Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci

[1]  Luke R. Lloyd-Jones,et al.  Bayesian analysis of GWAS summary data reveals differential signatures of natural selection across human complex traits and functional genomic categories , 2019, bioRxiv.

[2]  A. Rokas,et al.  Immune Regulation in Eutherian Pregnancy: Live Birth Coevolved with Novel Immune Genes and Gene Regulation. , 2019, BioEssays : news and reviews in molecular, cellular and developmental biology.

[3]  R. Nielsen,et al.  Detecting Natural Selection , 2019, Handbook of Statistical Genomics.

[4]  J. Jastrzębski,et al.  Placenta Transcriptome Profiling in Intrauterine Growth Restriction (IUGR) , 2019, International journal of molecular sciences.

[5]  J. Roman,et al.  Maternal undernutrition during pregnancy alters the epigenetic landscape and the expression of endothelial function genes in male progeny. , 2019, Nutrition research.

[6]  M. Pavlicev,et al.  Evolution of the human pelvis and obstructed labor: New explanations of an old obstetrical dilemma. , 2019, American journal of obstetrics and gynecology.

[7]  P. Visscher,et al.  Leveraging GWAS for complex traits to detect signatures of natural selection in humans. , 2018, Current opinion in genetics & development.

[8]  N. Jablonski,et al.  The roles of vitamin D and cutaneous vitamin D production in human evolution and health. , 2018, International journal of paleopathology.

[9]  N. Patterson,et al.  Extreme Polygenicity of Complex Traits Is Explained by Negative Selection. , 2019, American journal of human genetics.

[10]  J. Boardman,et al.  Preterm Birth and the Risk of Neurodevelopmental Disorders - Is There a Role for Epigenetic Dysregulation? , 2018, Current genomics.

[11]  Holly M Dunsworth There Is No "Obstetrical Dilemma": Towards a Braver Medicine with Fewer Childbirth Interventions , 2018, Perspectives in biology and medicine.

[12]  J. Martin,et al.  Births in the United States, 2017. , 2018, NCHS data brief.

[13]  G. Shaw,et al.  Natural Selection Has Differentiated the Progesterone Receptor among Human Populations. , 2018, American journal of human genetics.

[14]  P. Visscher,et al.  Global genetic differentiation of complex traits shaped by natural selection in humans , 2018, Nature Communications.

[15]  J. Coorssen,et al.  Proteomic analysis of first trimester maternal serum to identify candidate biomarkers potentially predictive of spontaneous preterm birth. , 2018, Journal of proteomics.

[16]  Luke R. Lloyd-Jones,et al.  Signatures of negative selection in the genetic architecture of human complex traits , 2018, Nature Genetics.

[17]  Daniel E. Miller,et al.  Genetic Associations With Gestational Duration and Spontaneous Preterm Birth , 2018, Obstetric Anesthesia Digest.

[18]  Astrid Gall,et al.  Ensembl 2018 , 2017, Nucleic Acids Res..

[19]  Jaume Bertranpetit,et al.  PopHuman: the human population genomics browser , 2017, Nucleic Acids Res..

[20]  Cédric Coulonges,et al.  Genetic Associations with Spontaneous Preterm Birth. , 2017, The New England journal of medicine.

[21]  P. Keightley,et al.  Detecting positive selection in the genome , 2017, BMC Biology.

[22]  Xiaoting Chen,et al.  Genetic Associations with Gestational Length and Spontaneous Preterm Birth , 2017, The New England journal of medicine.

[23]  Antonis Rokas,et al.  The transformative potential of an integrative approach to pregnancy. , 2017, Placenta.

[24]  C. Wagner,et al.  New insights into the vitamin D requirements during pregnancy , 2017, Bone Research.

[25]  P. Visscher,et al.  10 Years of GWAS Discovery: Biology, Function, and Translation. , 2017, American journal of human genetics.

