Biomedical Informatics Publications

Publications by CoreStaff

(Core Staff in Bold Italics)

1. Ishida-Yamamoto, A.,McGrath, J. A., Lam, H., Lizuka, H., Friedman, R. A.,and Christiano, A. M. The molecular basis of autosomal dominanterythrokeratoderma: A frameshift mutation in the loricrin gene. Am.J. Human. Genetics. 61: 381-389, 1997. PMID: 9326323; PMCID: PMC1715943.

2. Su, Z.-Z., Shi, Y.,Friedman, R., Qiao, L., McKinstry, R., Hinman, D.,Dent, P., Fisher, B., PEA3 sites within the progression elevatedgene-3 (PEG-3) promoter and mitogen activated protein kinasecontribute to differential PEG-3 expression in Ha-ras and v-rafoncogene transformed rat embryo cells. Nucl. Acids Res., 29,1661-1671, 2001. PMID: 11292838; PMCID:PMC31320.

3. Li, C.-M., M. Guo, A.Borzuck, C. Powell, M. Wei, H. Thaker, R. Friedman, U.Klein, and B. Tycko, Gene expression in Wilms tumors mimics theearliest committed stages in the metanephric mesenchymal-epithelialtransition. American Journal of Pathology, 2002. 160: p. 2181-2190.PMID: 12057921; PMCID: PMC1850829.

4. Chen, M.-W., A. de laTaille, R. Shen, F. Vacherot, S. Gil Diez de Medina, R.A.Friedman , J. Kitjajewski, M. Burchardt, D.K. Chopin,and R. Buttyan, The emergence of protocadherin-PC expression during the acquisition of apoptosis-resistance by prostate cancer cells.Oncogene, 2002. 21: p. 7861-7871. PMID: 12420223.[uid]

5. Borczuk,A C., Shah,L., Pearson, G. D.N., Walter, K., L. Wang, L., Austin, J. H.M.Friedman, R. A. and Powell, C. A. (2004). Molecular Signatures in Biopsy Specimensof Lung Cancer. American Journal of Respiratory and Critical CareMedicine, 170: 167-174. PMID: 15087295.

6. Borczuk AC, Kim HK,Yegen HA, Friedman RA , Powell CA. Lung AdenocarcinomaGlobal Profiling Identifies Type II TGF-Receptor as a Repressorof Invasiveness. Am J Respir Crit Care Med 2005;172:729-737.PMID: 15976377. 15976377

7. Einbond, L. S., Su,T., Wu, H. A., Friedman, R. , Wang, X., Ramirez, A., Kronenberg, F.,Weinstein, I.B. 2007. The growth inhibitory effect of actein on human breast cancercells is associated with activation of stress response pathways. Int J Cancer 121:2073-2083. PMID: 17465192

8. Einbond, L.S., Su,T., Wu, H.A, Friedman, R.A. , Wang, X., Jiang, B.,Hagan, T., Kennelly, X., Kronenberg, F., Weinstein, I.B. 2007. Geneexpression analysis of the mechanisms whereby black cohosh inhibitshuman breast cancer cell growth. Anticancer Res.27:697-712. PMID: 17465192

9. Wu, H.D., Maurer,M.S., Friedman, R.A. , Marboe, C.C., Ruiz-Vazquez,E.M., Ramakrishnan, R., Schwartz, A., Tilson, M.D., Stewart, A.S.,Winchester, R.W. 2007. The lymphocyticinfiltration in calcific aortic stenosis predominantly consists of clonally expanded Tcells. J. Immunol. 178:5329-5339. PMID: 17404318

10. Borczuk, A. C., N.Papanikolaou, R. L. Toonkel, M. Sole, L. A. Gorenstein, M. E. Ginsburg, J. R. Sonett, R. A. Friedman, and C. A. Powell. 2008. Lung adenocarcinoma invasionin TGFbetaRII-deficient cells is mediated by CCL5/RANTES. Oncogene27:557-564. PMID: 17653092

