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TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data.

Goubert C, Thomas J, Payer LM, Kidd JM, Feusier J, Watkins WS, Burns KH, Jorde LB, Feschotte C.

Nucleic Acids Res. 2020 Feb 18. pii: gkaa074. doi: 10.1093/nar/gkaa074. [Epub ahead of print]


Rapid, Paralog-Sensitive CNV Analysis of 2457 Human Genomes Using QuicK-mer2.

Shen F, Kidd JM.

Genes (Basel). 2020 Jan 29;11(2). pii: E141. doi: 10.3390/genes11020141.


The difficulties of identifying and treating Enterobacterales with OXA-48-like carbapenemases.

Kidd JM, Livermore DM, Nicolau DP.

Clin Microbiol Infect. 2019 Dec 31. pii: S1198-743X(19)30658-5. doi: 10.1016/j.cmi.2019.12.006. [Epub ahead of print] No abstract available.


Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology.

Zhou W, Emery SB, Flasch DA, Wang Y, Kwan KY, Kidd JM, Moran JV, Mills RE.

Nucleic Acids Res. 2020 Feb 20;48(3):1146-1163. doi: 10.1093/nar/gkz1173.


Pharmacokinetics of Telavancin in Adult Patients with Cystic Fibrosis during Acute Pulmonary Exacerbation.

Kidd JM, Sakon CM, Oleksiuk LM, Cies JJ, Pettit RS, Nicolau DP, Kuti JL.

Antimicrob Agents Chemother. 2019 Dec 20;64(1). pii: e01914-19. doi: 10.1128/AAC.01914-19. Print 2019 Dec 20.


Development of Neutropenic Murine Models of Iron Overload and Depletion To Study the Efficacy of Siderophore-Antibiotic Conjugates.

Kidd JM, Abdelraouf K, Nicolau DP.

Antimicrob Agents Chemother. 2019 Dec 20;64(1). pii: e01961-19. doi: 10.1128/AAC.01961-19. Print 2019 Dec 20.


Efficacy of Humanized Cefiderocol Exposure Is Unaltered by Host Iron Overload in the Thigh Infection Model.

Kidd JM, Abdelraouf K, Nicolau DP.

Antimicrob Agents Chemother. 2019 Dec 20;64(1). pii: e01767-19. doi: 10.1128/AAC.01767-19. Print 2019 Dec 20.


A Neofunctionalized X-Linked Ampliconic Gene Family Is Essential for Male Fertility and Equal Sex Ratio in Mice.

Kruger AN, Brogley MA, Huizinga JL, Kidd JM, de Rooij DG, Hu YC, Mueller JL.

Curr Biol. 2019 Nov 4;29(21):3699-3706.e5. doi: 10.1016/j.cub.2019.08.057. Epub 2019 Oct 17.


Dog10K: the International Consortium of Canine Genome Sequencing.

Wang GD, Larson G, Kidd JM, vonHoldt BM, Ostrander EA, Zhang YP.

Natl Sci Rev. 2019 Jul;6(4):611-613. doi: 10.1093/nsr/nwz068. Epub 2019 May 29. No abstract available.


Comparative In Vivo Antibacterial Activity of Human-Simulated Exposures of Cefiderocol and Ceftazidime against Stenotrophomonas maltophilia in the Murine Thigh Model.

Chen IH, Kidd JM, Abdelraouf K, Nicolau DP.

Antimicrob Agents Chemother. 2019 Oct 7. pii: AAC.01558-19. doi: 10.1128/AAC.01558-19. [Epub ahead of print]


Stable integrant-specific differences in bimodal HIV-1 expression patterns revealed by high-throughput analysis.

Read DF, Atindaana E, Pyaram K, Yang F, Emery S, Cheong A, Nakama KR, Burnett C, Larragoite ET, Battivelli E, Verdin E, Planelles V, Chang CH, Telesnitsky A, Kidd JM.

PLoS Pathog. 2019 Oct 4;15(10):e1007903. doi: 10.1371/journal.ppat.1007903. eCollection 2019 Oct.


Monte Carlo Simulation Methodologies for β-Lactam/β-Lactamase Inhibitor Combinations: Effect on Probability of Target Attainment Assessments.

Kidd JM, Stein GE, Nicolau DP, Kuti JL.

J Clin Pharmacol. 2020 Feb;60(2):172-180. doi: 10.1002/jcph.1510. Epub 2019 Aug 18.