[26]  Sudhir Kumar,et al.  TimeTree: A Resource for Timelines, Timetrees, and Divergence Times. , 2017, Molecular biology and evolution.

[27]  Katherine M. Siewert,et al.  Detecting Long-Term Balancing Selection Using Allele Frequency Correlation , 2017, bioRxiv.

[28]  A. Rokas,et al.  Mammalian pregnancy , 2017, Current Biology.

[29]  F. Tao,et al.  Vitamin D and risk of preterm birth: Up‐to‐date meta‐analysis of randomized controlled trials and observational studies , 2017, The journal of obstetrics and gynaecology research.

[30]  J. Gelernter,et al.  Widespread signatures of positive selection in common risk alleles associated to autism spectrum disorder , 2017, PLoS genetics.

[31]  A. Siepel,et al.  Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data , 2016, Nature Genetics.

[32]  X. Cui,et al.  Inhibition of the Arp2/3 complex impairs early embryo development of porcine parthenotes , 2016 .

[33]  M. Inouye,et al.  Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy , 2016, bioRxiv.

[34]  Ole A. Andreassen,et al.  Genetic Markers of Human Evolution Are Enriched in Schizophrenia , 2016, Biological Psychiatry.

[35]  M. Gautier,et al.  rehh 2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure , 2016, bioRxiv.

[36]  F. Cunningham,et al.  The Ensembl Variant Effect Predictor , 2016, Genome Biology.

[37]  K. Nakayama,et al.  Maternal TET3 is dispensable for embryonic development but is required for neonatal growth , 2015, Scientific Reports.

[38]  Gabor T. Marth,et al.  A global reference for human genetic variation , 2015, Nature.

[39]  David Bryant,et al.  popart: full‐feature software for haplotype network construction , 2015 .

[40]  M. Laan,et al.  Extensive shift in placental transcriptome profile in preeclampsia and placental origin of adverse pregnancy outcomes , 2015, Scientific Reports.

[41]  Antonis Rokas,et al.  Is preterm birth a human-specific syndrome? , 2015, Evolution, medicine, and public health.

[42]  B. Crespi,et al.  Genetic recapitulation of human pre-eclampsia risk during convergent evolution of reduced placental invasiveness in eutherian mammals , 2015, Philosophical Transactions of the Royal Society B: Biological Sciences.

[43]  D. Altman,et al.  The distribution of clinical phenotypes of preterm birth syndrome: implications for prevention. , 2015, JAMA pediatrics.

[44]  Joel Hirschhorn,et al.  SNPsnap: a Web-based tool for identification and annotation of matched SNPs , 2015, Bioinform..

[45]  M. Zeviani,et al.  A family with paroxysmal nonkinesigenic dyskinesias (PNKD): evidence of mitochondrial dysfunction. , 2015, European journal of paediatric neurology : EJPN : official journal of the European Paediatric Neurology Society.

[46]  R. Gáspár,et al.  Effects of nociceptin and nocistatin on uterine contraction. , 2015, Vitamins and hormones.

[47]  C. Pennell,et al.  Strategies to Prevent Preterm Birth , 2014, Front. Immunol..

[48]  K. Washington,et al.  Vitamin D deficiency in pregnant women of ethnic minority: a potential contributor to preeclampsia , 2014, Journal of Perinatology.

[49]  M. Esplin Overview of Spontaneous Preterm Birth: A Complex and Multifactorial Phenotype , 2014, Clinical obstetrics and gynecology.

[50]  S. Fisher,et al.  Preterm labor: One syndrome, many causes , 2014, Science.

[51]  Michael C Neale,et al.  The contribution of genetic and environmental factors to the duration of pregnancy. , 2014, American journal of obstetrics and gynecology.

[52]  M. Carrington,et al.  Maternal KIR in Combination with Paternal HLA-C2 Regulate Human Birth Weight , 2014, The Journal of Immunology.

[53]  Pavlos Pavlidis,et al.  1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans , 2013, Nucleic Acids Res..

