and Anders Krogh and Robert A. Foley and Marta M. Lahr and Francois Balloux and Thomas Sicheritz-Pontén and Richard Villems and Rasmus Nielsen and Jun Wang and Eske Willerslev
Science, ISSN 0036-8075, 10/2011, Volume 334, Issue 6052, pp. 94 - 98
We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in... 
Gene flow | Highlands | Aboriginal Australians | Genomics | REPORTS | Alleles | Admixtures | Genomes | Modeling | We they distinction | Asians | Y-CHROMOSOME | NEW-GUINEA | HUMAN-EVOLUTION | MULTIDISCIPLINARY SCIENCES | SEQUENCE | SETTLEMENT | DIVERSITY | MODEL | ESKIMO | HISTORY | Haplotypes | Western Australia | Humans | Asian Continental Ancestry Group - genetics | Male | Phylogeny | Hominidae - genetics | DNA, Mitochondrial - genetics | Ethnic Groups - genetics | Computer Simulation | Far East | Oceanic Ancestry Group - genetics | European Continental Ancestry Group - genetics | Gene Flow | Gene Frequency | Sequence Analysis, DNA | Linkage Disequilibrium | Animals | Genetics, Population - methods | Asia | Polymorphism, Single Nucleotide | Genome, Mitochondrial | African Continental Ancestry Group | Genome, Human | Emigration and Immigration | Physiological aspects | Australian aborigines | Genetic aspects | Research | Nucleotide sequencing | Population genetics | Human genetics | DNA sequencing | Mobility | Native peoples | Dispersal | Contamination | Index Medicus | Populations and Evolution | DNA, Mitochondrial | Humanities and Social Sciences | Life Sciences | Ethnic Groups | Biological anthropology | Genetics | Hominidae | Oceanic Ancestry Group | Genetics, Population | European Continental Ancestry Group | Asian Continental Ancestry Group
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7. Full Text Gut microbiome transition across a lifestyle gradient in Himalaya
by Jha, Aashish R and Jha, Aashish R and Davenport, Emily R and Gautam, Yoshina and Bhandari, Dinesh and Bhandari, Dinesh and Tandukar, Sarmila and Tandukar, Sarmila and Ng, Katharine M and Ng, Katharine M and Fragiadakis, Gabriela K and Holmes, Susan and Gautam, Guru Prasad and Leach, Jeff and Leach, Jeff and Sherchand, Jeevan Bahadur and Sherchand, Jeevan Bahadur and Bustamante, Carlos D and Bustamante, Carlos D and Sonnenburg, Justin L and Sonnenburg, Justin L
PLoS biology, ISSN 1544-9173, 11/2018, Volume 16, Issue 11, pp. e2005396 - e2005396
The composition of the gut microbiome in industrialized populations differs from those living traditional lifestyles. However, it has been difficult to... 
HEALTH | DIET | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOLOGY | Geography | Drinking water | Visualization | Divergence | Cooking | Populations | Arsenic | Laboratories | Funding | Communities | Microbiomes | Population genetics | Microorganisms | Immunology | Dependence | Genetics | Bacteria | Bioinformatics | Supervision | Public health | Medical research | Composition | Hunting | Environmental factors | Diet | Software | Lifestyles | Harbors | Farming | Reconfiguration | Index Medicus
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8. Full Text Tim-3 marks human natural killer cell maturation and suppresses cell-mediated cytotoxicity
by Ndhlovu, Lishomwa C and Lopez-Vergès, Sandra and Barbour, Jason D and Brad Jones, R and Jha, Aashish R and Long, Brian R and Schoeffler, Eric C and Fujita, Tsuyoshi and Nixon, Douglas F and Lanier, Lewis L
Blood, ISSN 0006-4971, 04/2012, Volume 119, Issue 16, pp. 3734 - 3743
Natural killer (NK) cells are innate lymphocytes that play an important role against viral infections and cancer. This effect is achieved through a complex... 
