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Items: 1 to 50 of 144

1.

Cyberinfrastructure and resources to enable an integrative approach to studying forest trees.

Wegrzyn JL, Falk T, Grau E, Buehler S, Ramnath R, Herndon N.

Evol Appl. 2019 Nov 3;13(1):228-241. doi: 10.1111/eva.12860. eCollection 2020 Jan.

2.

Comparative genomics of six Juglans species reveals disease-associated gene family contractions.

Trouern-Trend AJ, Falk T, Zaman S, Caballero M, Neale DB, Langley CH, Dandekar AM, Stevens KA, Wegrzyn JL.

Plant J. 2019 Dec 10. doi: 10.1111/tpj.14630. [Epub ahead of print]

PMID:
31823432
3.

Co-option of wing-patterning genes underlies the evolution of the treehopper helmet.

Fisher CR, Wegrzyn JL, Jockusch EL.

Nat Ecol Evol. 2020 Feb;4(2):250-260. doi: 10.1038/s41559-019-1054-4. Epub 2019 Dec 9.

PMID:
31819237
4.

Is Isolated Mobile Component Exchange an Option in the Management of Intraprosthetic Dislocation of a Dual Mobility Cup?

Wegrzyn J, Malatray M, Pibarot V, Anania G, Béjui-Hugues J.

Clin Orthop Relat Res. 2020 Feb;478(2):279-287. doi: 10.1097/CORR.0000000000001055.

PMID:
31794492
5.

Tripal MapViewer: A tool for interactive visualization and comparison of genetic maps.

Buble K, Jung S, Humann JL, Yu J, Cheng CH, Lee T, Ficklin SP, Hough H, Condon B, Staton ME, Wegrzyn JL, Main D.

Database (Oxford). 2019 Jan 1;2019. pii: baz100. doi: 10.1093/database/baz100.

6.

EnTAP: Bringing faster and smarter functional annotation to non-model eukaryotic transcriptomes.

Hart AJ, Ginzburg S, Xu MS, Fisher CR, Rahmatpour N, Mitton JB, Paul R, Wegrzyn JL.

Mol Ecol Resour. 2019 Oct 19. doi: 10.1111/1755-0998.13106. [Epub ahead of print]

PMID:
31628884
7.

Dual RNA-Seq Analysis of the Pine-Fusarium circinatum Interaction in Resistant (Pinus tecunumanii) and Susceptible (Pinus patula) Hosts.

Visser EA, Wegrzyn JL, Steenkamp ET, Myburg AA, Naidoo S.

Microorganisms. 2019 Sep 4;7(9). pii: E315. doi: 10.3390/microorganisms7090315.

8.

gFACs: Gene Filtering, Analysis, and Conversion to Unify Genome Annotations Across Alignment and Gene Prediction Frameworks.

Caballero M, Wegrzyn J.

Genomics Proteomics Bioinformatics. 2019 Jun;17(3):305-310. doi: 10.1016/j.gpb.2019.04.002. Epub 2019 Aug 19.

9.

Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases.

Spoor S, Cheng CH, Sanderson LA, Condon B, Almsaeed A, Chen M, Bretaudeau A, Rasche H, Jung S, Main D, Bett K, Staton M, Wegrzyn JL, Feltus FA, Ficklin SP.

Database (Oxford). 2019 Jan 1;2019. pii: baz077. doi: 10.1093/database/baz077.

10.

Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment.

Wegrzyn JL, Staton MA, Street NR, Main D, Grau E, Herndon N, Buehler S, Falk T, Zaman S, Ramnath R, Richter P, Sun L, Condon B, Almsaeed A, Chen M, Mannapperuma C, Jung S, Ficklin S.

Front Plant Sci. 2019 Jun 25;10:813. doi: 10.3389/fpls.2019.00813. eCollection 2019.

11.

Growing and cultivating the forest genomics database, TreeGenes.

Falk T, Herndon N, Grau E, Buehler S, Richter P, Zaman S, Baker EM, Ramnath R, Ficklin S, Staton M, Feltus FA, Jung S, Main D, Wegrzyn JL.