[54]  Matthew D. Rasmussen,et al.  Genome-Wide Inference of Ancestral Recombination Graphs , 2013, PLoS genetics.

[55]  Sharon R Grossman,et al.  Detecting natural selection in genomic data. , 2013, Annual review of genetics.

[56]  M. Permezel,et al.  Is Vitamin D Binding Protein a Novel Predictor of Labour? , 2013, PloS one.

[57]  Arcadi Navarro,et al.  Great ape genetic diversity and population history , 2013, Nature.

[58]  Nam-Hyung Kim,et al.  Actin nucleator Arp2/3 complex is essential for mouse preimplantation embryo development. , 2013, Reproduction, fertility, and development.

[59]  Louis J Muglia,et al.  The genomics of preterm birth: from animal models to human studies , 2013, Genome Medicine.

[60]  R. Gáspár,et al.  Uterus-Relaxing Effects of Nociceptin and Nocistatin: Studies on Preterm and Term-Pregnant Human Myometrium In vitro , 2013 .

[61]  Zengrui Wu,et al.  Serum Vitamin D Metabolites in Colorectal Cancer Patients Receiving Cholecalciferol Supplementation: Correlation with Polymorphisms in the Vitamin D Genes , 2013, Hormones and Cancer.

[62]  Eurie L. Hong,et al.  Annotation of functional variation in personal genomes using RegulomeDB , 2012, Genome research.

[63]  A. Litonjua,et al.  Plasma 25-hydroxyvitamin D during pregnancy and small-for-gestational age in black and white infants. , 2012, Annals of epidemiology.

[64]  Ann-Beth Moller,et al.  National, regional, and worldwide estimates of preterm birth rates in the year 2010 with time trends since 1990 for selected countries: a systematic analysis and implications , 2012, The Lancet.

[65]  C. Pennell,et al.  Preterm birth aetiology 2004–2008. Maternal factors associated with three phenotypes: spontaneous preterm labour, preterm pre-labour rupture of membranes and medically indicated preterm birth , 2012, The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians.

[66]  Ji-Young Kim,et al.  Associations of Vitamin D Binding Protein Gene Polymorphisms with the Development of Peripheral Arthritis and Uveitis in Ankylosing Spondylitis , 2011, The Journal of Rheumatology.

[67]  Z. Deng,et al.  The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes , 2011, Nature.

[68]  Gonçalo R. Abecasis,et al.  The variant call format and VCFtools , 2011, Bioinform..

[69]  B. Sibai,et al.  Admixture Mapping to Identify Spontaneous Preterm Birth Susceptibility Loci in African Americans , 2011, Obstetrics and gynecology.

[70]  C. Doglioni,et al.  Liprin-α1 regulates breast cancer cell invasion by affecting cell motility, invadopodia and extracellular matrix degradation , 2011, Oncogene.

[71]  Leena Peltonen,et al.  An Evolutionary Genomic Approach to Identify Genes Involved in Human Birth Timing , 2011, PLoS genetics.

[72]  Y. Li,et al.  Cytoskeletal remodelling proteins identified in fetal-maternal interface in pregnant women and rhesus monkeys , 2011, Journal of Molecular Histology.

[73]  Klaus Peter Schliep,et al.  phangorn: phylogenetic analysis in R , 2010, Bioinform..

[74]  Serafim Batzoglou,et al.  Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++ , 2010, PLoS Comput. Biol..

[75]  Justin C. Fay,et al.  Primate-specific evolution of noncoding element insertion into PLA2G4C and human preterm birth , 2010, BMC Medical Genomics.

[76]  Y. Li,et al.  Proteomic approach identifies alterations in cytoskeletal remodelling proteins during decidualization of human endometrial stromal cells. , 2010, Journal of proteome research.

[77]  G. Krikun,et al.  A genomic and proteomic investigation of the impact of preimplantation factor on human decidual cells. , 2010, American journal of obstetrics and gynecology.

