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Items: 45

1.

Author Correction: Best practices for benchmarking germline small-variant calls in human genomes.

Krusche P, Trigg L, Boutros PC, Mason CE, De La Vega FM, Moore BL, Gonzalez-Porta M, Eberle MA, Tezak Z, Lababidi S, Truty R, Asimenos G, Funke B, Fleharty M, Chapman BA, Salit M, Zook JM; Global Alliance for Genomics and Health Benchmarking Team.

Nat Biotechnol. 2019 May;37(5):567. doi: 10.1038/s41587-019-0108-0.

PMID:
30899106
2.

Best practices for benchmarking germline small-variant calls in human genomes.

Krusche P, Trigg L, Boutros PC, Mason CE, De La Vega FM, Moore BL, Gonzalez-Porta M, Eberle MA, Tezak Z, Lababidi S, Truty R, Asimenos G, Funke B, Fleharty M, Chapman BA, Salit M, Zook JM; Global Alliance for Genomics and Health Benchmarking Team.

Nat Biotechnol. 2019 May;37(5):555-560. doi: 10.1038/s41587-019-0054-x. Epub 2019 Mar 11. Erratum in: Nat Biotechnol. 2019 Mar 21;:.

PMID:
30858580
3.

Identification, characterization, and targeting of IL-4 receptor by IL-4-Pseudomonas exotoxin in mouse models of anaplastic thyroid cancer.

Joshi BH, Suzuki A, Fujisawa T, Leland P, Varrichio F, Lababidi S, Lloyd R, Kasperbauer J, Puri RK.

Discov Med. 2015 Nov;20(111):273-84.

4.

Overall conceptual framework for studying the genetics of autoimmune diseases following vaccination: a regulatory perspective.

Lababidi S, Sutherland A, Krasnicka B, Forshee RA, Anderson SA.

Biomark Med. 2015;9(11):1107-20. doi: 10.2217/bmm.15.67. Epub 2015 Nov 3.

PMID:
26526761
5.

Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.

Zhang W, Yu Y, Hertwig F, Thierry-Mieg J, Zhang W, Thierry-Mieg D, Wang J, Furlanello C, Devanarayan V, Cheng J, Deng Y, Hero B, Hong H, Jia M, Li L, Lin SM, Nikolsky Y, Oberthuer A, Qing T, Su Z, Volland R, Wang C, Wang MD, Ai J, Albanese D, Asgharzadeh S, Avigad S, Bao W, Bessarabova M, Brilliant MH, Brors B, Chierici M, Chu TM, Zhang J, Grundy RG, He MM, Hebbring S, Kaufman HL, Lababidi S, Lancashire LJ, Li Y, Lu XX, Luo H, Ma X, Ning B, Noguera R, Peifer M, Phan JH, Roels F, Rosswog C, Shao S, Shen J, Theissen J, Tonini GP, Vandesompele J, Wu PY, Xiao W, Xu J, Xu W, Xuan J, Yang Y, Ye Z, Dong Z, Zhang KK, Yin Y, Zhao C, Zheng Y, Wolfinger RD, Shi T, Malkas LH, Berthold F, Wang J, Tong W, Shi L, Peng Z, Fischer M.

Genome Biol. 2015 Jun 25;16:133. doi: 10.1186/s13059-015-0694-1.

6.

In silico analysis of autoimmune diseases and genetic relationships to vaccination against infectious diseases.

McGarvey PB, Suzek BE, Baraniuk JN, Rao S, Conkright B, Lababidi S, Sutherland A, Forshee R, Madhavan S.

BMC Immunol. 2014 Dec 9;15:61. doi: 10.1186/s12865-014-0061-0.

7.

Interleukin-4 receptor alpha overexpression in human bladder cancer correlates with the pathological grade and stage of the disease.

Joshi BH, Leland P, Lababidi S, Varrichio F, Puri RK.

Cancer Med. 2014 Dec;3(6):1615-28. doi: 10.1002/cam4.330. Epub 2014 Sep 10.

9.

Gene markers of cellular aging in human multipotent stromal cells in culture.

Bellayr IH, Catalano JG, Lababidi S, Yang AX, Lo Surdo JL, Bauer SR, Puri RK.

Stem Cell Res Ther. 2014 Apr 28;5(2):59. doi: 10.1186/scrt448.

10.

