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Items: 1 to 50 of 63

1.

Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.

Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, Becker C, Kudrna D, Zhang J, Londono CEM, Song X, Lee S, Sanchez P, Zuccolo A, Ammiraju JSS, Talag J, Danowitz A, Rivera LF, Gschwend AR, Noutsos C, Wu CC, Kao SM, Zeng JW, Wei FJ, Zhao Q, Feng Q, El Baidouri M, Carpentier MC, Lasserre E, Cooke R, da Rosa Farias D, da Maia LC, Dos Santos RS, Nyberg KG, McNally KL, Mauleon R, Alexandrov N, Schmutz J, Flowers D, Fan C, Weigel D, Jena KK, Wicker T, Chen M, Han B, Henry R, Hsing YC, Kurata N, de Oliveira AC, Panaud O, Jackson SA, Machado CA, Sanderson MJ, Long M, Ware D, Wing RA.

Nat Genet. 2018 Nov;50(11):1618. doi: 10.1038/s41588-018-0261-2.

PMID:
30291357
2.

Improved RNA-seq Workflows Using CyVerse Cyberinfrastructure.

Chougule KM, Wang L, Stein JC, Wang X, Devisetty UK, Klein RR, Ware D.

Curr Protoc Bioinformatics. 2018 Sep;63(1):e53. doi: 10.1002/cpbi.53. Epub 2018 Aug 31.

PMID:
30168903
3.

The maize W22 genome provides a foundation for functional genomics and transposon biology.

Springer NM, Anderson SN, Andorf CM, Ahern KR, Bai F, Barad O, Barbazuk WB, Bass HW, Baruch K, Ben-Zvi G, Buckler ES, Bukowski R, Campbell MS, Cannon EKS, Chomet P, Dawe RK, Davenport R, Dooner HK, Du LH, Du C, Easterling KA, Gault C, Guan JC, Hunter CT, Jander G, Jiao Y, Koch KE, Kol G, Köllner TG, Kudo T, Li Q, Lu F, Mayfield-Jones D, Mei W, McCarty DR, Noshay JM, Portwood JL 2nd, Ronen G, Settles AM, Shem-Tov D, Shi J, Soifer I, Stein JC, Stitzer MC, Suzuki M, Vera DL, Vollbrecht E, Vrebalov JT, Ware D, Wei S, Wimalanathan K, Woodhouse MR, Xiong W, Brutnell TP.

Nat Genet. 2018 Sep;50(9):1282-1288. doi: 10.1038/s41588-018-0158-0. Epub 2018 Jul 30.

PMID:
30061736
4.

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes.

Sun S, Zhou Y, Chen J, Shi J, Zhao H, Zhao H, Song W, Zhang M, Cui Y, Dong X, Liu H, Ma X, Jiao Y, Wang B, Wei X, Stein JC, Glaubitz JC, Lu F, Yu G, Liang C, Fengler K, Li B, Rafalski A, Schnable PS, Ware DH, Buckler ES, Lai J.

Nat Genet. 2018 Sep;50(9):1289-1295. doi: 10.1038/s41588-018-0182-0. Epub 2018 Jul 30.

PMID:
30061735
5.

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.

Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, Becker C, Kudrna D, Zhang J, Londono CEM, Song X, Lee S, Sanchez P, Zuccolo A, Ammiraju JSS, Talag J, Danowitz A, Rivera LF, Gschwend AR, Noutsos C, Wu CC, Kao SM, Zeng JW, Wei FJ, Zhao Q, Feng Q, El Baidouri M, Carpentier MC, Lasserre E, Cooke R, Rosa Farias DD, da Maia LC, Dos Santos RS, Nyberg KG, McNally KL, Mauleon R, Alexandrov N, Schmutz J, Flowers D, Fan C, Weigel D, Jena KK, Wicker T, Chen M, Han B, Henry R, Hsing YC, Kurata N, de Oliveira AC, Panaud O, Jackson SA, Machado CA, Sanderson MJ, Long M, Ware D, Wing RA.

Nat Genet. 2018 Feb;50(2):285-296. doi: 10.1038/s41588-018-0040-0. Epub 2018 Jan 22. Erratum in: Nat Genet. 2018 Nov;50(11):1618.

