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Published works
 

BOOKS

  1. Ganiraju Manyam, A Baranova. "Gene expression during carcinogenesis: A bioinformatics perspective" LAP Lambert Academic Publishing (May 7, 2010)

  2. MH Jarrar, ZM.Younossi, A Baranova. "Adipokines and Pathogenesis of Non Alcoholic Fatty Liver Disease" VDM Verlag Dr. Mueller e.K. (October 24, 2008)

BOOK CHAPTERS

  1. Baranova A, Birerdinc A, Younossi ZM. “Adipokines in Non-alcoholic Fatty Liver Diseases” In: Adipose tissue and adipokines in health and disease. Editors: Giamila Fantuzzi and Theodore Mazzone. Humana Press, 2014

  2. Baranova A , A. Birerdinc, M. Estep, ZM Younossi. ”Pathogenisis of Obesity Related Chronic Liver Diseases as a Study Case for the Systems Biology” In: Systems Biology for Signaling Networks, Springer; 1st Edition. (August 18, 2010)

  3. Baranova A , Petricoin E, Liotta L, Jarrar MH, Younossi ZM. ”Novel Technologies in Studying Chronic Liver Diseases” In: Practical Management of Liver Diseases, 1st Edition, Cambridge University Press, 2008

  4. Baranova A, Younossi ZM. “Adipokines in Non-alcoholic Fatty Liver Diseases” In: Adipose tissue and adipokines in health and disease. Editors: Giamila Fantuzzi and Theodore Mazzone. Humana Press, in press. (Book chapter), 2007

  5. Baranova A, Liotta L, Petricoin E, Younossi ZM. “The Role of Genomics and Proteomics Technologies in Studying Non-Alcoholic Fatty Liver Disease”. In: “Liver clinic”, Clinics of North America Series, in press (Book chapter)

  6. Methods in Virology. Textbook. Editor: Atabekov IG. Published in MGU, 2002. 1st edition: 3000 copies. In Russian.
    Chapter 4. Viral nucleic acids and protein: preparative methods. Pages 113-141.
    Baranova AV. Polimerase chain reaction. P113-121.
    Skoblov MY, Baranova AV. DNA sequencing: Sanger method P121-129
    Ivanov DV, Baranova AV. Hybridization of nucleic acids. P. 129-141
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Metabolic Syndrome (obesity, insulin resistance and non-alcoholoic fatty liver disease)

  1. Estep JM, Goodman Z, Sharma H, Younossi E, Elarainy H, Baranova A, Younossi Z. Adipocytokine expression associated with miRNA regulation and diagnosis of NASH in obese patients with NAFLD. Liver Int. 2015 Apr;35(4):1367-72. PMID: 24684403

  2. Birerdinc A, Jarrar M, Stotish T, Randhawa M, Baranova A. Manipulating molecular switches in brown adipocytes and their precursors: a therapeutic potential. Prog Lipid Res. 2013 Jan;52(1):51-61. PMID: 22960032.

  3. Mehta R, Neupane A, Wang L, Goodman Z, Baranova A, Younossi ZM.Expression of NALPs in adipose and the fibrotic progression of non-alcoholic fatty liver disease in obese subjects. BMC Gastroenterol. 2014 Dec 16;14:208. PMID: 25512222.

  4. Mehta R, Birerdinc A, Wang L, Younoszai Z, Moazzez A, Elariny H, Goodman Z, Chandhoke V, Baranova A, Younossi ZM. Expression of energy metabolism related genes in the gastric tissue of obese individuals with non-alcoholic fatty liver disease. BMC Gastroenterol. 2014 Apr 9;14:72. PMID: 24716593.

  5. Loria A, Doyle K, Weinstein AA, Winter P, Escheik C, Price J, Wang L, Birerdinc A, Baranova A, Gerber L, Younossi ZM. Multiple factors predict physical performance in people with chronic liver disease. MAm J Phys Med Rehabil. 2014 Jun;93(6):470-6. PMID: 24398583.

