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Items: 1 to 50 of 196

1.

Squeakr: an exact and approximate k-mer counting system.

Pandey P, Bender MA, Johnson R, Patro R, Berger B.

Bioinformatics. 2018 Feb 15;34(4):568-575. doi: 10.1093/bioinformatics/btx636.

PMID:
29444235
2.

deBGR: an efficient and near-exact representation of the weighted de Bruijn graph.

Pandey P, Bender MA, Johnson R, Patro R.

Bioinformatics. 2017 Jul 15;33(14):i133-i141. doi: 10.1093/bioinformatics/btx261.

PMID:
28881995
3.

Sickle Cell Disease.

Bender MA.

In: Adam MP, Ardinger HH, Pagon RA, Wallace SE, Bean LJH, Stephens K, Amemiya A, editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2018.
2003 Sep 15 [updated 2017 Aug 17].

4.

A New Generation of Comfort Care Order Sets: Aligning Protocols with Current Principles.

Bender MA, Hurd C, Solvang N, Colagrossi K, Matsuwaka D, Curtis JR.

J Palliat Med. 2017 Sep;20(9):922-929. doi: 10.1089/jpm.2016.0549. Epub 2017 May 24.

PMID:
28537773
5.

Increasing vertical resolution in US models to improve track forecasts of Hurricane Joaquin with HWRF as an example.

Zhang B, Lindzen RS, Tallapragada V, Weng F, Liu Q, Sippel JA, Ma Z, Bender MA.

Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):11765-11769. Epub 2016 Oct 3.

6.

Characterization of Deletions of the HBA and HBB Loci by Array Comparative Genomic Hybridization.

Sabath DE, Bender MA, Sankaran VG, Vamos E, Kentsis A, Yi HS, Greisman HA.

J Mol Diagn. 2016 Jan;18(1):92-9. doi: 10.1016/j.jmoldx.2015.07.011. Epub 2015 Nov 21.

7.

Copper and zinc accumulation and fractionation in a clayey Hapludox soil subject to long-term pig slurry application.

Formentini TA, Mallmann FJ, Pinheiro A, Fernandes CV, Bender MA, da Veiga M, dos Santos DR, Doelsch E.

Sci Total Environ. 2015 Dec 1;536:831-9. doi: 10.1016/j.scitotenv.2015.07.110. Epub 2015 Aug 6.

PMID:
26256309
8.

DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements.

Wilken MS, Brzezinski JA, La Torre A, Siebenthall K, Thurman R, Sabo P, Sandstrom RS, Vierstra J, Canfield TK, Hansen RS, Bender MA, Stamatoyannopoulos J, Reh TA.

Epigenetics Chromatin. 2015 Feb 28;8:8. doi: 10.1186/1756-8935-8-8. eCollection 2015.

9.

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.

Vierstra J, Rynes E, Sandstrom R, Zhang M, Canfield T, Hansen RS, Stehling-Sun S, Sabo PJ, Byron R, Humbert R, Thurman RE, Johnson AK, Vong S, Lee K, Bates D, Neri F, Diegel M, Giste E, Haugen E, Dunn D, Wilken MS, Josefowicz S, Samstein R, Chang KH, Eichler EE, De Bruijn M, Reh TA, Skoultchi A, Rudensky A, Orkin SH, Papayannopoulou T, Treuting PM, Selleri L, Kaul R, Groudine M, Bender MA, Stamatoyannopoulos JA.

Science. 2014 Nov 21;346(6212):1007-12. doi: 10.1126/science.1246426.

10.

Conservation of trans-acting circuitry during mammalian regulatory evolution.

Stergachis AB, Neph S, Sandstrom R, Haugen E, Reynolds AP, Zhang M, Byron R, Canfield T, Stelhing-Sun S, Lee K, Thurman RE, Vong S, Bates D, Neri F, Diegel M, Giste E, Dunn D, Vierstra J, Hansen RS, Johnson AK, Sabo PJ, Wilken MS, Reh TA, Treuting PM, Kaul R, Groudine M, Bender MA, Borenstein E, Stamatoyannopoulos JA.