PMID:
29358651
6.

Gramene 2018: unifying comparative genomics and pathway resources for plant research.

Tello-Ruiz MK, Naithani S, Stein JC, Gupta P, Campbell M, Olson A, Wei S, Preece J, Geniza MJ, Jiao Y, Lee YK, Wang B, Mulvaney J, Chougule K, Elser J, Al-Bader N, Kumari S, Thomason J, Kumar V, Bolser DM, Naamati G, Tapanari E, Fonseca N, Huerta L, Iqbal H, Keays M, Munoz-Pomer Fuentes A, Tang A, Fabregat A, D'Eustachio P, Weiser J, Stein LD, Petryszak R, Papatheodorou I, Kersey PJ, Lockhart P, Taylor C, Jaiswal P, Ware D.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1181-D1189. doi: 10.1093/nar/gkx1111.

7.

Improved maize reference genome with single-molecule technologies.

Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, Campbell MS, Stein JC, Wei X, Chin CS, Guill K, Regulski M, Kumari S, Olson A, Gent J, Schneider KL, Wolfgruber TK, May MR, Springer NM, Antoniou E, McCombie WR, Presting GG, McMullen M, Ross-Ibarra J, Dawe RK, Hastie A, Rank DR, Ware D.

Nature. 2017 Jun 22;546(7659):524-527. doi: 10.1038/nature22971. Epub 2017 Jun 12.

PMID:
28605751
8.

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing.

Wang B, Tseng E, Regulski M, Clark TA, Hon T, Jiao Y, Lu Z, Olson A, Stein JC, Ware D.

Nat Commun. 2016 Jun 24;7:11708. doi: 10.1038/ncomms11708.

9.

Clinician Perspectives on Challenges to Patient Centered Care at the End of Life.

Bardach SH, Dunn EJ, Stein JC.

J Appl Gerontol. 2017 Apr;36(4):401-415. doi: 10.1177/0733464815584668. Epub 2016 Jul 9.

PMID:
25956446
10.

Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica.

Schatz MC, Maron LG, Stein JC, Hernandez Wences A, Gurtowski J, Biggers E, Lee H, Kramer M, Antoniou E, Ghiban E, Wright MH, Chia JM, Ware D, McCouch SR, McCombie WR.

Genome Biol. 2014;15(11):506.

11.

Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes.

Law M, Childs KL, Campbell MS, Stein JC, Olson AJ, Holt C, Panchy N, Lei J, Jiao D, Andorf CM, Lawrence CJ, Ware D, Shiu SH, Sun Y, Jiang N, Yandell M.

Plant Physiol. 2015 Jan;167(1):25-39. doi: 10.1104/pp.114.245027. Epub 2014 Nov 10.

12.

Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3.

Zwickl DJ, Stein JC, Wing RA, Ware D, Sanderson MJ.

Syst Biol. 2014 Sep;63(5):645-59. doi: 10.1093/sysbio/syu027. Epub 2014 Apr 9.

PMID:
24721692
13.

Oblique-axis vs. short-axis view in ultrasound-guided central venous catheterization.

Wilson JG, Berona KM, Stein JC, Wang R.

J Emerg Med. 2014 Jul;47(1):45-50. doi: 10.1016/j.jemermed.2013.11.080. Epub 2014 Mar 27.

PMID:
24685453
14.

Root Cause Analysis of Ambulatory Adverse Drug Events That Present to the Emergency Department.

Gertler SA, Coralic Z, López A, Stein JC, Sarkar U.

J Patient Saf. 2016 Sep;12(3):119-24. doi: 10.1097/PTS.0000000000000072.

PMID:
24583958
15.

Intensive care unit scoring systems outperform emergency department scoring systems for mortality prediction in critically ill patients: a prospective cohort study.

Moseson EM, Zhuo H, Chu J, Stein JC, Matthay MA, Kangelaris KN, Liu KD, Calfee CS.

J Intensive Care. 2014 Jul 1;2:40. doi: 10.1186/2052-0492-2-40. eCollection 2014.

16.

MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations.

Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J, Achawanantakun R, Jiao D, Lawrence CJ, Ware D, Shiu SH, Childs KL, Sun Y, Jiang N, Yandell M.

