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1

Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals

Chen, Lu, Wolf, Aaron B., Fu, Wenqing, Li, Liming, Akey, Joshua M.

Journal:

Year:

2020

Language:

english

File:

PDF, 2.75 MB

english, 2020

2

Tracing the peopling of the world through genomics

Nielsen, Rasmus, Akey, Joshua M., Jakobsson, Mattias, Pritchard, Jonathan K., Tishkoff, Sarah, Willerslev, Eske

Journal:

Year:

2017

Language:

english

File:

PDF, 719 KB

english, 2017

3

The Date of Interbreeding between Neandertals and Modern Humans

Sankararaman, Sriram, Patterson, Nick, Li, Heng, Pääbo, Svante, Reich, David, Akey, Joshua M.

Journal:

Year:

2012

Language:

english

File:

PDF, 427 KB

english, 2012

4

Y-Chromosome Evidence for a Northward Migration of Modern Humans into Eastern Asia during the Last Ice Age

Bing Su, Junhua Xiao, Peter Underhill, Ranjan Deka, Weiling Zhang, Joshua Akey, Wei Huang, Di Shen, Daru Lu, Jingchun Luo, Jiayou Chu, Jiazhen Tan, Peidong Shen, Ron Davis, Luca Cavalli-Sforza, Ranaji

Journal:

The American Journal of Human Genetics

Year:

1999

Language:

english

File:

PDF, 1.53 MB

english, 1999

5

Complex History of Admixture between Modern Humans and Neandertals

Vernot, Benjamin, Akey, Joshua M.

Journal:

The American Journal of Human Genetics

Year:

2015

Language:

english

File:

PDF, 344 KB

english, 2015

6

Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression

McCoy, Rajiv C., Wakefield, Jon, Akey, Joshua M.

Journal:

Year:

2017

Language:

english

File:

PDF, 4.40 MB

english, 2017

7

Models of archaic admixture and recent history from two-locus statistics

Ragsdale, Aaron P., Gravel, Simon, Akey, Joshua M.

Journal:

Year:

2019

Language:

english

File:

PDF, 2.35 MB

english, 2019

8

The Case for Junk DNA

Palazzo, Alexander F., Gregory, T. Ryan, Akey, Joshua M.

Journal:

Year:

2014

Language:

english

File:

PDF, 365 KB

english, 2014

9

Methods and models for unravelling human evolutionary history

Schraiber, Joshua G., Akey, Joshua M.

Journal:

Nature Reviews Genetics

Year:

2015

Language:

english

File:

PDF, 362 KB

english, 2015

10

Archaic Hominin Admixture Facilitated Adaptation to Out-of-Africa Environments

Gittelman, Rachel M., Schraiber, Joshua G., Vernot, Benjamin, Mikacenic, Carmen, Wurfel, Mark M., Akey, Joshua M.

Journal:

Current Biology

Year:

2016

Language:

english

File:

PDF, 1.75 MB

english, 2016

11

Outstanding questions in the study of archaic hominin admixture

Wolf, Aaron B., Akey, Joshua M., Barsh, Gregory S.

Journal:

Year:

2018

Language:

english

File:

PDF, 2.47 MB

english, 2018

12

The long walk to African genomics

Tucci, Serena, Akey, Joshua M.

Journal:

Year:

2019

Language:

english

File:

PDF, 301 KB

english, 2019

13

Sequence diversity, natural selection and linkage disequilibrium in the human T cell receptor alpha/delta locus

Rachel Mackelprang, Robert J. Livingston, Michael A. Eberle, Christopher S. Carlson, Qian Yi, Joshua M. Akey, Deborah A. Nickerson

Journal:

Year:

2006

Language:

english

File:

PDF, 557 KB

english, 2006

14

Highly Punctuated Patterns of Population Structure on the X Chromosome and Implications for African Evolutionary History

Charla A. Lambert, Caitlin F. Connelly, Jennifer Madeoy, Ruolan Qiu, Maynard V. Olson, Joshua M. Akey

Journal:

The American Journal of Human Genetics

Year:

2010

Language:

english

File:

PDF, 1.10 MB

english, 2010

15

Estimators of the Human Effective Sex Ratio Detect Sex Biases on Different Timescales

Leslie S. Emery, Joseph Felsenstein, Joshua M. Akey

Journal:

The American Journal of Human Genetics

Year:

2010

Language:

english

File:

PDF, 370 KB

english, 2010

16

Genomic insights into positive selection

Shameek Biswas, Joshua M. Akey

Journal:

Trends in Genetics

Year:

2006

Language:

english

File:

PDF, 222 KB

english, 2006

17

Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers

Joseph Lachance, Benjamin Vernot, Clara C. Elbers, Bart Ferwerda, Alain Froment, Jean-Marie Bodo, Godfrey Lema, Wenqing Fu, Thomas B. Nyambo, Timothy R. Rebbeck, Kun Zhang, Joshua M. Akey, Sarah A. Ti

Journal:

Year:

2012

Language:

english

File:

PDF, 62 KB

english, 2012

18

Selection and Adaptation in the Human Genome

Fu, Wenqing, Akey, Joshua M.

