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Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection.

Song H, Giorgi EE, Ganusov VV, Cai F, Athreya G, Yoon H, Carja O, Hora B, Hraber P, Romero-Severson E, Jiang C, Li X, Wang S, Li H, Salazar-Gonzalez JF, Salazar MG, Goonetilleke N, Keele BF, Montefiori DC, Cohen MS, Shaw GM, Hahn BH, McMichael AJ, Haynes BF, Korber B, Bhattacharya T, Gao F.

Nat Commun. 2018 May 15;9(1):1928. doi: 10.1038/s41467-018-04217-5.


Women's periconceptional diet and risk of biliary atresia in offspring.

Carmichael SL, Ma C, Van Zutphen AR, Moore CA, Shaw GM; National Birth Defects Prevention Study.

Birth Defects Res. 2018 May 15. doi: 10.1002/bdr2.1340. [Epub ahead of print]


Failed umbilical artery catheterization and adverse outcomes in extremely low birth weight infants.

Wallenstein MB, Shaw GM, Yang W, Stevenson DK.

J Matern Fetal Neonatal Med. 2018 May 2:1-5. doi: 10.1080/14767058.2018.1468430. [Epub ahead of print]


Genetic variation in biotransformation enzymes, air pollution exposures, and risk of spina bifida.

Padula AM, Yang W, Schultz K, Lurmann F, Hammond SK, Shaw GM.

Am J Med Genet A. 2018 May;176(5):1055-1090. doi: 10.1002/ajmg.a.38661.


Herpesvirus Infection in Infants with Gastroschisis.

Francis SS, Wiemels JL, Yang W, Shaw GM.

Epidemiology. 2018 Apr 6. doi: 10.1097/EDE.0000000000000844. [Epub ahead of print]


Residential agricultural pesticide exposures and risks of preeclampsia.

Shaw GM, Yang W, Roberts EM, Aghaeepour N, Mayo JA, Weber KA, Maric I, Carmichael SL, Winn VD, Stevenson DK, English PB.

Environ Res. 2018 Jul;164:546-555. doi: 10.1016/j.envres.2018.03.020. Epub 2018 Mar 31.


Nutrient intake in women before conception and risks of anophthalmia and microphthalmia in their offspring.

Weber KA, Yang W, Carmichael SL, Shaw GM; National Birth Defects Prevention Study.

Birth Defects Res. 2018 Mar 5. doi: 10.1002/bdr2.1201. [Epub ahead of print]


Next-generation, personalised, model-based critical care medicine: a state-of-the art review of in silico virtual patient models, methods, and cohorts, and how to validation them.

Chase JG, Preiser JC, Dickson JL, Pironet A, Chiew YS, Pretty CG, Shaw GM, Benyo B, Moeller K, Safaei S, Tawhai M, Hunter P, Desaive T.

Biomed Eng Online. 2018 Feb 20;17(1):24. doi: 10.1186/s12938-018-0455-y. Review.


Nutrition delivery of a model-based ICU glycaemic control system.

Stewart KW, Chase JG, Pretty CG, Shaw GM.

Ann Intensive Care. 2018 Jan 10;8(1):4. doi: 10.1186/s13613-017-0351-9.


A genome-wide association study identifies only two ancestry specific variants associated with spontaneous preterm birth.

Rappoport N, Toung J, Hadley D, Wong RJ, Fujioka K, Reuter J, Abbott CW, Oh S, Hu D, Eng C, Huntsman S, Bodian DL, Niederhuber JE, Hong X, Zhang G, Sikora-Wohfeld W, Gignoux CR, Wang H, Oehlert J, Jelliffe-Pawlowski LL, Gould JB, Darmstadt GL, Wang X, Bustamante CD, Snyder MP, Ziv E, Patsopoulos NA, Muglia LJ, Burchard E, Shaw GM, O'Brodovich HM, Stevenson DK, Butte AJ, Sirota M.

Sci Rep. 2018 Jan 9;8(1):226. doi: 10.1038/s41598-017-18246-5.


A proteomic clock of human pregnancy.