[78]  Cory Y. McLean,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

[79]  G. Mor,et al.  REVIEW ARTICLE: The Immune System in Pregnancy: A Unique Complexity , 2010, American journal of reproductive immunology.

[80]  Louis J Muglia,et al.  The enigma of spontaneous preterm birth. , 2010, The New England journal of medicine.

[81]  L. Mincheva-Nilsson,et al.  REVIEW ARTICLE: The Role of Placental Exosomes in Reproduction , 2010, American journal of reproductive immunology.

[82]  J. J. Moore,et al.  Decreased adherence and spontaneous separation of fetal membrane layers--amnion and choriodecidua--a possible part of the normal weakening process. , 2010, Placenta.

[83]  K. Pollard,et al.  Detection of nonneutral substitution rates on mammalian phylogenies. , 2010, Genome research.

[84]  E. Birney,et al.  Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt , 2009, Nature Protocols.

[85]  Michael F. Wangler,et al.  Mother’s Genome or Maternally-Inherited Genes Acting in the Fetus Influence Gestational Age in Familial Preterm Birth , 2009, Human Heredity.

[86]  G. Acharya,et al.  Differential placental gene expression in severe preeclampsia. , 2009, Placenta.

[87]  Joshua M Akey,et al.  Where do we go from here? Constructing genomic maps of positive selection in humans: , 2009 .

[88]  P. Villesen,et al.  Gene conversion and purifying selection of a placenta-specific ERV-V envelope gene during simian evolution , 2008, BMC Evolutionary Biology.

[89]  T. Marquès-Bonet,et al.  Balancing Selection Is the Main Force Shaping the Evolution of Innate Immunity Genes1 , 2008, The Journal of Immunology.

[90]  D. Wildman,et al.  The human progesterone receptor shows evidence of adaptive evolution associated with its ability to act as a transcription factor. , 2008, Molecular phylogenetics and evolution.

[91]  Roberto Romero,et al.  Epidemiology and causes of preterm birth , 2008, The Lancet.

[92]  G. Willemsen,et al.  Heritability of parturition timing: an extended twin design analysis. , 2007, American journal of obstetrics and gynecology.

[93]  Alissa M. Weaver,et al.  Cortactin is an essential regulator of matrix metalloproteinase secretion and extracellular matrix degradation in invadopodia. , 2007, Cancer research.

[94]  Bart De Moor,et al.  BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis , 2005, Bioinform..

[95]  S. Batzoglou,et al.  Distribution and intensity of constraint in mammalian genomic sequence. , 2005, Genome research.

[96]  K. Rosenberg,et al.  Bipedalism and human birth: The obstetrical dilemma revisited , 2005 .

[97]  Terrence S. Furey,et al.  The UCSC Table Browser data retrieval tool , 2004, Nucleic Acids Res..

[98]  K. Rosenberg,et al.  Birth, obstetrics and human evolution , 2002, BJOG : an international journal of obstetrics and gynaecology.

[99]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[100]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[101]  International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome , 2001, Nature.

[102]  S Cnattingius,et al.  Genetic influence on birthweight and gestational length determined by studies in offspring of twins , 2000, BJOG : an international journal of obstetrics and gynaecology.

[103]  H. Bandelt,et al.  Median-joining networks for inferring intraspecific phylogenies. , 1999, Molecular biology and evolution.

[104]  Y W Loke,et al.  Trophoblast migration during human placental implantation. , 1996, Human reproduction update.

[105]  Marc Parmentier,et al.  Isolation and structure of the endogenous agonist of opioid receptor-like ORL1 receptor , 1995, Nature.

[106]  R. Hynes,et al.  Cell adhesion events mediated by alpha 4 integrins are essential in placental and cardiac development. , 1995, Development.

[107]  J. Crawford,et al.  Births in the United States , 1964 .

[108]  W. M. Krogman The Scars of Human Evolution , 1951 .