11. Compagno M, Lim WK,Grunn A, Nandula SV, Brahmachary M, Shen Q, Bertoni F, Ponzoni M,Scandurra M, Califano A, Bhagat G, Chadburn A, Dalla-Favera R,Pasqualucci L. Mutations of multiple genes cause deregulation ofNF-kappaB in diffuse large B-cell lymphoma. Nature 2009;459:717-21.PMID: 19412164

12. Zhao X, D DA, LimWK, Brahmachary M, Carro MS, Ludwig T, Cardo CC, Guillemot F,Aldape K, Califano A, Iavarone A, Lasorella A.
The N-Myc-DLL3 cascadeis suppressed by the ubiquitin ligase Huwe1 to inhibitproliferation and promote neurogenesis in the developing brain. DevCell 2009;17:210-21. PMID: 19686682; PMCID:PMC2769073

13. Basso K, Sumazin P,Morozov P, Schneider C, Maute RL, Kitagawa Y, Mandelbaum J, Haddad J,Jr., Chen CZ, Califano A, Dalla-Favera R. Identification of thehuman mature B cell miRNome. Immunity 2009;30:744-52. PMID: 19446474; PubMedCentral PMCID: PMC2764486.

14. Mandelbaum J, BhagatG, Tang H, Mo T, Brahmachary M, Shen Q, Chadburn A, Rajewsky K,Tarakhovsky A, Pasqualucci L, Dalla-Favera R. BLIMP1 is a tumorsuppressor gene frequently disrupted in activated B cell-like diffuse largeB cell lymphoma. Cancer Cell 2010;18:568-79. PMID: 21156281 PMCID:PMC3030476

15. Bu, D. X., V. Rai,X. Shen, R. Rosario, Y. Lu, V. D'Agati, S. F. Yan,R. A. Friedman,E. Nuglozeh, Schmidt, A. M. 2010. Activation of the ROCK1 branch of the transforming growth factor- pathway contributes to RAGE-dependent acceleration of atherosclerosis in diabetic ApoE-null mice. Circ Res 106:1040-1051.PMID: 20133903; PMCID: PMC2848909

16. Reiniger, N., Lau,K., McCalla, D.,Eby, B., Cheng, B., Lu, Y. Qu, W., Quadri, N..Ananthakrishnan, R.,Furmansky, M., Rosario, R., Song, F., Rai,V.,Weinberg, A. Friedman, R., Ramasamy,R., D'Agati, V.,and Schmidt, A.M. 2010. Deletion of the Receptor for AdvancedGlycation Endproducts Reduces Glomerulosclerosis and Preserves RenalFunction in the Diabetic OVE26 Mouse. Diabetes 59:2043-54. PMID: 20627935; PMCID:PMC2911065

17. Basso K, Mussolin L,Lettieri A, Brahmachary M, Lim WK, Califano A, Basso G, Biondi A, Cazzaniga G,Rosolen A. T-cell lymphoblastic lymphoma shows differences and similarities with T-cell acute lymphoblastic leukemia by genomic and gene expression analyses. Genes Chromosomes Cancer 2011;50:1063-75. PMID: 21987448

18. Vlad G, King J,Chang CC, Liu Z, Friedman RA, Torkamani AA, Suciu-FocaN. Gene profile analysis of CD8(+) ILT3-Fc induced T suppressorcells. 2011 Hum Immunol 72, 107-114.PMID: 20974207

19. Borczuk, A.C., SoleM., Lu, P., Chen, J., Wilgus, M.L., Friedman, R.A.,Albelda, S.M., Powell, C.A. 2011. Progression of humanbronchioloalveolar carcinoma to invasive adenocarcinoma is modeled ina transgenic mouse model of K-ras-induced lung cancer by loss of theTGFb type II receptor. Cancer Res 71:6665-75. PMID: 21911454

20. Quante, M., Tu,S.P., Tomita, H., Gonda, T., Wang, S.S., Takashi, S., Baik, G.H.,Shibata, W., Diprete, B., Betz, K.S., Friedman, R.,Varro, A., Tycko, B., Wang, T.C. 2011. Bone marrow-derivedmyofibroblasts contribute to the mesenchymal stem cell niche andpromote tumor growth. Cancer Cell.19:257-72. PMID: 21316604