Aghaeepour N, Lehallier B, Baca Q, Ganio EA, Wong RJ, Ghaemi MS, Culos A, El-Sayed YY, Blumenfeld YJ, Druzin ML, Winn VD, Gibbs RS, Tibshirani R, Shaw GM, Stevenson DK, Gaudilliere B, Angst MS.

Am J Obstet Gynecol. 2018 Mar;218(3):347.e1-347.e14. doi: 10.1016/j.ajog.2017.12.208. Epub 2017 Dec 24.


First Trimester Plasma Glucose Values in Women without Diabetes are Associated with Risk for Congenital Heart Disease in Offspring.

Helle EIT, Biegley P, Knowles JW, Leader JB, Pendergrass S, Yang W, Reaven GR, Shaw GM, Ritchie M, Priest JR.

J Pediatr. 2018 Apr;195:275-278. doi: 10.1016/j.jpeds.2017.10.046. Epub 2017 Dec 15.


Divergent Patterns of Mitochondrial and Nuclear Ancestry Are Associated with the Risk for Preterm Birth.

Crawford N, Prendergast D, Oehlert JW, Shaw GM, Stevenson DK, Rappaport N, Sirota M, Tishkoff SA, Sondheimer N.

J Pediatr. 2018 Mar;194:40-46.e4. doi: 10.1016/j.jpeds.2017.10.052. Epub 2017 Dec 14.


Hypovitaminosis C and vitamin C deficiency in critically ill patients despite recommended enteral and parenteral intakes.

Carr AC, Rosengrave PC, Bayer S, Chambers S, Mehrtens J, Shaw GM.

Crit Care. 2017 Dec 11;21(1):300. doi: 10.1186/s13054-017-1891-y.


Copy number variants in Ebstein anomaly.

Giannakou A, Sicko RJ, Zhang W, Romitti P, Browne ML, Caggana M, Brody LC, Jelliffe-Pawlowski L, Shaw GM, Kay DM, Mills JL.

PLoS One. 2017 Dec 7;12(12):e0188168. doi: 10.1371/journal.pone.0188168. eCollection 2017.


Risky Business: Meeting the Structural Needs of Transdisciplinary Science.

Wise PH, Shaw GM, Druzin ML, Darmstadt GL, Quaintance C, Mäkinen E, Relman DA, Quake SR, Butte AJ, Angst MS, Muglia LJ, Macones G, Driscoll D, Ober C, Simpson JL, Katz M, Howse J, Stevenson DK.

J Pediatr. 2017 Dec;191:255-258. doi: 10.1016/j.jpeds.2017.08.072. No abstract available.


Wild bonobos host geographically restricted malaria parasites including a putative new Laverania species.

Liu W, Sherrill-Mix S, Learn GH, Scully EJ, Li Y, Avitto AN, Loy DE, Lauder AP, Sundararaman SA, Plenderleith LJ, Ndjango JN, Georgiev AV, Ahuka-Mundeke S, Peeters M, Bertolani P, Dupain J, Garai C, Hart JA, Hart TB, Shaw GM, Sharp PM, Hahn BH.

Nat Commun. 2017 Nov 21;8(1):1635. doi: 10.1038/s41467-017-01798-5.


Out-of-hospital births in California 1991-2011.

Girsen AI, Mayo JA, Lyell DJ, Blumenfeld YJ, Stevenson DK, El-Sayed YY, Shaw GM, Druzin ML.

J Perinatol. 2018 Jan;38(1):41-45. doi: 10.1038/jp.2017.156. Epub 2017 Nov 9.


Continuous Glucose Monitoring Measures Can Be Used for Glycemic Control in the ICU: An In-Silico Study.

Zhou T, Dickson JL, Shaw GM, Chase JG.

J Diabetes Sci Technol. 2018 Jan;12(1):7-19. doi: 10.1177/1932296817738791. Epub 2017 Nov 6.


Occurrence of Selected Structural Birth Defects Among Women With Preeclampsia and Other Hypertensive Disorders.

Weber KA, Mayo JA, Carmichael SL, Stevenson DK, Winn VD, Shaw GM.

Am J Epidemiol. 2018 Apr 1;187(4):668-676. doi: 10.1093/aje/kwx269.


Residential Agricultural Pesticide Exposures and Risks of Spontaneous Preterm Birth.