IMMUNITY | MULTIPLE-SCLEROSIS | ELEVATED FREQUENCIES | APOPTOTIC CELLS | INHIBITORY RECEPTOR | CD56(DIM) NK CELLS | HEMATOLOGY | EXPRESSION | CD8(+) T-CELLS | CONTAINING MOLECULE-3 TIM-3 | Biomarkers - metabolism | T-Lymphocytes, Cytotoxic - immunology | CD56 Antigen - metabolism | Cell Line | GPI-Linked Proteins - immunology | Humans | Immunophenotyping | Membrane Proteins - immunology | Receptors, IgG - immunology | Hepatitis A Virus Cellular Receptor 2 | GPI-Linked Proteins - metabolism | Lymphocyte Subsets - immunology | Receptors, IgG - metabolism | Cross-Linking Reagents - metabolism | Cell Differentiation - immunology | Killer Cells, Natural - cytology | Lymphocyte Subsets - metabolism | Up-Regulation - immunology | Killer Cells, Natural - immunology | Ligands | Membrane Proteins - metabolism | CD56 Antigen - immunology | T-Lymphocytes, Cytotoxic - cytology | Index Medicus | Abridged Index Medicus | Immunobiology
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9. Full Text Tim-3 expression defines a novel population of dysfunctional T cells with highly elevated frequencies in progressive HIV-1 infection
by Jones, R. Brad and Ndhlovu, Lishomwa C and Barbour, Jason D and Sheth, Prameet M and Jha, Aashish R and Long, Brian R and Wong, Jessica C and Satkunarajah, Malathy and Schweneker, Marc and Chapman, Joan M and Gyenes, Gabor and Vali, Bahareh and Hyrcza, Martin D and Yue, Feng Yun and Kovacs, Colin and Sassi, Aref and Loutfy, Mona and Halpenny, Roberta and Persad, Desmond and Spotts, Gerald and Hecht, Frederick M and Chun, Tae-Wook and McCune, Joseph M and Kaul, Rupert and Rini, James M and Nixon, Douglas F and Ostrowski, Mario A
Journal of Experimental Medicine, ISSN 0022-1007, 11/2008, Volume 205, Issue 12, pp. 2763 - 2779
Progressive loss of T cell functionality is a hallmark of chronic infection with human immunodeficiency virus 1 (HIV-1). We have identified a novel population... 
MEDICINE, RESEARCH & EXPERIMENTAL | SKEWED MATURATION | ACTIVATION | MULTIPLE-SCLEROSIS | IMMUNODEFICIENCY-VIRUS-INFECTION | IMPAIRED FUNCTION | CD4(+) | IMMUNOLOGY | CHRONIC VIRAL-INFECTION | DISEASE PROGRESSION | LYMPHOCYTES | ANTIGEN | GATA3 Transcription Factor - genetics | T-Lymphocyte Subsets - immunology | Antigens, CD - immunology | HIV-1 - pathogenicity | T-Lymphocyte Subsets - cytology | GATA3 Transcription Factor - immunology | Humans | STAT5 Transcription Factor - immunology | T-Box Domain Proteins - immunology | Antigens, CD - genetics | Extracellular Signal-Regulated MAP Kinases - genetics | Extracellular Signal-Regulated MAP Kinases - immunology | HIV Infections - immunology | STAT5 Transcription Factor - genetics | Signal Transduction - immunology | HIV Infections - pathology | Apoptosis Regulatory Proteins - genetics | Apoptosis Regulatory Proteins - immunology | Membrane Proteins - genetics | p38 Mitogen-Activated Protein Kinases - genetics | Membrane Proteins - immunology | p38 Mitogen-Activated Protein Kinases - immunology | Hepatitis A Virus Cellular Receptor 2 | T-Box Domain Proteins - genetics | Disease Progression | Antiretroviral Therapy, Highly Active | HIV-1 - immunology | Phenotype | Animals | T-Lymphocytes - cytology | HIV Infections - drug therapy | Programmed Cell Death 1 Receptor | T-Lymphocytes - immunology | HIV Infections - physiopathology | HLA Antigens | Index Medicus
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10. Full Text Whole-genome resequencing of experimental populations reveals polygenic basis of egg-size variation in drosophila melanogaster
by Jha, Aashish R and Miles, Cecelia M and Lippert, Nodia R and Brown, Christopher D and White, Kevin P and Kreitman, Martin
Molecular Biology and Evolution, ISSN 0737-4038, 10/2015, Volume 32, Issue 10, pp. 2616 - 2632
Complete genome resequencing of populations holds great promise in deconstructing complex polygenic traits to elucidate molecular and developmental mechanisms... 