In vitro activity of ampicillin and ceftriaxone against ampicillin-susceptible Enterococcus faecium.

Lorenzo MP, Kidd JM, Jenkins SG, Nicolau DP, Housman ST.

J Antimicrob Chemother. 2019 Aug 1;74(8):2269-2273. doi: 10.1093/jac/dkz173.


Origin and recent expansion of an endogenous gammaretroviral lineage in domestic and wild canids.

Halo JV, Pendleton AL, Jarosz AS, Gifford RJ, Day ML, Kidd JM.

Retrovirology. 2019 Mar 7;16(1):6. doi: 10.1186/s12977-019-0468-z.


Correction: A 32 kb Critical Region Excluding Y402H in CFH Mediates Risk for Age-Related Macular Degeneration.

Sivakumaran TA, Igo RP Jr, Kidd JM, Itsara A, Kopplin LJ, Chen W, Hagstrom SA, Peachey NS, Francis PJ, Klein ML, Chew EY, Ramprasad VL, Tay WT, Mitchell P, Seielstad M, Stambolian DE, Edwards AO, Lee KE, Leontiev DV, Jun G, Wang Y, Tian L, Qiu F, Henning AK, LaFramboise T, Sen P, Aarthi M, George R, Raman R, Das MK, Vijaya L, Kumaramanickavel G, Wong TY, Swaroop A, Abecasis GR, Klein R, Klein BEK, Nickerson DA, Eichler EE, Iyengar SK.

PLoS One. 2018 Dec 20;13(12):e0209943. doi: 10.1371/journal.pone.0209943. eCollection 2018.


Optimizing Antibiotic Administration for Pneumonia.

Motos A, Kidd JM, Nicolau DP.

Clin Chest Med. 2018 Dec;39(4):837-852. doi: 10.1016/j.ccm.2018.08.006. Review.


Pharmacokinetic and Pharmacodynamic Analysis of Ceftazidime/Avibactam in Critically Ill Patients.

Stein GE, Smith CL, Scharmen A, Kidd JM, Cooper C, Kuti J, Mitra S, Nicolau DP, Havlichek DH.

Surg Infect (Larchmt). 2019 Jan;20(1):55-61. doi: 10.1089/sur.2018.141. Epub 2018 Oct 23.


Corrigendum to Physical Compatibility of Meropenem and Vaborbactam with Select Intravenous Drugs During Simulated Y-site Administration [Clinical Therapeutics 40 (2018) 261-269].

Kidd JM, Avery LM, Asempa TE, Nicolau DP, Kuti JL.

Clin Ther. 2018 Nov;40(11):1956. doi: 10.1016/j.clinthera.2018.09.013. Epub 2018 Oct 16. No abstract available.


Developing and interpreting aqueous functional assays for comparative property-activity relationships of different nanoparticles.

Kidd JM, Hanigan D, Truong L, Hristovski K, Tanguay R, Westerhoff P.

Sci Total Environ. 2018 Jul 1;628-629:1609-1616. doi: 10.1016/j.scitotenv.2018.02.107. Epub 2018 Feb 28.


Pharmacodynamics of Daptomycin against Enterococcus faecium and Enterococcus faecalis in the Murine Thigh Infection Model.

Kidd JM, Abdelraouf K, Asempa TE, Humphries RM, Nicolau DP.

Antimicrob Agents Chemother. 2018 Sep 24;62(10). pii: e00506-18. doi: 10.1128/AAC.00506-18. Print 2018 Oct.


Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication.

Pendleton AL, Shen F, Taravella AM, Emery S, Veeramah KR, Boyko AR, Kidd JM.

BMC Biol. 2018 Jun 28;16(1):64. doi: 10.1186/s12915-018-0535-2.


Physical compatibility of plazomicin with select i.v. drugs during simulated Y-site administration.

Asempa TE, Avery LM, Kidd JM, Kuti JL, Nicolau DP.

Am J Health Syst Pharm. 2018 Jul 15;75(14):1048-1056. doi: 10.2146/ajhp170839. Epub 2018 Jun 12. Erratum in: Am J Health Syst Pharm. 2018 Dec 1;75(23):1848.


Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs.

Oetjens MT, Martin A, Veeramah KR, Kidd JM.

BMC Genomics. 2018 May 10;19(1):350. doi: 10.1186/s12864-018-4749-z.


Spliced integrated retrotransposed element (SpIRE) formation in the human genome.

Larson PA, Moldovan JB, Jasti N, Kidd JM, Beck CR, Moran JV.