Plant Physiol. 2014 Feb;164(2):513-24. doi: 10.1104/pp.113.230144. Epub 2013 Dec 4.

17.

Physician accuracy in interpreting potential ST-segment elevation myocardial infarction electrocardiograms.

McCabe JM, Armstrong EJ, Ku I, Kulkarni A, Hoffmayer KS, Bhave PD, Waldo SW, Hsue P, Stein JC, Marcus GM, Kinlay S, Ganz P.

J Am Heart Assoc. 2013 Oct 4;2(5):e000268. doi: 10.1161/JAHA.113.000268.

18.

Copeptin helps in the early detection of patients with acute myocardial infarction: primary results of the CHOPIN trial (Copeptin Helps in the early detection Of Patients with acute myocardial INfarction).

Maisel A, Mueller C, Neath SX, Christenson RH, Morgenthaler NG, McCord J, Nowak RM, Vilke G, Daniels LB, Hollander JE, Apple FS, Cannon C, Nagurney JT, Schreiber D, deFilippi C, Hogan C, Diercks DB, Stein JC, Headden G, Limkakeng AT Jr, Anand I, Wu AHB, Papassotiriou J, Hartmann O, Ebmeyer S, Clopton P, Jaffe AS, Peacock WF.

J Am Coll Cardiol. 2013 Jul 9;62(2):150-160. doi: 10.1016/j.jacc.2013.04.011. Epub 2013 Apr 30.

19.

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor.

Luo MC, Gu YQ, You FM, Deal KR, Ma Y, Hu Y, Huo N, Wang Y, Wang J, Chen S, Jorgensen CM, Zhang Y, McGuire PE, Pasternak S, Stein JC, Ware D, Kramer M, McCombie WR, Kianian SF, Martis MM, Mayer KF, Sehgal SK, Li W, Gill BS, Bevan MW, Simková H, Dolezel J, Weining S, Lazo GR, Anderson OD, Dvorak J.

Proc Natl Acad Sci U S A. 2013 May 7;110(19):7940-5. doi: 10.1073/pnas.1219082110. Epub 2013 Apr 22.

20.

Benefit or burden? A sociotechnical analysis of diagnostic computer kiosks in four California hospital emergency departments.

Ackerman SL, Tebb K, Stein JC, Frazee BW, Hendey GW, Schmidt LA, Gonzales R.

Soc Sci Med. 2012 Dec;75(12):2378-85. doi: 10.1016/j.socscimed.2012.09.013. Epub 2012 Sep 26.

21.

Impact of door-to-activation time on door-to-balloon time in primary percutaneous coronary intervention for ST-segment elevation myocardial infarctions: a report from the Activate-SF registry.

McCabe JM, Armstrong EJ, Hoffmayer KS, Bhave PD, MacGregor JS, Hsue P, Stein JC, Kinlay S, Ganz P.

Circ Cardiovasc Qual Outcomes. 2012 Sep 1;5(5):672-9. Epub 2012 Sep 4.

PMID:
22949494
22.

Electrocardiographic criteria for ST-elevation myocardial infarction in patients with left ventricular hypertrophy.

Armstrong EJ, Kulkarni AR, Bhave PD, Hoffmayer KS, Macgregor JS, Stein JC, Kinlay S, Ganz P, McCabe JM.

Am J Cardiol. 2012 Oct 1;110(7):977-83. doi: 10.1016/j.amjcard.2012.05.032. Epub 2012 Jun 26.

PMID:
22738872
23.

Prevalence and factors associated with false-positive ST-segment elevation myocardial infarction diagnoses at primary percutaneous coronary intervention–capable centers: a report from the Activate-SF registry.

McCabe JM, Armstrong EJ, Kulkarni A, Hoffmayer KS, Bhave PD, Garg S, Patel A, MacGregor JS, Hsue P, Stein JC, Kinlay S, Ganz P.

Arch Intern Med. 2012 Jun 11;172(11):864-71. doi: 10.1001/archinternmed.2012.945.

PMID:
22566489
24.

Delaying primary percutaneous coronary intervention for computed tomographic scans in the emergency department.

Armstrong EJ, Kulkarni AR, Hoffmayer KS, Bhave PD, MacGregor JS, Hsue P, Stein JC, Kinlay S, Ganz P, McCabe JM.