21. Yang, X.D., Ai, W.,Asfaha S., Bhagat, G. , Friedman, R.A., Jin, G., Park,H., Shykind, B., Diacovo, T.G., Falus, A., Wang, al. 2011.Histamine deficiency promotes inflammation-associated carcinogenesisthrough reduced myeloid maturation and accumulation ofCD11b(+)Ly6G(+) immature myeloid cells. Nat Med 17:87-95 PMID:21170045; PMCID: PMC3075560.

22. Fisher JC, GanderJW, Haley MJ, Hernandez SL, Huang J, Chang YJ, Johung TB, Guarnieri P,O'Toole K, Yamashiro DJ, Kandel JJ. Inhibition of cyclo-oxygenase 2reduces tumor metastasis and inflammatory signaling during blockadeof vascular endothelial growth factor. Vasc Cell 2011;3:22. PMID: 21978392; PMCID:PMC3198683.

23. Lei L, Sonabend AM,Guarnieri P, Soderquist C, Ludwig T, Rosenfeld S, Bruce JN, Canoll P. Glioblastomamodels reveal the connection between adult glial progenitors and theproneural phenotype. PLoS One 2011;6:e20041. PMID: 21625383; PMCID:PMC3100315.

24. Sumazin P, Yang X,Chiu HS, Chung WJ, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M,Guarnieri P, Silva J, Califano A. An extensivemicroRNA-mediated network of RNA-RNA interactions regulatesestablished oncogenic pathways in glioblastoma. Cell 2011;147:370-81. PMID: 22000015; PMCID:PMC3214599.

25. Kitagawa Y,Brahmachary M, Tiacci E, Dalla-Favera R, Falini B,Basso K. A microRNA signaturespecific for hairy cell leukemia and associated with modulation of the MAPK-JNK pathways. Leukemia 2012;26:2564-7. PMID: 22660186

26. Zeng, S., Zhang,Q.Y., Huang, J., Vedantham, S., Rosario, R., Ananthakrishnan, R.,Yan, S.F., Ramasamy R, Dematteo, R.P., Emond, J.C, Friedman,R.A, Schmidt, A.M. 2012. Opposing roles of RAGE and Myd88signaling in extensive liver resection. FASEB J. 26,882-893 PMID:22075646 PMCID: PMC3365861

27. Quante M, Bhagat G,Abrams JA, Marache F, Good P, Lee MD, Lee Y, Friedman R,Asfaha S, Dubeykovskaya Z, Mahmood U, Figueiredo JL, Kitajewski J,Shawbe C, Lightdale CJ, Rustgi AK, Wang TC. Bile acid andinflammation activate gastric cardia stem cells in a mouse model ofBarrett-like metaplasia. 2012 Cancer Cell 21, 36-51 PMID:22264787.PMCID: PMC3266546

28.Dapito DH, Mencin A,Gwak GY, Pradere JP, Jang MK, Mederacke I, Caviglia JM, Khiabanian H, Adeyemi A,Bataller R, Lefkowitch JH, Bower M, Friedman R , SartorRB, Rabadan R, Schwabe RF.Promotion of Hepatocellular Carcinoma bythe Intestinal Microbiota and TLR4. Cancer Cell 2012; 21:504-16.PMID: 22516259. PMCID: PMC3332000.

29. Troeger, J. S.,Mederacke, I.,Gwak, G. Y., Dapito, D. H., Mu, X., Hsu, C. C., Pradere, J. P.,Friedman, R. A. ,Schwabe, R. F., Deactivation ofhepatic stellate cells during liver fibrosis resolution in mice. Gastroenterology, 2012. 143(4): p. 1073-83. PMID: 22750464

30. Berkovits BD, WangL, Guarnieri P, Wolgemuth DJ. The testis-specific double bromodomain-containing protein BRDT forms a complex with multiple spliceosome components and is required for mRNA splicing and 3'-UTR truncation in round spermatids. Nucleic Acids Res 2012;40:7162-75. PMID: 22570411 PMCID:PMC3424537

31. Doege CA, Inoue K,Yamashita T, Rhee DB, Travis S, Fujita R, Guarnieri P,Bhagat G, Vanti WB, Shih A, Levine RL, Nik S, Chen EI, Abeliovich A.Early-stage epigenetic modification during somatic cell reprogrammingby Parp1 and Tet2. Nature 2012;488:652-5. PMID: 22902501.