PLoS Biol. 2018 Mar 5;16(3):e2003067. doi: 10.1371/journal.pbio.2003067. eCollection 2018 Mar.


Novel pharmacotherapy for the treatment of hospital-acquired and ventilator-associated pneumonia caused by resistant gram-negative bacteria.

Kidd JM, Kuti JL, Nicolau DP.

Expert Opin Pharmacother. 2018 Mar;19(4):397-408. doi: 10.1080/14656566.2018.1438408. Epub 2018 Feb 19. Review.


Physical Compatibility of Meropenem and Vaborbactam With Select Intravenous Drugs During Simulated Y-site Administration.

Kidd JM, Avery LM, Asempa TE, Nicolau DP, Kuti JL.

Clin Ther. 2018 Feb;40(2):261-269. doi: 10.1016/j.clinthera.2017.12.007. Epub 2017 Dec 28. Erratum in: Clin Ther. 2018 Nov;40(11):1956.


Ancient European dog genomes reveal continuity since the Early Neolithic.

Botigué LR, Song S, Scheu A, Gopalan S, Pendleton AL, Oetjens M, Taravella AM, Seregély T, Zeeb-Lanz A, Arbogast RM, Bobo D, Daly K, Unterländer M, Burger J, Kidd JM, Veeramah KR.

Nat Commun. 2017 Jul 18;8:16082. doi: 10.1038/ncomms16082.


Production and economic responses to intensification of pasture-based dairy production systems.

Macdonald KA, Penno JW, Lancaster JAS, Bryant AM, Kidd JM, Roche JR.

J Dairy Sci. 2017 Aug;100(8):6602-6619. doi: 10.3168/jds.2016-12497. Epub 2017 Jun 7.


Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network.

McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, Cortes-Ciriano I, Erwin JA, Fasching L, Flasch DA, Freed D, Ganz J, Jaffe AE, Kwan KY, Kwon M, Lodato MA, Mills RE, Paquola ACM, Rodin RE, Rosenbluh C, Sestan N, Sherman MA, Shin JH, Song S, Straub RE, Thorpe J, Weinberger DR, Urban AE, Zhou B, Gage FH, Lehner T, Senthil G, Walsh CA, Chess A, Courchesne E, Gleeson JG, Kidd JM, Park PJ, Pevsner J, Vaccarino FM; Brain Somatic Mosaicism Network.

Science. 2017 Apr 28;356(6336). pii: eaal1641. doi: 10.1126/science.aal1641. Epub 2017 Apr 27. Review.


Modeling Human Population Separation History Using Physically Phased Genomes.

Song S, Sliwerska E, Emery S, Kidd JM.

Genetics. 2017 Jan;205(1):385-395. doi: 10.1534/genetics.116.192963. Epub 2016 Nov 9.


Renal Survival in Patients with Collapsing Compared with Not Otherwise Specified FSGS.

Laurin LP, Gasim AM, Derebail VK, McGregor JG, Kidd JM, Hogan SL, Poulton CJ, Detwiler RK, Jennette JC, Falk RJ, Nachman PH.

Clin J Am Soc Nephrol. 2016 Oct 7;11(10):1752-1759. doi: 10.2215/CJN.13091215. Epub 2016 Jul 21.


Y-Chromosome Structural Diversity in the Bonobo and Chimpanzee Lineages.

Oetjens MT, Shen F, Emery SB, Zou Z, Kidd JM.

Genome Biol Evol. 2016 Aug 3;8(7):2231-40. doi: 10.1093/gbe/evw150.


Resolving complex structural genomic rearrangements using a randomized approach.

Zhao X, Emery SB, Myers B, Kidd JM, Mills RE.

Genome Biol. 2016 Jun 10;17(1):126. doi: 10.1186/s13059-016-0993-1.


Discovery of unfixed endogenous retrovirus insertions in diverse human populations.

Wildschutte JH, Williams ZH, Montesion M, Subramanian RP, Kidd JM, Coffin JM.

Proc Natl Acad Sci U S A. 2016 Apr 19;113(16):E2326-34. doi: 10.1073/pnas.1602336113. Epub 2016 Mar 21.


Ipilimumab-associated minimal-change disease.

Kidd JM, Gizaw AB.

Kidney Int. 2016 Mar;89(3):720. doi: 10.1016/j.kint.2015.11.028. No abstract available.


Distance from sub-Saharan Africa predicts mutational load in diverse human genomes.