Nature. 2014 Nov 20;515(7527):365-70. doi: 10.1038/nature13972.

11.

A comparative encyclopedia of DNA elements in the mouse genome.

Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium.

Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.

12.

Excitatory and inhibitory brain metabolites as targets of motor cortex transcranial direct current stimulation therapy and predictors of its efficacy in fibromyalgia.

Foerster BR, Nascimento TD, DeBoer M, Bender MA, Rice IC, Truong DQ, Bikson M, Clauw DJ, Zubieta JK, Harris RE, DaSilva AF.

Arthritis Rheumatol. 2015 Feb;67(2):576-81.

13.

3D-neuronavigation in vivo through a patient's brain during a spontaneous migraine headache.

DaSilva AF, Nascimento TD, Love T, DosSantos MF, Martikainen IK, Cummiford CM, DeBoer M, Lucas SR, Bender MA, Koeppe RA, Hall T, Petty S, Maslowski E, Smith YR, Zubieta JK.

J Vis Exp. 2014 Jun 2;(88). doi: 10.3791/50682.

14.

Real-time sharing and expression of migraine headache suffering on Twitter: a cross-sectional infodemiology study.

Nascimento TD, DosSantos MF, Danciu T, DeBoer M, van Holsbeeck H, Lucas SR, Aiello C, Khatib L, Bender MA; UMSoD (Under)Graduate Class Of 2014, Zubieta JK, DaSilva AF.

J Med Internet Res. 2014 Apr 3;16(4):e96. doi: 10.2196/jmir.3265.

15.

Missed opportunities in providing palliative care for the urban poor: a case discussion.

Bender MA, Clarke E, Guilbe RM, Selwyn PA.

J Palliat Med. 2013 May;16(5):587-90. doi: 10.1089/jpm.2012.0095. Epub 2012 Dec 16.

PMID:
23240868
16.

Liver and heart MR relaxometry in iron loading: reproducibility of three methods.

Ferguson MR, Otto RK, Bender MA, Kolokythas O, Friedman SD.

J Magn Reson Imaging. 2013 Oct;38(4):987-90. doi: 10.1002/jmri.23937. Epub 2012 Nov 21.

PMID:
23172590
17.

An expansive human regulatory lexicon encoded in transcription factor footprints.

Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender MA, Groudine M, Kaul R, Stamatoyannopoulos JA.

Nature. 2012 Sep 6;489(7414):83-90. doi: 10.1038/nature11212.

18.

The hypersensitive sites of the murine β-globin locus control region act independently to affect nuclear localization and transcriptional elongation.

Bender MA, Ragoczy T, Lee J, Byron R, Telling A, Dean A, Groudine M.

Blood. 2012 Apr 19;119(16):3820-7. doi: 10.1182/blood-2011-09-380485. Epub 2012 Feb 29.

19.

The cost-effectiveness of routine tuberculosis screening with Xpert MTB/RIF prior to initiation of antiretroviral therapy: a model-based analysis.

Andrews JR, Lawn SD, Rusu C, Wood R, Noubary F, Bender MA, Horsburgh CR, Losina E, Freedberg KA, Walensky RP.

AIDS. 2012 May 15;26(8):987-95. doi: 10.1097/QAD.0b013e3283522d47.

20.

A functional element necessary for fetal hemoglobin silencing.

Sankaran VG, Xu J, Byron R, Greisman HA, Fisher C, Weatherall DJ, Sabath DE, Groudine M, Orkin SH, Premawardhena A, Bender MA.

N Engl J Med. 2011 Sep 1;365(9):807-14. doi: 10.1056/NEJMoa1103070.

21.

Cohesin mediates chromatin interactions that regulate mammalian β-globin expression.

Chien R, Zeng W, Kawauchi S, Bender MA, Santos R, Gregson HC, Schmiesing JA, Newkirk DA, Kong X, Ball AR Jr, Calof AL, Lander AD, Groudine MT, Yokomori K.

J Biol Chem. 2011 May 20;286(20):17870-8. doi: 10.1074/jbc.M110.207365. Epub 2011 Mar 29.