Database (Oxford). 2019 Jan 1;2019. pii: baz043. doi: 10.1093/database/baz043. No abstract available.

12.

Hospital Length of Stay Reduction Over Time and Patient Readmission for Severe Adverse Events Following Surgery.

Pascal L, Polazzi S, Piriou V, Cotte E, Wegrzyn J, Carty MJ, Chollet F, Sanchez S, Lifante JC, Duclos A.

Ann Surg. 2019 Jan 19. doi: 10.1097/SLA.0000000000003206. [Epub ahead of print]

PMID:
30676380
13.

15 years of GDR: New data and functionality in the Genome Database for Rosaceae.

Jung S, Lee T, Cheng CH, Buble K, Zheng P, Yu J, Humann J, Ficklin SP, Gasic K, Scott K, Frank M, Ru S, Hough H, Evans K, Peace C, Olmstead M, DeVetter LW, McFerson J, Coe M, Wegrzyn JL, Staton ME, Abbott AG, Main D.

Nucleic Acids Res. 2019 Jan 8;47(D1):D1137-D1145. doi: 10.1093/nar/gky1000.

14.

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture.

Harper L, Campbell J, Cannon EKS, Jung S, Poelchau M, Walls R, Andorf C, Arnaud E, Berardini TZ, Birkett C, Cannon S, Carson J, Condon B, Cooper L, Dunn N, Elsik CG, Farmer A, Ficklin SP, Grant D, Grau E, Herndon N, Hu ZL, Humann J, Jaiswal P, Jonquet C, Laporte MA, Larmande P, Lazo G, McCarthy F, Menda N, Mungall CJ, Munoz-Torres MC, Naithani S, Nelson R, Nesdill D, Park C, Reecy J, Reiser L, Sanderson LA, Sen TZ, Staton M, Subramaniam S, Tello-Ruiz MK, Unda V, Unni D, Wang L, Ware D, Wegrzyn J, Williams J, Woodhouse M, Yu J, Main D.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay088.

15.

Growing and cultivating the forest genomics database, TreeGenes.

Falk T, Herndon N, Grau E, Buehler S, Richter P, Zaman S, Baker EM, Ramnath R, Ficklin S, Staton M, Feltus FA, Jung S, Main D, Wegrzyn JL.

Database (Oxford). 2018 Jan 1;2018:1-11. doi: 10.1093/database/bay084. Erratum in: Database (Oxford). 2019 Jan 1;2019:.

16.

Defence transcriptome assembly and pathogenesis related gene family analysis in Pinus tecunumanii (low elevation).

Visser EA, Wegrzyn JL, Myburg AA, Naidoo S.

BMC Genomics. 2018 Aug 23;19(1):632. doi: 10.1186/s12864-018-5015-0.

17.

Bone and parietal anterior iliac crest reconstruction for trans-iliac hernia after tricortical graft harvesting: An original technique.

Malatray M, Al Qahtani T, Monneuse O, Pibarot V, Wegrzyn J.

Orthop Traumatol Surg Res. 2018 Nov;104(7):1069-1072. doi: 10.1016/j.otsr.2018.06.010. Epub 2018 Aug 13.

18.

miR-143/145 differentially regulate hematopoietic stem and progenitor activity through suppression of canonical TGFβ signaling.

Lam J, van den Bosch M, Wegrzyn J, Parker J, Ibrahim R, Slowski K, Chang L, Martinez-Høyer S, Condorelli G, Boldin M, Deng Y, Umlandt P, Fuller M, Karsan A.

Nat Commun. 2018 Jun 20;9(1):2418. doi: 10.1038/s41467-018-04831-3.

19.

Total Hip Arthroplasty for Periacetabular Metastatic Disease. An Original Technique of Reconstruction According to the Harrington Classification.

Wegrzyn J, Malatray M, Al-Qahtani T, Pibarot V, Confavreux C, Freyer G.