Henn BM, Botigué LR, Peischl S, Dupanloup I, Lipatov M, Maples BK, Martin AR, Musharoff S, Cann H, Snyder MP, Excoffier L, Kidd JM, Bustamante CD.

Proc Natl Acad Sci U S A. 2016 Jan 26;113(4):E440-9. doi: 10.1073/pnas.1510805112. Epub 2015 Dec 28.


The Time Scale of Recombination Rate Evolution in Great Apes.

Stevison LS, Woerner AE, Kidd JM, Kelley JL, Veeramah KR, McManus KF; Great Ape Genome Project, Bustamante CD, Hammer MF, Wall JD.

Mol Biol Evol. 2016 Apr;33(4):928-45. doi: 10.1093/molbev/msv331. Epub 2015 Dec 15.


Discovery and characterization of Alu repeat sequences via precise local read assembly.

Wildschutte JH, Baron A, Diroff NM, Kidd JM.

Nucleic Acids Res. 2015 Dec 2;43(21):10292-307. doi: 10.1093/nar/gkv1089. Epub 2015 Oct 25.


An integrated map of structural variation in 2,504 human genomes.

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO.

Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394.


All that leaks is not blood.

Gizaw A, Kidd JM.

Kidney Int. 2015 Sep;88(3):645. doi: 10.1038/ki.2015.7. No abstract available.


The development of a prototype measure of the co-production of health in routine consultations for people with long-term conditions.

Realpe AX, Wallace LM, Adams AE, Kidd JM.

Patient Educ Couns. 2015 Jul 8. pii: S0738-3991(15)30014-8. doi: 10.1016/j.pec.2015.07.005. [Epub ahead of print]


Adverse events and infectious burden, microbes and temporal outline from immunosuppressive therapy in antineutrophil cytoplasmic antibody-associated vasculitis with native renal function.

McGregor JG, Negrete-Lopez R, Poulton CJ, Kidd JM, Katsanos SL, Goetz L, Hu Y, Nachman PH, Falk RJ, Hogan SL.

Nephrol Dial Transplant. 2015 Apr;30 Suppl 1:i171-81. doi: 10.1093/ndt/gfv045.


Rituximab as an immunosuppressant in antineutrophil cytoplasmic antibody-associated vasculitis.

McGregor JG, Hogan SL, Kotzen ES, Poulton CJ, Hu Y, Negrete-Lopez R, Kidd JM, Katsanos SL, Bunch DO, Nachman PH, Falk RJ.

Nephrol Dial Transplant. 2015 Apr;30 Suppl 1:i123-31. doi: 10.1093/ndt/gfv076.


Inference of gorilla demographic and selective history from whole-genome sequence data.

McManus KF, Kelley JL, Song S, Veeramah KR, Woerner AE, Stevison LS, Ryder OA, Ape Genome Project G, Kidd JM, Wall JD, Bustamante CD, Hammer MF.

Mol Biol Evol. 2015 Mar;32(3):600-12. doi: 10.1093/molbev/msu394. Epub 2014 Dec 21.


The genomic landscape of polymorphic human nuclear mitochondrial insertions.

Dayama G, Emery SB, Kidd JM, Mills RE.

Nucleic Acids Res. 2014 Nov 10;42(20):12640-9. doi: 10.1093/nar/gku1038. Epub 2014 Oct 27.


Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture.

Martin AR, Costa HA, Lappalainen T, Henn BM, Kidd JM, Yee MC, Grubert F, Cann HM, Snyder M, Montgomery SB, Bustamante CD.

PLoS Genet. 2014 Aug 14;10(8):e1004549. doi: 10.1371/journal.pgen.1004549. eCollection 2014 Aug.


Exome capture from saliva produces high quality genomic and metagenomic data.

Kidd JM, Sharpton TJ, Bobo D, Norman PJ, Martin AR, Carpenter ML, Sikora M, Gignoux CR, Nemat-Gorgani N, Adams A, Guadalupe M, Guo X, Feng Q, Li Y, Liu X, Parham P, Hoal EG, Feldman MW, Pollard KS, Wall JD, Bustamante CD, Henn BM.

BMC Genomics. 2014 Apr 4;15:262. doi: 10.1186/1471-2164-15-262.


How do early emotional experiences in the operating theatre influence medical student learning in this environment?

Bowrey DJ, Kidd JM.

Teach Learn Med. 2014;26(2):113-20. doi: 10.1080/10401334.2014.883986.


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