Journal:

Annual Review of Genomics and Human Genetics

Year:

2013

Language:

english

File:

PDF, 753 KB

english, 2013

19

Human Evolution: Genomic Gifts from Archaic Hominins

Vernot, Benjamin, Akey, Joshua M.

Journal:

Current Biology

Year:

2014

Language:

english

File:

PDF, 1.08 MB

english, 2014

20

Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution

Fumagalli, Matteo, Sironi, Manuela, Pozzoli, Uberto, Ferrer-Admettla, Anna, Pattini, Linda, Nielsen, Rasmus, Akey, Joshua M.

Journal:

Year:

2011

Language:

english

File:

PDF, 391 KB

english, 2011

21

Selection plays the hand it was dealt: evidence that human adaptation commonly targets standing genetic variation

McCoy, Rajiv C., Akey, Joshua M.

Journal:

Year:

2017

Language:

english

File:

PDF, 304 KB

english, 2017

22

Implications of localized charge for human influenza A H1N1 hemagglutinin evolution: Insights from deep mutational scans

Saad-Roy, Chadi M., Arinaminpathy, Nimalan, Wingreen, Ned S., Levin, Simon A., Akey, Joshua M., Grenfell, Bryan T., Antia, Rustom

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 1.91 MB

2020

23

High-throughput single-nucleotide polymorphism analysis of the IL1RN locus in patients with ankylosing spondylitis by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry

Walter P. Maksymowych, Jeff P. Reeve, John D. Reveille, Joshua M. Akey, Heidi Buenviaje, Lori O'Brien, Paul M. Peloso, Glen T. Thomson, Li Jin, Anthony S. Russell

Journal:

Arthritis & Rheumatism

Year:

2003

Language:

english

File:

PDF, 82 KB

english, 2003

24

Lack of linkage of IL1RN genotypes with ankylosing spondylitis susceptibility

Li Jin, Ge Zhang, Joshua M. Akey, Jingchun Luo, Juwon Lee, Michael H. Weisman, Jane Bruckel, Robert D. Inman, Millicent A. Stone, Muhammad A. Khan, H. Ralph Schumacher, Walter P. Maksymowych, Maren L.

Journal:

Arthritis & Rheumatism

Year:

2004

Language:

english

File:

PDF, 119 KB

english, 2004

25

A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog

Thomas J Nicholas, Carl Baker, Evan E Eichler, Joshua M Akey

Journal:

Year:

2011

Language:

english

File:

PDF, 497 KB

english, 2011

26

Copy number variation in the domestic dog

Carlos E. Alvarez, Joshua M. Akey

Journal:

Mammalian Genome

Year:

2012

Language:

english

File:

PDF, 728 KB

english, 2012

27

Randomly distributed crossovers may generate block-like patterns of linkage disequilibrium: an act of genetic drift

Kun Zhang, Joshua M. Akey, Ning Wang, Momiao Xiong, Ranajit Chakraborty, Li Jin

Journal:

Year:

2003

Language:

english

File:

PDF, 1.92 MB

english, 2003

28

Interaction between the melanocortin-1 receptor andPgenes contributes to inter-individual variation in skin pigmentation phenotypes in a Tibetan population

Joshua M. Akey, Hong Wang, Momiao Xiong, Hong Wu, Weida Liu, Mark D. Shriver, Li Jin

Journal:

Year:

2001

Language:

english

File:

PDF, 60 KB

english, 2001

29

On the design and analysis of gene expression studies in human populations

Akey, Joshua M, Biswas, Shameek, Leek, Jeffrey T, Storey, John D

Journal:

Nature Genetics

Year:

2007

Language:

english

File:

PDF, 391 KB

english, 2007

30

Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors

Yvert, Gaël, Brem, Rachel B, Whittle, Jacqueline, Akey, Joshua M, Foss, Eric, Smith, Erin N, Mackelprang, Rachel, Kruglyak, Leonid

Journal:

Nature Genetics

Year:

2003

Language:

english

File:

PDF, 812 KB

english, 2003

31

Haplotypes vs single marker linkage disequilibrium tests: what do we gain?

Akey, Joshua, Jin, Li, Xiong, Momiao

Journal:

European Journal of Human Genetics

Year:

2001

Language:

english

File:

PDF, 208 KB

english, 2001

32

Global genetic variation at nine short tandem repeat loci and implications on forensic genetics

Sun, Guangyun, McGarvey, Stephen T, Bayoumi, Riad, Mulligan, Connie J, Barrantes, Ramiro, Raskin, Salmo, Zhong, Yixi, Akey, Joshua, Chakraborty, Ranajit, Deka, Ranjan

Journal:

European Journal of Human Genetics

Year:

2003

Language:

english

File:

PDF, 144 KB

english, 2003

33

A polymorphism in the promoter region of catalase is associated with blood pressure levels

Jiang, Zhengwen, Akey, Joshua, Shi, Jinxiu, Xiong, Momiao, Wang, Ying, Shen, Yayun, Xu, Xiaoyun, Chen, Hua, Wu, Hong, Xiao, Junhua