J Arthroplasty. 2018 Aug;33(8):2546-2555. doi: 10.1016/j.arth.2018.02.096. Epub 2018 Mar 17.

PMID:
29656965
20.

Bone metastases from lung cancer: A paradigm for multidisciplinary onco-rheumatology management.

Confavreux CB, Pialat JB, Bellière A, Brevet M, Decroisette C, Tescaru A, Wegrzyn J, Barrey C, Mornex F, Souquet PJ, Girard N.

Joint Bone Spine. 2019 Mar;86(2):185-194. doi: 10.1016/j.jbspin.2018.03.005. Epub 2018 Apr 6.

PMID:
29631067
21.

Comparative Transcriptomics Among Four White Pine Species.

Baker EAG, Wegrzyn JL, Sezen UU, Falk T, Maloney PE, Vogler DR, Delfino-Mix A, Jensen C, Mitton J, Wright J, Knaus B, Rai H, Cronn R, Gonzalez-Ibeas D, Vasquez-Gross HA, Famula RA, Liu JJ, Kueppers LM, Neale DB.

G3 (Bethesda). 2018 May 4;8(5):1461-1474. doi: 10.1534/g3.118.200257.

22.

JAK/STAT3 regulated global gene expression dynamics during late-stage reprogramming process.

Wang L, Jiang Z, Huang D, Duan J, Huang C, Sullivan S, Vali K, Yin Y, Zhang M, Wegrzyn J, Tian XC, Tang Y.

BMC Genomics. 2018 Mar 6;19(1):183. doi: 10.1186/s12864-018-4507-2.

23.

The tridimensional geometry of the proximal femur should determine the design of cementless femoral stem in total hip arthroplasty.

Wegrzyn J, Roux JP, Loriau C, Bonin N, Pibarot V.

Int Orthop. 2018 Oct;42(10):2329-2334. doi: 10.1007/s00264-018-3843-9. Epub 2018 Feb 22.

PMID:
29468265
24.

Practice makes the deficiency of global motion detection in people with pattern-related visual stress more apparent.

Han D, Wegrzyn J, Bi H, Wei R, Zhang B, Li X.

PLoS One. 2018 Feb 15;13(2):e0193215. doi: 10.1371/journal.pone.0193215. eCollection 2018.

25.

Bone, muscle, and metabolic parameters predict survival in patients with synchronous bone metastases from lung cancers.

Chambard L, Girard N, Ollier E, Rousseau JC, Duboeuf F, Carlier MC, Brevet M, Szulc P, Pialat JB, Wegrzyn J, Clezardin P, Confavreux CB.

Bone. 2018 Mar;108:202-209. doi: 10.1016/j.bone.2018.01.004. Epub 2018 Jan 11.

PMID:
29337225
26.

New extension software modules to enhance searching and display of transcriptome data in Tripal databases.

Chen M, Henry N, Almsaeed A, Zhou X, Wegrzyn J, Ficklin S, Staton M.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax052.

27.

Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL.

Gigascience. 2017 Oct 1;6(10):1. doi: 10.1093/gigascience/gix072.

28.

The predictive factors of secondary patellar resurfacing in computer-assisted total knee arthroplasty. A prospective cohort study.

Franck F, Ouanezar H, Jacquel A, Pibarot V, Wegrzyn J.

Int Orthop. 2018 May;42(5):1051-1060. doi: 10.1007/s00264-017-3630-z. Epub 2017 Sep 9.

PMID:
28889222
29.

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

Neale DB, McGuire PE, Wheeler NC, Stevens KA, Crepeau MW, Cardeno C, Zimin AV, Puiu D, Pertea GM, Sezen UU, Casola C, Koralewski TE, Paul R, Gonzalez-Ibeas D, Zaman S, Cronn R, Yandell M, Holt C, Langley CH, Yorke JA, Salzberg SL, Wegrzyn JL.

G3 (Bethesda). 2017 Sep 7;7(9):3157-3167. doi: 10.1534/g3.117.300078.

30.

Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir needles.