22.

A survey of perioperative management of sickle cell disease in North America.

Firth PG, McMillan KN, Haberkern CM, Yaster M, Bender MA, Goodwin SR.

Paediatr Anaesth. 2011 Jan;21(1):43-9. doi: 10.1111/j.1460-9592.2010.03415.x. Epub 2010 Sep 29.

PMID:
20880153
23.

Cost-effectiveness of HIV testing referral strategies among tuberculosis patients in India.

Uhler LM, Kumarasamy N, Mayer KH, Saxena A, Losina E, Muniyandi M, Stoler AW, Lu Z, Walensky RP, Flanigan TP, Bender MA, Freedberg KA, Swaminathan S; CEPAC International investigators.

PLoS One. 2010 Sep 16;5(9). pii: e12747. doi: 10.1371/journal.pone.0012747.

24.

Multiple functions of Ldb1 required for beta-globin activation during erythroid differentiation.

Song SH, Kim A, Ragoczy T, Bender MA, Groudine M, Dean A.

Blood. 2010 Sep 30;116(13):2356-64. doi: 10.1182/blood-2010-03-272252. Epub 2010 Jun 22.

25.

Modeled impact of anthropogenic warming on the frequency of intense Atlantic hurricanes.

Bender MA, Knutson TR, Tuleya RE, Sirutis JJ, Vecchi GA, Garner ST, Held IM.

Science. 2010 Jan 22;327(5964):454-8. doi: 10.1126/science.1180568.

26.

Cost-effectiveness of tenofovir as first-line antiretroviral therapy in India.

Bender MA, Kumarasamy N, Mayer KH, Wang B, Walensky RP, Flanigan T, Schackman BR, Scott CA, Lu Z, Freedberg KA.

Clin Infect Dis. 2010 Feb 1;50(3):416-25. doi: 10.1086/649884.

27.

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J.

Science. 2009 Oct 9;326(5950):289-93. doi: 10.1126/science.1181369.

28.

Histone hyperacetylation within the beta-globin locus is context-dependent and precedes high-level gene expression.

Fromm G, de Vries C, Byron R, Fields J, Fiering S, Groudine M, Bender MA, Palis J, Bulger M.

Blood. 2009 Oct 15;114(16):3479-88. doi: 10.1182/blood-2009-03-210690. Epub 2009 Aug 18.

29.

Developmental and species-divergent globin switching are driven by BCL11A.

Sankaran VG, Xu J, Ragoczy T, Ippolito GC, Walkley CR, Maika SD, Fujiwara Y, Ito M, Groudine M, Bender MA, Tucker PW, Orkin SH.

Nature. 2009 Aug 27;460(7259):1093-7. doi: 10.1038/nature08243. Epub 2009 Aug 5.

30.

H3 K79 dimethylation marks developmental activation of the beta-globin gene but is reduced upon LCR-mediated high-level transcription.

Sawado T, Halow J, Im H, Ragoczy T, Bresnick EH, Bender MA, Groudine M.

Blood. 2008 Jul 15;112(2):406-14. doi: 10.1182/blood-2007-12-128983. Epub 2008 Apr 25.

31.

Clinical impact and cost-effectiveness of antiretroviral therapy in India: starting criteria and second-line therapy.

Freedberg KA, Kumarasamy N, Losina E, Cecelia AJ, Scott CA, Divi N, Flanigan TP, Lu Z, Weinstein MC, Wang B, Ganesh AK, Bender MA, Mayer KH, Walensky RP.

AIDS. 2007 Jul;21 Suppl 4:S117-28.

32.

The locus control region is required for association of the murine beta-globin locus with engaged transcription factories during erythroid maturation.

Ragoczy T, Bender MA, Telling A, Byron R, Groudine M.

Genes Dev. 2006 Jun 1;20(11):1447-57. Epub 2006 May 16.

33.

Flanking HS-62.5 and 3' HS1, and regions upstream of the LCR, are not required for beta-globin transcription.

Bender MA, Byron R, Ragoczy T, Telling A, Bulger M, Groudine M.