pooled sequencing | experimental evolution | polygenic adaptation | egg size | adaptation | complex traits | evolution | MORPHOLOGICAL TRAITS | FITNESS-RELATED TRAITS | PHENOTYPIC PLASTICITY | BIOCHEMISTRY & MOLECULAR BIOLOGY | OVARIOLE NUMBER | TROPICAL POPULATIONS | EVOLUTIONARY BIOLOGY | POSITIVE SELECTION | SELECTION EXPERIMENTS | LIFE-HISTORY CONSEQUENCES | GENETICS & HEREDITY | STANDING GENETIC-VARIATION | Multifactorial Inheritance - genetics | Gene Frequency - genetics | Genetic Association Studies | Drosophila melanogaster - cytology | Gene Expression Regulation | Cell Size | Male | Directed Molecular Evolution | Drosophila melanogaster - genetics | Genetic Variation | Ovum - cytology | Phenotype | Animals | Female | Genome, Insect | Sequence Analysis, DNA - methods | Gene Ontology | Crosses, Genetic | Genomes | Biological variation | Genomics | Genes | Generalized linear models | Polymorphism | Index Medicus | Discoveries
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11. Full Text Shared Genetic Signals of Hypoxia Adaptation inDrosophilaand in High-Altitude Human Populations
by Jha, Aashish R and Zhou, Dan and Brown, Christopher D and Kreitman, Martin and Haddad, Gabriel G and White, Kevin P
Molecular Biology and Evolution, ISSN 0737-4038, 02/2016, Volume 33, Issue 2, pp. 501 - 517
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12. Full Text miR-9a Minimizes the Phenotypic Impact of Genomic Diversity by Buffering a Transcription Factor
by Cassidy, Justin J and Jha, Aashish R and Posadas, Diana M and Giri, Ritika and Venken, Koen J.T and Ji, Jingran and Jiang, Hongmei and Bellen, Hugo J and White, Kevin P and Carthew, Richard W
Cell, ISSN 0092-8674, 12/2013, Volume 155, Issue 7, pp. 1556 - 1567
Gene expression has to withstand stochastic, environmental, and genomic perturbations. For example, in the latter case, 0.5%–1% of the human genome is... 
DNA-BINDING | EVOLUTION | DROSOPHILA-MELANOGASTER | ACHAETE | CANALIZATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | GENES | SCUTE | BRISTLES | MICRORNAS | SENSELESS | CELL BIOLOGY | Drosophila melanogaster - metabolism | Genetic Variation | Transcription Factors - metabolism | Animals | Female | Male | MicroRNAs - metabolism | Nuclear Proteins - metabolism | Genome, Insect | Drosophila Proteins - metabolism | Gene Regulatory Networks | Drosophila melanogaster - genetics | MicroRNA | Gene expression | Developmental biology | Analysis | Genes | Genomics | Index Medicus
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13. Full Text Global diversity, population stratification, and selection of human copy-number variation
by Sudmant, Peter H and Mallick, Swapan and Nelson, Bradley J and Hormozdiari, Fereydoun and Krumm, Niklas and Huddleston, John and Coe, Bradley P and Baker, Carl and Nordenfelt, Susanne and Bamshad, Michael and Jorde, Lynn B and Posukh, Olga L and Sahakyan, Hovhannes and Watkins, W. Scott and Yepiskoposyan, Levon and Abdullah, M. Syafiq and Bravi, Claudio M and Capelli, Cristian and Hervig, Tor and Wee, Joseph T. S and Tyler-Smith, Chris and Van Driem, George and Romero, Irene Gallego and Jha, Aashish R and Karachanak-Yankova, Sena and Toncheva, Draga and Comas, David and Henn, Brenna and Kivisild, Toomas and Ruiz-Linares, Andres and Sajantila, Antti and Metspalu, Ene and Parik, Jüri and Villems, Richard and Starikovskaya, Elena B and Ayodo, George and Beall, Cynthia M and Di Rienzo, Anna and Hammer, Michael F and Khusainova, Rita and Khusnutdinova, Elza and Klitz, William and Winkler, Cheryl and Labuda, Damian and Metspalu, Mait and Tishkoff, Sarah A and Dryomov, Stanislav and Sukernik, Rem and Patterson, Nick and Reich, David and Eichler, Evan E
Science, ISSN 0036-8075, 09/2015, Volume 349, Issue 6253, pp. aab3761 - aab3761
In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125... 
MICRODELETION | POLYMORPHISMS | AUTISM | HUMAN GENOME SEQUENCE | CODING VARIATION | MULTIDISCIPLINARY SCIENCES | REGIONS | SEGMENTAL DUPLICATIONS | ASSOCIATION | DELETION | HISTORY | Gene Duplication | African Continental Ancestry Group - classification | Sequence Deletion | Humans | Selection, Genetic | Oceanic Ancestry Group - classification | Phylogeny | Hominidae - genetics | Genome, Human - genetics | DNA Copy Number Variations | Animals | Polymorphism, Single Nucleotide | African Continental Ancestry Group - genetics | Oceanic Ancestry Group - genetics | Population - genetics | Evolution, Molecular | Population genetics | Genomics | Genetic diversity | Index Medicus | Reproduction | Genes | Deletion | Genetics | Genomes | High frequencies | Signatures | Loci | Polimorfisme genètic | Duplicació cromosòmica | Evolució molecular | Genoma humà
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