Early hyperglycemia is associated with poor gross motor outcome in asphyxiated term newborns.

Spies EE, Lababidi SL, McBride MC.

Pediatr Neurol. 2014 Jun;50(6):586-90. doi: 10.1016/j.pediatrneurol.2014.01.043. Epub 2014 Jan 31.

PMID:
24731484
11.

Mutation in osteoactivin decreases bone formation in vivo and osteoblast differentiation in vitro.

Abdelmagid SM, Belcher JY, Moussa FM, Lababidi SL, Sondag GR, Novak KM, Sanyurah AS, Frara NA, Razmpour R, Del Carpio-Cano FE, Safadi FF.

Am J Pathol. 2014 Mar;184(3):697-713. doi: 10.1016/j.ajpath.2013.11.031. Epub 2014 Jan 23.

12.

Osteoactivin induces transdifferentiation of C2C12 myoblasts into osteoblasts.

Sondag GR, Salihoglu S, Lababidi SL, Crowder DC, Moussa FM, Abdelmagid SM, Safadi FF.

J Cell Physiol. 2014 Jul;229(7):955-66. doi: 10.1002/jcp.24512.

PMID:
24265122
13.
14.

Impact of different ionization methods on the molecular assignments of asphaltenes by FT-ICR mass spectrometry.

Gaspar A, Zellermann E, Lababidi S, Reece J, Schrader W.

Anal Chem. 2012 Jun 19;84(12):5257-67. doi: 10.1021/ac300133p. Epub 2012 Jun 6.

PMID:
22607608
15.

Molecular characterization of Ethiopian indigenous goat populations.

Hassen H, Lababidi S, Rischkowsky B, Baum M, Tibbo M.

Trop Anim Health Prod. 2012 Aug;44(6):1239-46. doi: 10.1007/s11250-011-0064-2. Epub 2012 Jan 12.

PMID:
22237413
16.

Measurement of bacterial volume by transmission-through-dye imaging.

Lababidi SL, Pelts M, Moitra M, Leff LG, Model MA.

J Microbiol Methods. 2011 Dec;87(3):375-7. doi: 10.1016/j.mimet.2011.08.019. Epub 2011 Sep 25.

PMID:
21982927
17.

First Report of Chickpea chlorotic stunt virus Infecting Legume Crops in Tunisia.

Najar A, Kumari S, Attar N, Lababidi S.

Plant Dis. 2011 Oct;95(10):1321. doi: 10.1094/PDIS-10-10-0708.

PMID:
30731675
18.

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.

Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD Jr, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas AB, Berthold F, Brennan RJ, Buness A, Catalano JG, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe JC, Gatto L, Ge W, Goldstein DR, Guo L, Halbert DN, Han J, Harris SC, Hatzis C, Herman D, Huang J, Jensen RV, Jiang R, Johnson CD, Jurman G, Kahlert Y, Khuder SA, Kohl M, Li J, Li L, Li M, Li QZ, Li S, Li Z, Liu J, Liu Y, Liu Z, Meng L, Madera M, Martinez-Murillo F, Medina I, Meehan J, Miclaus K, Moffitt RA, Montaner D, Mukherjee P, Mulligan GJ, Neville P, Nikolskaya T, Ning B, Page GP, Parker J, Parry RM, Peng X, Peterson RL, Phan JH, Quanz B, Ren Y, Riccadonna S, Roter AH, Samuelson FW, Schumacher MM, Shambaugh JD, Shi Q, Shippy R, Si S, Smalter A, Sotiriou C, Soukup M, Staedtler F, Steiner G, Stokes TH, Sun Q, Tan PY, Tang R, Tezak Z, Thorn B, Tsyganova M, Turpaz Y, Vega SC, Visintainer R, von Frese J, Wang C, Wang E, Wang J, Wang W, Westermann F, Willey JC, Woods M, Wu S, Xiao N, Xu J, Xu L, Yang L, Zeng X, Zhang J, Zhang L, Zhang M, Zhao C, Puri RK, Scherf U, Tong W, Wolfinger RD; MAQC Consortium.

Nat Biotechnol. 2010 Aug;28(8):827-38. doi: 10.1038/nbt.1665. Epub 2010 Jul 30.

19.

Targeting angiogenesis via a c-Myc/hypoxia-inducible factor-1alpha-dependent pathway in multiple myeloma.