Am J Cardiol. 2012 Aug 1;110(3):345-9. doi: 10.1016/j.amjcard.2012.03.032. Epub 2012 Apr 23.

PMID:
22534052
25.

Regional differences in emergency medical services use for patients with acute stroke (findings from the National Hospital Ambulatory Medical Care Survey Emergency Department Data File).

Govindarajan P, Gonzales R, Maselli JH, Johnston SC, Fahimi J, Poisson S, Stein JC.

J Stroke Cerebrovasc Dis. 2013 Nov;22(8):e257-63. doi: 10.1016/j.jstrokecerebrovasdis.2012.02.014. Epub 2012 Mar 31.

PMID:
22465209
26.

Predictors of depressed left ventricular function in patients presenting with ST-elevation myocardial infarction.

Bhave PD, Hoffmayer KS, Armstrong EJ, Garg S, Patel A, Macgregor JS, Stein JC, Kinlay S, Ganz P, McCabe JM.

Am J Cardiol. 2012 Feb 1;109(3):327-31. doi: 10.1016/j.amjcard.2011.09.015. Epub 2011 Nov 11.

PMID:
22078964
27.

A randomized trial of computer kiosk-expedited management of cystitis in the emergency department.

Stein JC, Navab B, Frazee B, Tebb K, Hendey G, Maselli J, Gonzales R.

Acad Emerg Med. 2011 Oct;18(10):1053-9. doi: 10.1111/j.1553-2712.2011.01167.x.

28.

Hypertensive encephalopathy presenting as status epilepticus in a three year old.

Sanford EF, Stein JC.

J Emerg Med. 2012 Jun;42(6):e141-5. doi: 10.1016/j.jemermed.2011.05.062. Epub 2011 Sep 8. Review.

PMID:
21903352
29.

Antimicrobial resistance in uncomplicated urinary tract infections in 3 California EDs.

Moffett SE, Frazee BW, Stein JC, Navab B, Maselli J, Takhar SS, Gonzales R.

Am J Emerg Med. 2012 Jul;30(6):942-9. doi: 10.1016/j.ajem.2011.05.008. Epub 2011 Jul 29.

PMID:
21802879
30.

Differential use of diagnostic ultrasound in u.s. Emergency departments by time of day.

Stein JC, Jacoby VL, Vittinghoff E, Wang R, Kwan E, Reynolds T, McAlpine I, Gonzales R.

West J Emerg Med. 2011 Feb;12(1):90-5.

31.

Use of a β-hCG discriminatory zone with bedside pelvic ultrasonography.

Wang R, Reynolds TA, West HH, Ravikumar D, Martinez C, McAlpine I, Jacoby VL, Stein JC.

Ann Emerg Med. 2011 Jul;58(1):12-20. doi: 10.1016/j.annemergmed.2010.12.023. Epub 2011 Feb 18.

PMID:
21310509
32.

Gramene database in 2010: updates and extensions.

Youens-Clark K, Buckler E, Casstevens T, Chen C, Declerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D.

Nucleic Acids Res. 2011 Jan;39(Database issue):D1085-94. doi: 10.1093/nar/gkq1148. Epub 2010 Nov 13.

33.

Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor.

Swanson-Wagner RA, Eichten SR, Kumari S, Tiffin P, Stein JC, Ware D, Springer NM.

Genome Res. 2010 Dec;20(12):1689-99. doi: 10.1101/gr.109165.110. Epub 2010 Oct 29.

34.

Constipation in a 7-year-old boy: congenital band causing a strangulated small bowel and pulseless electrical activity.

Fang AC, Carnell J, Stein JC.

J Emerg Med. 2012 Mar;42(3):283-7. doi: 10.1016/j.jemermed.2010.05.092. Epub 2010 Sep 15.

PMID:
20832966
35.

Emergency physician ultrasonography for evaluating patients at risk for ectopic pregnancy: a meta-analysis.

Stein JC, Wang R, Adler N, Boscardin J, Jacoby VL, Won G, Goldstein R, Kohn MA.

Ann Emerg Med. 2010 Dec;56(6):674-83. doi: 10.1016/j.annemergmed.2010.06.563. Epub 2010 Sep 15.