Shaw GM, Yang W, Roberts EM, Kegley SE, Stevenson DK, Carmichael SL, English PB.

Epidemiology. 2018 Jan;29(1):8-21. doi: 10.1097/EDE.0000000000000757.


Correction: Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection.

Kijak GH, Sanders-Buell E, Chenine AL, Eller MA, Goonetilleke N, Thomas R, Leviyang S, Harbolick EA, Bose M, Pham P, Oropeza C, Poltavee K, O'Sullivan AM, Billings E, Merbah M, Costanzo MC, Warren JA, Slike B, Li H, Peachman KK, Fischer W, Gao F, Cicala C, Arthos J, Eller LA, O'Connell RJ, Sinei S, Maganga L, Kibuuka H, Nitayaphan S, Rao M, Marovich MA, Krebs SJ, Rolland M, Korber BT, Shaw GM, Michael NL, Robb ML, Tovanabutra S, Kim JH.

PLoS Pathog. 2017 Sep 14;13(9):e1006620. doi: 10.1371/journal.ppat.1006620. eCollection 2017 Sep.


Simultaneously Monitoring Immune Response and Microbial Infections during Pregnancy through Plasma cfRNA Sequencing.

Pan W, Ngo TTM, Camunas-Soler J, Song CX, Kowarsky M, Blumenfeld YJ, Wong RJ, Shaw GM, Stevenson DK, Quake SR.

Clin Chem. 2017 Nov;63(11):1695-1704. doi: 10.1373/clinchem.2017.273888. Epub 2017 Sep 13.


A Multivariate Dynamic Spatial Factor Model for Speciated Pollutants and Adverse Birth Outcomes.

Kaufeld KA, Fuentes M, Reich BJ, Herring AH, Shaw GM, Terres MA.

Int J Environ Res Public Health. 2017 Sep 11;14(9). pii: E1046. doi: 10.3390/ijerph14091046.


Antioxidant Consumption is Associated with Decreased Odds of Congenital Limb Deficiencies.

Pace ND, Desrosiers TA, Carmichael SL, Shaw GM, Olshan AF, Siega-Riz AM; National Birth Defects Prevention Study.

Paediatr Perinat Epidemiol. 2018 Jan;32(1):90-99. doi: 10.1111/ppe.12403. Epub 2017 Sep 4.


An immune clock of human pregnancy.

Aghaeepour N, Ganio EA, Mcilwain D, Tsai AS, Tingle M, Van Gassen S, Gaudilliere DK, Baca Q, McNeil L, Okada R, Ghaemi MS, Furman D, Wong RJ, Winn VD, Druzin ML, El-Sayed YY, Quaintance C, Gibbs R, Darmstadt GL, Shaw GM, Stevenson DK, Tibshirani R, Nolan GP, Lewis DB, Angst MS, Gaudilliere B.

Sci Immunol. 2017 Sep 1;2(15). pii: eaan2946. doi: 10.1126/sciimmunol.aan2946.


Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women.

Callahan BJ, DiGiulio DB, Goltsman DSA, Sun CL, Costello EK, Jeganathan P, Biggio JR, Wong RJ, Druzin ML, Shaw GM, Stevenson DK, Holmes SP, Relman DA.

Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):9966-9971. doi: 10.1073/pnas.1705899114. Epub 2017 Aug 28.


Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA.

Kowarsky M, Camunas-Soler J, Kertesz M, De Vlaminck I, Koh W, Pan W, Martin L, Neff NF, Okamoto J, Wong RJ, Kharbanda S, El-Sayed Y, Blumenfeld Y, Stevenson DK, Shaw GM, Wolfe ND, Quake SR.

Proc Natl Acad Sci U S A. 2017 Sep 5;114(36):9623-9628. doi: 10.1073/pnas.1707009114. Epub 2017 Aug 22.


Social disadvantage and the black-white disparity in spontaneous preterm delivery among California births.

Carmichael SL, Kan P, Padula AM, Rehkopf DH, Oehlert JW, Mayo JA, Weber AM, Wise PH, Shaw GM, Stevenson DK.

PLoS One. 2017 Aug 11;12(8):e0182862. doi: 10.1371/journal.pone.0182862. eCollection 2017.