Zhang J, Sattler M, Tonon G, Grabher C, Lababidi S, Zimmerhackl A, Raab MS, Vallet S, Zhou Y, Cartron MA, Hideshima T, Tai YT, Chauhan D, Anderson KC, Podar K.

Cancer Res. 2009 Jun 15;69(12):5082-90. doi: 10.1158/0008-5472.CAN-08-4603. Epub 2009 Jun 9.

21.

Challenges in DNA microarray studies from the regulatory perspective.

Lababidi S.

J Biopharm Stat. 2008;18(1):183-202.

PMID:
18161548
22.

Detailed DNA methylation profiles of the E-cadherin promoter in the NCI-60 cancer cells.

Reinhold WC, Reimers MA, Maunakea AK, Kim S, Lababidi S, Scherf U, Shankavaram UT, Ziegler MS, Stewart C, Kouros-Mehr H, Cui H, Dolginow D, Scudiero DA, Pommier YG, Munroe DJ, Feinberg AP, Weinstein JN.

Mol Cancer Ther. 2007 Feb;6(2):391-403. Epub 2007 Feb 1.

23.

Women participating in a dietary intervention trial maintain dietary changes without much effect on household members.

Radakovich K, Heilbrun LK, Venkatranamamoorthy R, Lababidi S, Klurfeld DM, Djuric Z.

Nutr Cancer. 2006;55(1):44-52.

PMID:
16965240
24.

Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel.

Bussey KJ, Chin K, Lababidi S, Reimers M, Reinhold WC, Kuo WL, Gwadry F, Ajay, Kouros-Mehr H, Fridlyand J, Jain A, Collins C, Nishizuka S, Tonon G, Roschke A, Gehlhaus K, Kirsch I, Scudiero DA, Gray JW, Weinstein JN.

Mol Cancer Ther. 2006 Apr;5(4):853-67.

25.

Karyotypic "state" as a potential determinant for anticancer drug discovery.

Roschke AV, Lababidi S, Tonon G, Gehlhaus KS, Bussey K, Weinstein JN, Kirsch IR.

Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2964-9. Epub 2005 Feb 9.

26.

Predicting drug sensitivity and resistance: profiling ABC transporter genes in cancer cells.

Szakács G, Annereau JP, Lababidi S, Shankavaram U, Arciello A, Bussey KJ, Reinhold W, Guo Y, Kruh GD, Reimers M, Weinstein JN, Gottesman MM.

Cancer Cell. 2004 Aug;6(2):129-37.

27.
28.

Development of gene ontology tool for biological interpretation of genomic and proteomic data.

Feng W, Wang G, Zeeberg BR, Guo K, Fojo AT, Kane DW, Reinhold WC, Lababidi S, Weinstein JN, Wang MD.

AMIA Annu Symp Proc. 2003:839.

29.

Karyotypic complexity of the NCI-60 drug-screening panel.

Roschke AV, Tonon G, Gehlhaus KS, McTyre N, Bussey KJ, Lababidi S, Scudiero DA, Weinstein JN, Kirsch IR.

Cancer Res. 2003 Dec 15;63(24):8634-47.

30.

Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells.

Lee JK, Bussey KJ, Gwadry FG, Reinhold W, Riddick G, Pelletier SL, Nishizuka S, Szakacs G, Annereau JP, Shankavaram U, Lababidi S, Smith LH, Gottesman MM, Weinstein JN.

Genome Biol. 2003;4(12):R82. Epub 2003 Nov 25.

31.

Diagnostic markers that distinguish colon and ovarian adenocarcinomas: identification by genomic, proteomic, and tissue array profiling.

Nishizuka S, Chen ST, Gwadry FG, Alexander J, Major SM, Scherf U, Reinhold WC, Waltham M, Charboneau L, Young L, Bussey KJ, Kim S, Lababidi S, Lee JK, Pittaluga S, Scudiero DA, Sausville EA, Munson PJ, Petricoin EF 3rd, Liotta LA, Hewitt SM, Raffeld M, Weinstein JN.

Cancer Res. 2003 Sep 1;63(17):5243-50.

32.

Cytochrome p450 and glutathione transferase expression in human breast cancer.

El-Rayes BF, Ali S, Heilbrun LK, Lababidi S, Bouwman D, Visscher D, Philip PA.

Clin Cancer Res. 2003 May;9(5):1705-9.