32. Stoecklin-Wasmer C,Guarnieri P, Celenti R, Demmer RT, Kebschull M,Papapanou PN. MicroRNAs and theirtarget genes in gingival tissues. J Dent Res 2012;91:934-40. PMID: 22879578; PMCID:PMC3446831.

33. Phatnani HP,Guarnieri P, Friedman BA, Carrasco MA, Muratet M,O'Keeffe S, Nwakeze C, Pauli-Behn F, Newberry KM, Meadows SK, Tapia JC, Myers RM, Maniatis T. Intricateinterplay between astrocytes and motor neurons in ALS. Proc Natl AcadSci U S A 2013;110:E756-65. PMID: 23388633 PMCID:PMC3581928

34. Totary-Jain H,Sanoudou D, Ben-Dov IZ, Dautriche CN, Guarnieri P, MarxSO, Tuschl T, Marks AR.Reprogramming of the microRNA transcriptome mediates resistance torapamycin. J Biol Chem 2013. PMID: 23300087; PMCID:PMC3585042.

35. Asfaha, S.,Dubeykovskiy, A. N., Tomita, H., Yang, X., Stokes, S.,Shibata, W., Friedman, R.A.,Ariyama, H., Dubeykovskaya, Z. A., Muthupalani, S.,Ericksen, R.,Frucht, H.,Fox, J.G., Wang, T.C. Mice that express human interleukin-8 have increased mobilization of immature myeloid cells, which exacerbates inflammation and accelerates colon carcinogenesis. Gastroenterology, 2013. 144:155-66,PMID: 23041326

36. Pradere J.P,. KluweJ,, De Minicis S. , Jiao J.J., Gwak G.Y., Dapito D.H., Jang M.K.,Guenther N. D,, Mederacke I, Friedman R. , DragomirA.C., Aloman C., Schwabe R.F,.Hepatic macrophages but not dendriticcells contribute to liver fibrosis by promoting the survival of activated hepatic stellate cells. Hepatology 2013. Mar 28.[Epub aheadof print] PubMed PMID: 23553591.

37. Vasileva A, HopkinsKM, Wang X, Weissbach MM, Friedman RA , Wolgemuth DJ,Lieberman HB. The DNA damage checkpoint protein RAD9A is essentialfor male meiosis in the mouse. J Cell Sci. 2013 Jun 20. [Epub aheadof print] PubMed PMID: 23788429.

38. Ericksen R.E., RoseS., Westphalen C.B., Shibata W., Muthupalani S., Tailor Y., FriedmanR.A. , Han W,, Fox J.G,, Ferrante A.W. Jr, Wang T.C. Obesityaccelerates Helicobacter felis-induced gastric carcinogenesis byenhancing immature myeloid cell trafficking and TH17 response. Gut.2013 May 31. [Epub ahead of print] PubMed PMID: 23729675

39 . Guangchun J,Westphalen CB, Worthley DL, Asfaha S, Yang X, Chen X, Friedman RA, Wang TC. Progastrin stimulates colonic proliferation andcrypt fission through CCK2R-dependent suppression of Bmp2. [Epubahead of print] Gasteroenterology 2013.[Epub ahead of print] PubMed PMID: 23891976.

40. Kebschull M, Guarnieri P, Demmer RT, Boulesteix AL, Pavlidis P, Papapanou PN. Molecular Differences between Chronic and Aggressive Periodontitis. J Dent Res. 2013 Oct 11. [Epub ahead of print] PubMed PMID: 24122488.