Journal:

Year:

2001

Language:

english

File:

PDF, 42 KB

english, 2001

34

Genome-wide Insights into the Patterns and Determinants of Fine-Scale Population Structure in Humans

Shameek Biswas, Laura B. Scheinfeldt, Joshua M. Akey

Journal:

The American Journal of Human Genetics

Year:

2009

Language:

english

File:

PDF, 522 KB

english, 2009

35

A Genome-wide In Vitro Bacterial-Infection Screen Reveals Human Variation in the Host Response Associated with Inflammatory Disease

Dennis C. Ko, Kajal P. Shukla, Christine Fong, Michael Wasnick, Mitchell J. Brittnacher, Mark M. Wurfel, Tarah D. Holden, Grant E. O'Keefe, Brian Van Yserloo, Joshua M. Akey, Samuel I. Miller

Journal:

The American Journal of Human Genetics

Year:

2009

Language:

english

File:

PDF, 1017 KB

english, 2009

36

High-Frequency Persistence of an Impaired Allele of the Retroviral Defense Gene TRIM5α in Humans

Sara L. Sawyer, Lily I. Wu, Joshua M. Akey, Michael Emerman, Harmit S. Malik

Journal:

Current Biology

Year:

2006

Language:

english

File:

PDF, 395 KB

english, 2006

37

Parallel Selection: Evolution's Surprising Predictability

Journal:

Current Biology

Year:

2012

Language:

english

File:

PDF, 209 KB

english, 2012

38

The genomic architecture of segmental duplications and copy number variants in dogs

Thomas J. Nicholas, Ze Cheng, Katrina L. Mealey, Evan E. Eichler, Joshua M. Akey

Journal:

Journal of Veterinary Behavior: Clinical Applications and Research

Year:

2009

Language:

english

File:

PDF, 54 KB

english, 2009

39

Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis

Shameek Biswas, John D Storey, Joshua M Akey

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 2.13 MB

english, 2008

40

Assaying DNA Methylation Based on High-Throughput Melting Curve Approaches

Dayna T Akey, Joshua M Akey, Kun Zhang, Li Jin

Journal:

Year:

2002

Language:

english

File:

PDF, 289 KB

english, 2002

41

Estimating African American Admixture Proportions by Use of Population-Specific Alleles

Esteban J. Parra, Amy Marcini, Joshua Akey, Jeremy Martinson, Mark A. Batzer, Richard Cooper, Terrence Forrester, David B. Allison, Ranjan Deka, Robert E. Ferrell, Mark D. Shriver

Journal:

The American Journal of Human Genetics

Year:

1998

Language:

english

File:

PDF, 123 KB

english, 1998

42

The Effect That Genotyping Errors Have on the Robustness of Common Linkage-Disequilibrium Measures

Joshua M. Akey, Kun Zhang, Momiao Xiong, Peter Doris, Li Jin

Journal:

The American Journal of Human Genetics

Year:

2001

Language:

english

File:

PDF, 940 KB

english, 2001

43

Distribution of Recombination Crossovers and the Origin of Haplotype Blocks: The Interplay of Population History, Recombination, and Mutation

Ning Wang, Joshua M. Akey, Kun Zhang, Ranajit Chakraborty, Li Jin

Journal:

The American Journal of Human Genetics

Year:

2002

Language:

english

File:

PDF, 414 KB

english, 2002

44

Gene-Expression Variation Within and Among Human Populations

John D. Storey, Jennifer Madeoy, Jeanna L. Strout, Mark Wurfel, James Ronald, Joshua M. Akey

Journal:

The American Journal of Human Genetics

Year:

2007

Language:

english

File:

PDF, 401 KB

english, 2007

45

The promise and limitations of population exomics for human evolution studies

Jacob A Tennessen, Timothy D O’Connor, Michael J Bamshad, Joshua M Akey

Journal:

Year:

2011

Language:

english

File:

PDF, 456 KB

english, 2011

46

Understanding human evolutionary history: a meeting report of the Swedish Royal Academy of Sciences symposium of modern human genetic variation

Journal:

Investigative Genetics

Year:

2012

Language:

english

File:

PDF, 90 KB

english, 2012

47

Inherited Variation in Gene Expression

Skelly, Daniel A., Ronald, James, Akey, Joshua M.

Journal:

Annual Review of Genomics and Human Genetics

Year:

2009

Language:

english

File:

PDF, 1.18 MB

english, 2009

48

Analysis of 2,440 human exomes highlights the evolution and functional impact of rare coding variation

Journal:

Year:

2011

Language:

english

File:

PDF, 356 KB

english, 2011

49

Analysis of 2,440 human exomes highlights the evolution and functional impact of rare coding variation

Journal:

Year:

2011

Language:

english

File:

PDF, 333 KB

english, 2011

50

Identification and antiviral activity of common polymorphisms in the APOBEC3 locus in human populations

Duggal, Nisha K., Fu, Wenqing, Akey, Joshua M., Emerman, Michael

Journal:

Year:

2013

Language:

english

File:

PDF, 651 KB

english, 2013