Cronn R, Dolan PC, Jogdeo S, Wegrzyn JL, Neale DB, St Clair JB, Denver DR.

BMC Genomics. 2017 Jul 24;18(1):558. doi: 10.1186/s12864-017-3916-y.

31.

Transcriptome Analysis Reveals Differential Gene Expression and a Possible Role of Gibberellins in a Shade-Tolerant Mutant of Perennial Ryegrass.

Li W, Katin-Grazzini L, Gu X, Wang X, El-Tanbouly R, Yer H, Thammina C, Inguagiato J, Guillard K, McAvoy RJ, Wegrzyn J, Gu T, Li Y.

Front Plant Sci. 2017 May 26;8:868. doi: 10.3389/fpls.2017.00868. eCollection 2017.

32.

ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.

Sablok G, Chen TW, Lee CC, Yang C, Gan RC, Wegrzyn JL, Porta NL, Nayak KC, Huang PJ, Varotto C, Tang P.

DNA Res. 2017 Jun 1;24(3):327-332. doi: 10.1093/dnares/dsw044.

33.

An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL.

Gigascience. 2017 Jan 1;6(1):1-4. doi: 10.1093/gigascience/giw016. Erratum in: Gigascience. 2017 Oct 1;6(10):1.

34.

Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA.

Lind BM, Friedline CJ, Wegrzyn JL, Maloney PE, Vogler DR, Neale DB, Eckert AJ.

Mol Ecol. 2017 Jun;26(12):3168-3185. doi: 10.1111/mec.14106. Epub 2017 May 6.

PMID:
28316116
35.

Transcriptomic imprints of adaptation to fresh water: parallel evolution of osmoregulatory gene expression in the Alewife.

Velotta JP, Wegrzyn JL, Ginzburg S, Kang L, Czesny S, O'Neill RJ, McCormick SD, Michalak P, Schultz ET.

Mol Ecol. 2017 Feb;26(3):831-848. doi: 10.1111/mec.13983. Epub 2017 Jan 27.

PMID:
28012221
36.

Highly crosslinked polyethylene: a safe alternative to conventional polyethylene for dual mobility cup mobile component. A biomechanical validation.

Malatray M, Roux JP, Gunst S, Pibarot V, Wegrzyn J.

Int Orthop. 2017 Mar;41(3):507-512. doi: 10.1007/s00264-016-3334-9. Epub 2016 Nov 11.

PMID:
27837329
37.

Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana).

Gonzalez-Ibeas D, Martinez-Garcia PJ, Famula RA, Delfino-Mix A, Stevens KA, Loopstra CA, Langley CH, Neale DB, Wegrzyn JL.

G3 (Bethesda). 2016 Dec 7;6(12):3787-3802. doi: 10.1534/g3.116.032805.

38.

Sequence of the Sugar Pine Megagenome.

Stevens KA, Wegrzyn JL, Zimin A, Puiu D, Crepeau M, Cardeno C, Paul R, Gonzalez-Ibeas D, Koriabine M, Holtz-Morris AE, Martínez-García PJ, Sezen UU, Marçais G, Jermstad K, McGuire PE, Loopstra CA, Davis JM, Eckert A, de Jong P, Yorke JA, Salzberg SL, Neale DB, Langley CH.

Genetics. 2016 Dec;204(4):1613-1626. Epub 2016 Oct 28.

39.

Does computer-assisted surgery influence survivorship of cementless total knee arthroplasty in patients with primary osteoarthritis? A 10-year follow-up study.

Ouanezar H, Franck F, Jacquel A, Pibarot V, Wegrzyn J.

Knee Surg Sports Traumatol Arthrosc. 2016 Nov;24(11):3448-3456. Epub 2016 Apr 7.

PMID:
27056689
40.

Quantitative trait loci influencing forking defects in an outbred pedigree of loblolly pine.

Xiong JS, McKeand SE, Isik F, Wegrzyn J, Neale DB, Zeng ZB, da Costa E Silva L, Whetten RW.

BMC Genet. 2016 Oct 18;17(1):138.

41.