Population-based case-control study of the association between weather-related extreme heat events and neural tube defects.

Soim A, Lin S, Sheridan SC, Hwang SA, Hsu WH, Luben TJ, Shaw GM, Feldkamp ML, Romitti PA, Reefhuis J, Langlois PH, Browne ML; National Birth Defects Prevention Study.

Birth Defects Res. 2017 Nov 1;109(18):1482-1493. doi: 10.1002/bdr2.1086. Epub 2017 Aug 2.


Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection.

Kijak GH, Sanders-Buell E, Chenine AL, Eller MA, Goonetilleke N, Thomas R, Leviyang S, Harbolick EA, Bose M, Pham P, Oropeza C, Poltavee K, O'Sullivan AM, Billings E, Merbah M, Costanzo MC, Warren JA, Slike B, Li H, Peachman KK, Fischer W, Gao F, Cicala C, Arthos J, Eller LA, O'Connell RJ, Sinei S, Maganga L, Kibuuka H, Nitayaphan S, Rao M, Marovich MA, Krebs SJ, Rolland M, Korber BT, Shaw GM, Michael NL, Robb ML, Tovanabutra S, Kim JH.

PLoS Pathog. 2017 Jul 31;13(7):e1006510. doi: 10.1371/journal.ppat.1006510. eCollection 2017 Jul. Erratum in: PLoS Pathog. 2017 Sep 14;13(9):e1006620.


'The obesity paradox': a reconsideration of obesity and the risk of preterm birth.

Tsur A, Mayo JA, Wong RJ, Shaw GM, Stevenson DK, Gould JB.

J Perinatol. 2017 Oct;37(10):1088-1092. doi: 10.1038/jp.2017.104. Epub 2017 Jul 27.


Interpregnancy Interval and Adverse Pregnancy Outcomes: An Analysis of Successive Pregnancies and: Interpregnancy Interval and Pregnancy Outcomes: Causal or Not?

Mayo JA, Shachar BZ, Stevenson DK, Shaw GM.

Obstet Gynecol. 2017 Aug;130(2):463. doi: 10.1097/AOG.0000000000002171. No abstract available.


Selected birth defects among males following the United States terrorist attacks of 11 September 2001.

Singh P, Yang W, Shaw GM, Catalano R, Bruckner TA.

Birth Defects Res. 2017 Oct 2;109(16):1277-1283. doi: 10.1002/bdr2.1072. Epub 2017 Jul 19.


Untangling glycaemia and mortality in critical care.

Uyttendaele V, Dickson JL, Shaw GM, Desaive T, Chase JG.

Crit Care. 2017 Jun 24;21(1):152. doi: 10.1186/s13054-017-1725-y.


Maternal Smoking, Alcohol, and Caffeine Exposures and Risk of Hypospadias.

Carmichael SL, Ma C, Shaw GM; National Birth Defects Prevention Study.

Birth Defects Res. 2017 Aug 15;109(14):1127-1133. doi: 10.1002/bdr2.1044. Epub 2017 Jun 21.


DNA Methylome Profiling on the Infinium HumanMethylation450 Array from Limiting Quantities of Genomic DNA from a Single, Small Archived Bloodspot.

Asrani K, Shaw GM, Rine J, Marini NJ.

Genet Test Mol Biomarkers. 2017 Aug;21(8):516-519. doi: 10.1089/gtmb.2017.0019. Epub 2017 Jun 13.


Effective treatment of SIVcpz-induced immunodeficiency in a captive western chimpanzee.

Barbian HJ, Jackson-Jewett R, Brown CS, Bibollet-Ruche F, Learn GH, Decker T, Kreider EF, Li Y, Denny TN, Sharp PM, Shaw GM, Lifson J, Acosta EP, Saag MS, Bar KJ, Hahn BH.

Retrovirology. 2017 Jun 2;14(1):35. doi: 10.1186/s12977-017-0359-0.


Proof of concept non-invasive estimation of peripheral venous oxygen saturation.

Khan M, Pretty CG, Amies AC, Balmer J, Banna HE, Shaw GM, Geoffrey Chase J.

Biomed Eng Online. 2017 May 19;16(1):60. doi: 10.1186/s12938-017-0351-x.