41. Irshad S, Bansal M, Castillo-Martin M, Zheng T, Aytes A, Wenske S, Le Magnen C, Guarnieri P, Sumazin P, Benson MC, Shen MM, Califano A, Abate-Shen C. A molecular signature predictive of indolent prostate cancer. Sci Transl Med. 2013 Sep 11;5(202):202ra122. PubMed PMID: 24027026.

42. Sonabend AM, Bansal M, Guarnieri P, Lei L, Amendolara B, Soderquist C, Leung R, Yun J, Kennedy B, Sisti J, Bruce S, Bruce R, Shakya R, Ludwig T, Rosenfeld S, Sims PA, Bruce JN, Califano A, Canoll P. The Transcriptional Regulatory Network of Proneural Glioma Determines the Genetic Alterations Selected During Tumor Progression. Cancer Res. 2014 Jan 3. [Epub ahead of print] PubMed PMID: 24390738.

43. Kode A, Manavalan JS, Mosialou I, Bhagat G, Rathinam CV, Luo N, Khiabanian H, Lee A, Murty VV, Friedman R, Brum A, Park D, Galili N, Mukherjee S, Teruya-Feldstein J, Raza A, Rabadan R, Berman E, Kousteni S. Leukaemogenesis induced by an activating β-catenin mutation in osteoblasts. Nature. 2014 Jan 15. doi: 10.1038/nature12883. [Epub ahead of print] PubMed PMID: 24429522.

44. Song F, Hurtado Del Pozo C, Rosario R, Zou YS, Ananthakrishnan R, Xu X, Patel PR, Benoit VM, Yan SF, Li H, Friedman RA, Kim JK, Ramasamy R, Ferrante AW Jr, Schmidt AM. RAGE Regulates the Metabolic and Inflammatory Response to High Fat Feeding in Mice. Diabetes. 2014 Feb 11. [Epub ahead of print] PubMed PMID: 24520121.

45. Huebener P, Gwak GY, Pradere JP, Quinzii CM, Friedman R, Lin CS, Trent CM, Mederacke I, Zhao E, Dapito DH, Lin Y, Goldberg IJ, Czaja MJ, Schwabe RF. High-mobility group box 1 is dispensable for autophagy, mitochondrial quality control, and organ function in vivo. Cell Metab. 2014 Mar 4;19(3):539-47. PubMed PMID: 24606906.

46. Zhao CM, Hayakawa Y, Kodama Y, Muthupalani S, Westphalen CB, Andersen GT, Flatberg A, Johannessen H, Friedman RA, Renz BW, Sandvik AK, Beisvag V, Tomita H, Hara A, Quante M, Li Z, Gershon MD, Kaneko K, Fox JG, Wang TC, Chen D. Denervation suppresses gastric tumorigenesis. Sci Transl Med. 2014 Aug 20;6(250) PubMed PMID: 25143365.

47. Kebschull M, Demmer RT, Grün B, , Pavlidis P, Papapanou PN. Gingival tissue transcriptomes identify distinct periodontitis phenotypes. J Dent Res. 2014 May;93(5):459-68. doi: 10.1177/0022034514527288. Epub 2014 Mar 19. PubMed PMID: 24646639; PubMed Central PMCID: PMC3988627.

48. Jiang K, Sawle AD, Frank MB, Chen Y, Wallace CA, Jarvis JN. Whole blood gene expression profiling predicts therapeutic response at six months in patients with polyarticular juvenile idiopathic arthritis. Arthritis Rheumatol. 2014 May;66(5):1363-71. doi: 10.1002/art.38341. PubMed PMID: 24782192; PubMed Central PMCID: PMC4077198.

49. Zhang Y, Chen K, Sloan SA, Bennett ML, Scholze AR, O'Keeffe S, Phatnani HP, Guarnieri P, Caneda C, Ruderisch N, Deng S, Liddelow SA, Zhang C, Daneman R, Maniatis T, Barres BA, Wu JQ. An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. J Neurosci. 2014 Sep 3;34(36):11929-47. doi: 10.1523/JNEUROSCI.1860-14.2014. PubMed PMID: 25186741; PubMed Central PMCID: PMC4152602.