PMID:
20828874
36.

The B73 maize genome: complexity, diversity, and dynamics.

Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK.

Science. 2009 Nov 20;326(5956):1112-5. doi: 10.1126/science.1178534. Erratum in: Science. 2012 Aug 31;337(6098):1040.

37.

A genome-wide characterization of microRNA genes in maize.

Zhang L, Chia JM, Kumari S, Stein JC, Liu Z, Narechania A, Maher CA, Guill K, McMullen MD, Ware D.

PLoS Genet. 2009 Nov;5(11):e1000716. doi: 10.1371/journal.pgen.1000716. Epub 2009 Nov 20.

38.

Detailed analysis of a contiguous 22-Mb region of the maize genome.

Wei F, Stein JC, Liang C, Zhang J, Fulton RS, Baucom RS, De Paoli E, Zhou S, Yang L, Han Y, Pasternak S, Narechania A, Zhang L, Yeh CT, Ying K, Nagel DH, Collura K, Kudrna D, Currie J, Lin J, Kim H, Angelova A, Scara G, Wissotski M, Golser W, Courtney L, Kruchowski S, Graves TA, Rock SM, Adams S, Fulton LA, Fronick C, Courtney W, Kramer M, Spiegel L, Nascimento L, Kalyanaraman A, Chaparro C, Deragon JM, Miguel PS, Jiang N, Wessler SR, Green PJ, Yu Y, Schwartz DC, Meyers BC, Bennetzen JL, Martienssen RA, McCombie WR, Aluru S, Clifton SW, Schnable PS, Ware D, Wilson RK, Wing RA.

PLoS Genet. 2009 Nov;5(11):e1000728. doi: 10.1371/journal.pgen.1000728. Epub 2009 Nov 20.

39.

Necrotizing vasculitis as a complication of propylthiouracil.

Stein JC, Hernandez S, Hebig A.

West J Emerg Med. 2008 Nov;9(4):212-5.

40.

A survey of bedside ultrasound use by emergency physicians in California.

Stein JC, River G, Kalika I, Hebig A, Price D, Jacoby VL, Filly R.

J Ultrasound Med. 2009 Jun;28(6):757-63.

PMID:
19470816
41.

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes.

Kurtz S, Narechania A, Stein JC, Ware D.

BMC Genomics. 2008 Oct 31;9:517. doi: 10.1186/1471-2164-9-517.

42.

A severe sore throat in a middle-aged man: calcific tendonitis of the longus colli tendon.

Kanzaria H, Stein JC.

J Emerg Med. 2011 Aug;41(2):151-3. doi: 10.1016/j.jemermed.2008.01.016. Epub 2008 Sep 23.

PMID:
18815000
43.

Emergency Department Ultrasound Credentialing: a sample policy and procedure.

Stein JC, Nobay F.

J Emerg Med. 2009 Aug;37(2):153-9. doi: 10.1016/j.jemermed.2007.10.078. Epub 2008 Jun 2.

PMID:
18514473
44.

Engineering vitamin E content: from Arabidopsis mutant to soy oil.

Van Eenennaam AL, Lincoln K, Durrett TP, Valentin HE, Shewmaker CK, Thorne GM, Jiang J, Baszis SR, Levering CK, Aasen ED, Hao M, Stein JC, Norris SR, Last RL.

Plant Cell. 2003 Dec;15(12):3007-19. Epub 2003 Nov 20.

45.
46.
47.
48.

Signaling the arrest of pollen tube development in self-incompatible plants.

Nasrallah JB, Stein JC, Kandasamy MK, Nasrallah ME.

Science. 1994 Dec 2;266(5190):1505-8.

PMID:
17841712
49.

Capillary oxygen transport during severe hypoxia: role of hemoglobin oxygen affinity.

Stein JC, Ellsworth ML.

J Appl Physiol (1985). 1993 Oct;75(4):1601-7.

PMID:
8282609
50.

Relationship between capillary and systemic venous PO2 during nonhypoxic and hypoxic ventilation.

Stein JC, Ellis CG, Ellsworth ML.

Am J Physiol. 1993 Aug;265(2 Pt 2):H537-42.

PMID:
8368357

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