Maternal Exposure to Nitrogen Dioxide, Intake of Methyl Nutrients, and Congenital Heart Defects in Offspring.

Stingone JA, Luben TJ, Carmichael SL, Aylsworth AS, Botto LD, Correa A, Gilboa SM, Langlois PH, Nembhard WN, Richmond-Bryant J, Shaw GM, Olshan AF; National Birth Defects Prevention Study.

Am J Epidemiol. 2017 Sep 15;186(6):719-729. doi: 10.1093/aje/kwx139.


Maternal Stressors and Social Support and Risks of Delivering Babies With Gastroschisis or Hypospadias.

Carmichael SL, Ma C, Tinker S, Shaw GM; National Birth Defects Prevention Study.

Am J Epidemiol. 2017 Jun 15;185(12):1240-1246. doi: 10.1093/aje/kww121.


Broadly neutralizing antibodies with few somatic mutations and hepatitis C virus clearance.

Bailey JR, Flyak AI, Cohen VJ, Li H, Wasilewski LN, Snider AE, Wang S, Learn GH, Kose N, Loerinc L, Lampley R, Cox AL, Pfaff JM, Doranz BJ, Shaw GM, Ray SC, Crowe JE Jr.

JCI Insight. 2017 May 4;2(9). pii: 92872. doi: 10.1172/jci.insight.92872. [Epub ahead of print]


A new class of Cu/ZnO catalysts derived from zincian georgeite precursors prepared by co-precipitation.

Smith PJ, Kondrat SA, Chater PA, Yeo BR, Shaw GM, Lu L, Bartley JK, Taylor SH, Spencer MS, Kiely CJ, Kelly GJ, Park CW, Hutchings GJ.

Chem Sci. 2017 Mar 1;8(3):2436-2447. doi: 10.1039/c6sc04130b. Epub 2017 Jan 3.


Improved pressure contour analysis for estimating cardiac stroke volume using pulse wave velocity measurement.

Kamoi S, Pretty C, Balmer J, Davidson S, Pironet A, Desaive T, Shaw GM, Chase JG.

Biomed Eng Online. 2017 Apr 24;16(1):51. doi: 10.1186/s12938-017-0341-z.


Risk for spontaneous preterm birth among inter-racial/ethnic couples.

Shachar BZ, Mayo JA, Lyell DJ, Stevenson DK, Shaw GM, Blumenfeld YJ.

J Matern Fetal Neonatal Med. 2018 Mar;31(5):633-639. doi: 10.1080/14767058.2017.1293029. Epub 2017 Apr 12.


Maternal prepregnancy body mass index and risk of bronchopulmonary dysplasia.

Carmichael SL, Kan P, Gould JB, Stevenson DK, Shaw GM, Lee HC.

Pediatr Res. 2017 Jul;82(1):8-13. doi: 10.1038/pr.2017.90. Epub 2017 May 31.


Air pollution, neighborhood acculturation factors, and neural tube defects among Hispanic women in California.

Padula AM, Yang W, Carmichael SL, Lurmann F, Balmes J, Hammond SK, Shaw GM.

Birth Defects Res. 2017 Apr 3;109(6):403-422. doi: 10.1002/bdra.23602. Epub 2017 Feb 21.


Fetal de novo mutations and preterm birth.

Li J, Oehlert J, Snyder M, Stevenson DK, Shaw GM.

PLoS Genet. 2017 Apr 7;13(4):e1006689. doi: 10.1371/journal.pgen.1006689. eCollection 2017 Apr.


Generalisability of a Virtual Trials Method for Glycaemic Control in Intensive Care.

Dickson JL, Stewart KW, Pretty CG, Flechet M, Desaive T, Penning S, Lambermont BC, Benyo B, Shaw GM, Chase G.

IEEE Trans Biomed Eng. 2017 Mar 24. doi: 10.1109/TBME.2017.2686432. [Epub ahead of print]


Cohort Variation in Selection During Pregnancy and Risk of Selected Birth Defects Among Males.

Bruckner TA, Karasek D, Yang W, Shaw GM, Catalano RA.

Epidemiology. 2017 Jul;28(4):580-586. doi: 10.1097/EDE.0000000000000661.


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