Poor maternal nutrition during gestation alters the expression of genes involved in muscle development and metabolism in lambs.

Hoffman ML, Peck KN, Wegrzyn JL, Reed SA, Zinn SA, Govoni KE.

J Anim Sci. 2016 Jul;94(7):3093-9. doi: 10.2527/jas.2016-0570.

PMID:
27482696
42.

Targeted Capture Sequencing in Whitebark Pine Reveals Range-Wide Demographic and Adaptive Patterns Despite Challenges of a Large, Repetitive Genome.

Syring JV, Tennessen JA, Jennings TN, Wegrzyn J, Scelfo-Dalbey C, Cronn R.

Front Plant Sci. 2016 Apr 21;7:484. doi: 10.3389/fpls.2016.00484. eCollection 2016.

43.

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols.

Martínez-García PJ, Crepeau MW, Puiu D, Gonzalez-Ibeas D, Whalen J, Stevens KA, Paul R, Butterfield TS, Britton MT, Reagan RL, Chakraborty S, Walawage SL, Vasquez-Gross HA, Cardeno C, Famula RA, Pratt K, Kuruganti S, Aradhya MK, Leslie CA, Dandekar AM, Salzberg SL, Wegrzyn JL, Langley CH, Neale DB.

Plant J. 2016 Sep;87(5):507-32. doi: 10.1111/tpj.13207. Epub 2016 Jul 18.

44.

Vertebral body morphology is associated with incident lumbar vertebral fracture in postmenopausal women. The OFELY study.

Roux JP, Belghali S, Wegrzyn J, Rendu ES, Chapurlat R.

Osteoporos Int. 2016 Aug;27(8):2507-13. doi: 10.1007/s00198-016-3558-y. Epub 2016 Mar 8.

PMID:
26957288
45.

YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut.

Chakraborty S, Britton M, Wegrzyn J, Butterfield T, Martínez-García PJ, Reagan RL, Rao BJ, Leslie CA, Aradhaya M, Neale D, Woeste K, Dandekar AM.

Version 2. F1000Res. 2015 Jun 17 [revised 2015 Jan 1];4:155. doi: 10.12688/f1000research.6617.2. eCollection 2015.

46.

Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome.

Visser EA, Wegrzyn JL, Steenkmap ET, Myburg AA, Naidoo S.

BMC Genomics. 2015 Dec 12;16:1057. doi: 10.1186/s12864-015-2277-7.

47.

Lineage, fate, and fate potential of NG2-glia.

Nishiyama A, Boshans L, Goncalves CM, Wegrzyn J, Patel KD.

Brain Res. 2016 May 1;1638(Pt B):116-128. doi: 10.1016/j.brainres.2015.08.013. Epub 2015 Aug 21. Review.

48.

Performance of Porous Tantalum vs. Titanium Cup in Total Hip Arthroplasty: Randomized Trial with Minimum 10-Year Follow-Up.

Wegrzyn J, Kaufman KR, Hanssen AD, Lewallen DG.

J Arthroplasty. 2015 Jun;30(6):1008-13. doi: 10.1016/j.arth.2015.01.013. Epub 2015 Jan 21.

PMID:
25765132
49.

Can Dual Mobility Cups prevent Dislocation in All Situations After Revision Total Hip Arthroplasty?

Wegrzyn J, Tebaa E, Jacquel A, Carret JP, Béjui-Hugues J, Pibarot V.

J Arthroplasty. 2015 Apr;30(4):631-40. doi: 10.1016/j.arth.2014.10.034. Epub 2014 Nov 10.

PMID:
25443363
50.

Discovering candidate genes that regulate resin canal number in Pinus taeda stems by integrating genetic analysis across environments, ages, and populations.

Westbrook JW, Walker AR, Neves LG, Munoz P, Resende MF Jr, Neale DB, Wegrzyn JL, Huber DA, Kirst M, Davis JM, Peter GF.

New Phytol. 2015 Jan;205(2):627-41. doi: 10.1111/nph.13074. Epub 2014 Sep 30.

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