33.

GoMiner: a resource for biological interpretation of genomic and proteomic data.

Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, Narasimhan S, Kane DW, Reinhold WC, Lababidi S, Bussey KJ, Riss J, Barrett JC, Weinstein JN.

Genome Biol. 2003;4(4):R28. Epub 2003 Mar 25.

34.

Plasma carotenoids, tocopherols, and antioxidant capacity in a 12-week intervention study to reduce fat and/or energy intakes.

Djuric Z, Uhley VE, Naegeli L, Lababidi S, Macha S, Heilbrun LK.

Nutrition. 2003 Mar;19(3):244-9.

PMID:
12620527
35.

Apoptotic susceptibility of cancer cells selected for camptothecin resistance: gene expression profiling, functional analysis, and molecular interaction mapping.

Reinhold WC, Kouros-Mehr H, Kohn KW, Maunakea AK, Lababidi S, Roschke A, Stover K, Alexander J, Pantazis P, Miller L, Liu E, Kirsch IR, Urasaki Y, Pommier Y, Weinstein JN.

Cancer Res. 2003 Mar 1;63(5):1000-11.

36.

Methods to increase fruit and vegetable intake with and without a decrease in fat intake: compliance and effects on body weight in the nutrition and breast health study.

Djuric Z, Poore KM, Depper JB, Uhley VE, Lababidi S, Covington C, Klurfeld DM, Simon MS, Kucuk O, Heilbrun LK.

Nutr Cancer. 2002;43(2):141-51.

PMID:
12588694
37.

Effect of participant motivation on rapid dietary changes in an intervention trial.

Poore KM, Depper JB, Heilbrun LK, Lababidi S, Covington C, Djuric Z.

J Hum Nutr Diet. 2002 Jun;15(3):211-4.

PMID:
12028517
38.

Comparison of dietary assessment methods in a low-fat dietary intervention program.

Simon MS, Lababidi S, Djuric Z, Uhley V, Depper J, Kresge C, Klurfeld DM, Heilbrun LK.

Nutr Cancer. 2001;40(2):108-17.

PMID:
11962245
39.

Effect of low-fat and/or low-energy diets on anthropometric measures in participants of the women's diet study.

Djuric Z, Lababidi S, Heilbrun LK, Depper JB, Poore KM, Uhley VE.

J Am Coll Nutr. 2002 Feb;21(1):38-46.

PMID:
11838886
40.

An Evaluation of Plasma Antioxidant Levels and the Risk of Breast Cancer: A Pilot Case Control Study.

Simon MS, Djuric Z, Dunn B, Stephens D, Lababidi S, Heilbrun LK.

Breast J. 2000 Nov;6(6):388-395.

PMID:
11348397
41.

Levels of 5-hydroxymethyl-2'-deoxyuridine in DNA from blood of women scheduled for breast biopsy.

Djuric Z, Heilbrun LK, Lababidi S, Berzinkas E, Simon MS, Kosir MA.

Cancer Epidemiol Biomarkers Prev. 2001 Feb;10(2):147-9.

42.

Recruitment for a pilot case control study of oxidative DNA damage and breast cancer risk.

Simon MS, Heilbrun LK, Stephens D, Lababidi S, Djuric Z.

Am J Clin Oncol. 2000 Jun;23(3):283-7.

PMID:
10857894
43.

A clinical trial to selectively change dietary fat and/or energy intake in women: the Women's Diet Study.

Djuric Z, Uhley VE, Depper JB, Brooks KM, Lababidi S, Heilbrun LK.

Nutr Cancer. 1999;34(1):27-35.

PMID:
10453438
44.

Oxidative DNA damage levels in blood from women at high risk for breast cancer are associated with dietary intakes of meats, vegetables, and fruits.

Djuric Z, Depper JB, Uhley V, Smith D, Lababidi S, Martino S, Heilbrun LK.

J Am Diet Assoc. 1998 May;98(5):524-8.

PMID:
9597024
45.

Growth inhibition of MCF-7 and MCF-10A human breast cells by alpha-tocopheryl hemisuccinate, cholesteryl hemisuccinate and their ether analogs.

Djuric Z, Heilbrun LK, Lababidi S, Everett-Bauer CK, Fariss MW.

Cancer Lett. 1997 Jan 1;111(1-2):133-9.

PMID:
9022138

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