50. Worthley DL, Churchill M, Compton JT, Tailor Y, Rao M, Si Y, Levin D, Schwartz MG, Uygur A, Hayakawa Y, Gross S, Renz BW, Setlik W, Martinez AN, Chen X, Nizami S, Lee HG, Kang HP, Caldwell JM, Asfaha S, Westphalen CB, Graham T, Jin G, Nagar K, Wang H, Kheirbek MA, Kolhe A, Carpenter J, Glaire M, Nair A, Renders S, Manieri N, Muthupalani S, Fox JG, Reichert M, Giraud AS, Schwabe RF, Pradere JP, Walton K, Prakash A, Gumucio D, Rustgi AK, Stappenbeck TS, Friedman RA, Gershon MD, Sims P, Grikscheit T, Lee FY, Karsenty G, Mukherjee S, Wang TC. Gremlin 1 identifies a skeletal stem cell with bone, cartilage, and reticular stromal potential. Cell. 2015 Jan 15;160(1-2):269-84. doi: 10.1016/j.cell.2014.11.042. PubMed PMID: 25594183.


51. Kaukua N, Chen M, Guarnieri P, Dahl M, Lim ML, Yucel-Lindberg T, Sundström E, Adameyko I, Mao JJ, Fried K. Molecular differences between stromal cell populations from deciduous and permanent human teeth. Stem Cell Res Ther. 2015 Apr 18;6:59. doi: 10.1186/s13287-015-0056-7. PubMed PMID: 25927523; PubMed Central PMCID: PMC4417277.

52. Yu L, Sawle AD, Wynn J, Aspelund G, Stolar CJ, Arkovitz MS, Potoka D, Azarow KS, Mychaliska GB, Shen Y, Chung WK. Increased burden of de novo predicted deleterious variants in complex congenital diaphragmatic hernia. Hum Mol Genet. 2015 Jun 1. pii: ddv196. [Epub ahead of print] PubMed PMID: 26034137.

53. Nicoletti P, Bansal M, Lefebvre C, Guarnieri , Shen Y, Pe'er I, Califano A, Floratos A. ABC Transporters and the Proteasome Complex Are Implicated in Susceptibility to Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis across Multiple Drugs. PLoS One. 2015 Jun 25;10(6):e0131038. eCollection 2015. PubMed PMID: 26110827.

54. Kode A, Mosialou I, Manavalan SJ, Rathinam CV, Friedman RA, Teruya-Feldstein J, Bhagat G, Berman E, Kousteni S. FoxO1-Dependent induction of acute myeloid leukemia by osteoblasts in mice. Leukemia. 2015 Jun 25. [Epub ahead of print] PubMed PMID: 26108693.

55. Daffu G, Shen X, Senatus L, Thiagarajan D, Abedini A, Hurtado Del Pozo C, Rosario R, Song F, Friedman RA, Ramasamy R, Schmidt AM. RAGE Suppresses ABCG1-Mediated Macrophage Cholesterol Efflux in Diabetes. Diabetes. 2015 Aug 7. [Epub ahead of print] PubMed PMID: 26253613.

56. Hayakawa Y, Ariyama H, Stancikova J, Sakitani K, Asfaha S, Renz BW, Dubeykovskaya ZA, Shibata W, Wang H, Westphalen CB, Chen X, Takemoto Y, Kim W, Khurana SS, Tailor Y, Nagar K, Tomita H, Hara A, Sepulveda AR, Setlik W, Gershon MD, Saha S, Ding L, Shen Z, Fox JG, Friedman RA, Konieczny SF, Worthley DL, Korinek V, Wang TC. Mist1 Expressing Gastric Stem Cells Maintain the Normal and Neoplastic Gastric Epithelium and Are Supported by a Perivascular Stem Cell Niche. Cancer Cell. 2015 Nov 11. [Epub ahead of print] PubMed PMID: 26585400.