Blood. 2006 Aug 15;108(4):1395-401. Epub 2006 Apr 27.

34.
35.

Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1.

Vakoc CR, Letting DL, Gheldof N, Sawado T, Bender MA, Groudine M, Weiss MJ, Dekker J, Blobel GA.

Mol Cell. 2005 Feb 4;17(3):453-62.

36.

Kegels and communication.

Engberg SJ, Bender MA, Stilley CS.

Am J Nurs. 2003 Jul;103(7):93-4. No abstract available.

PMID:
12877134
37.

A complex chromatin landscape revealed by patterns of nuclease sensitivity and histone modification within the mouse beta-globin locus.

Bulger M, Schübeler D, Bender MA, Hamilton J, Farrell CM, Hardison RC, Groudine M.

Mol Cell Biol. 2003 Aug;23(15):5234-44.

38.
39.

Additive impact of childhood emotional, physical, and sexual abuse on suicide attempts among low-income African American women.

Anderson PL, Tiro JA, Price AW, Bender MA, Kaslow NJ.

Suicide Life Threat Behav. 2002 Summer;32(2):131-8.

PMID:
12079029
40.

Targeted deletion of 5'HS1 and 5'HS4 of the beta-globin locus control region reveals additive activity of the DNaseI hypersensitive sites.

Bender MA, Roach JN, Halow J, Close J, Alami R, Bouhassira EE, Groudine M, Fiering SN.

Blood. 2001 Oct 1;98(7):2022-7.

41.

The murine beta-globin locus control region regulates the rate of transcription but not the hyperacetylation of histones at the active genes.

Schübeler D, Groudine M, Bender MA.

Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11432-7. Epub 2001 Sep 11.

42.

Discontinuing prophylaxis against Pneumocystis carinii pneumonia.

Bender MA, Sax PE.

N Engl J Med. 2001 May 24;344(21):1639; author reply 1640-1. No abstract available.

PMID:
11374364
43.

Comparative structural and functional analysis of the olfactory receptor genes flanking the human and mouse beta-globin gene clusters.

Bulger M, Bender MA, van Doorninck JH, Wertman B, Farrell CM, Felsenfeld G, Groudine M, Hardison R.

Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14560-5.

44.
45.

Independent formation of DnaseI hypersensitive sites in the murine beta-globin locus control region.

Bender MA, Mehaffey MG, Telling A, Hug B, Ley TJ, Groudine M, Fiering S.

Blood. 2000 Jun 1;95(11):3600-4.

46.

Deletions within the mouse beta-globin locus control region preferentially reduce beta(min) globin gene expression.

Alami R, Bender MA, Feng YQ, Fiering SN, Hug BA, Ley TJ, Groudine M, Bouhassira EE.

Genomics. 2000 Feb 1;63(3):417-24.

PMID:
10704289
47.

Analysis of mammalian cis-regulatory DNA elements by homologous recombination.

Fiering S, Bender MA, Groudine M.

Methods Enzymol. 1999;306:42-66. Review.

PMID:
10432447
48.

Conservation of sequence and structure flanking the mouse and human beta-globin loci: the beta-globin genes are embedded within an array of odorant receptor genes.

Bulger M, van Doorninck JH, Saitoh N, Telling A, Farrell C, Bender MA, Felsenfeld G, Axel R, Groudine M.

Proc Natl Acad Sci U S A. 1999 Apr 27;96(9):5129-34. Erratum in: Proc Natl Acad Sci U S A 1999 Jul 6;96(14):8307. von Doorninck JH [corrected to van Doorninck JH].

49.

Antihyperalgesic effects of infection with a preproenkephalin-encoding herpes virus.

Wilson SP, Yeomans DC, Bender MA, Lu Y, Goins WF, Glorioso JC.

Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):3211-6.

50.

Description and targeted deletion of 5' hypersensitive site 5 and 6 of the mouse beta-globin locus control region.

Bender MA, Reik A, Close J, Telling A, Epner E, Fiering S, Hardison R, Groudine M.

Blood. 1998 Dec 1;92(11):4394-403.

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