  6. Page S, Birerdinc A, Estep M, Stepanova M, Afendy A, Petricoin E, Younossi Z, Chandhoke V, Baranova A. Knowledge-based identification of soluble biomarkers: hepatic fibrosis in NAFLD as an example. PLoS One. 2013;8(2):e56009.PMC3566090.

  7. Baranova A, Tran TP, Afendy A, Wang L, Shamsaddini A, Mehta R, Chandhoke V, Birerdinc A, Younossi ZM. Molecular signature of adipose tissue in patients with both non-alcoholic fatty liver disease (NAFLD) and polycystic ovarian syndrome (PCOS). J Transl Med. 2013 May 31;11:133.PMID: 23721173.

  8. Sharma H, Estep M, Birerdinc A, Afendy A, Moazzez A, Elariny H, Goodman Z, Chandhoke V, Baranova A, Younossi ZM. Expression of genes for microRNA-processing enzymes is altered in advanced non-alcoholic fatty liver disease. J Gastroenterol Hepatol. 2013 Aug;28(8):1410-5. PMID: 23663110.

  9. de Oliveira MR, Elangovan N, Ljubkovic M, Baranova A. The roads to mitochondrial dysfunction. Biomed Res Int. 2015;2015:235370.PMID: 25654089 (Editorial Note to Special Issue)

  10. Mayburd A, Baranova A. Knowledge-based compact disease models identify new molecular players contributing to early-stage Alzheimer's disease. BMC Syst Biol. 2013 Nov 7;7:121. PMID: 24196233.

  11. Mehta R, Birerdinc A, Neupane A, Shamsaddini A, Afendy A, Elariny H, Chandhoke V, Baranova A, Younossi ZM. Expression of Inflammation-Related Genes Is Altered in Gastric Tissue of Patients with Advanced Stages of NAFLD. Mediators Inflamm. 2013;2013:684237. doi: 10.1155/2013/684237. Epub 2013 Mar 30. PubMed PMID:
    23661906.

  12. Page S, Birerdinc A, Estep M, Stepanova M, Afendy A, Petricoin E, Younossi Z, Chandhoke V, Baranova A. Knowledge-based identification of soluble biomarkers: hepatic fibrosis in NAFLD as an example. PLoS One. 2013;8(2):e56009. Epub 2013 Feb 6. PubMed PMID: 23405244

  13. Birerdinc A, Estep M, Afendy A, Stepanova M, Younossi I, Baranova A, Younossi ZM. Gene expression profiles associated with anaemia and ITPA genotypes in patients with chronic hepatitis C (CH-C). J Viral Hepat. 2012 Jun;19(6):414-22. PMID: 22571903.

  14. Birerdinc A, Stepanova M, Pawloski L, Younossi ZM. Caffeine is protective in patients with non-alcoholic fatty liver disease. Aliment Pharmacol Ther. 2012 Jan;35(1):76-82. PMID: 22059453.

  15. Younossi ZM, Birerdinc A, Estep M, Stepanova M, Afendy A, Baranova A. The impact of IL28B genotype on the gene expression profile of patients with chronic hepatitis C treated with pegylated interferon alpha and ribavirin. J Transl Med. 2012 Feb 7;10:25. PMID: 22313623.

  16. Birerdinc A, Mehta R, Alhussain R, Afendi A, Chandhoke V, Younossi Z, Baranova A. Selection of reliable reference genes for qRT-PCR analysis in human non-cancerous gastric tissue. Mol Biol (Mosk). 2012 Jan-Feb;46(1):166-75. PMID: 22642115.

  17. Mehta R, Baranova A, Birerdinc A. Do-It-Yourself device for recovery of cryopreserved samples accidentally dropped into cryogenic storage tanks. J Vis Exp. 2012 May 11;(63):e3903. PMID: 22617806.

  18. Birerdinc A, Afendy A, Stepanova M, Younossi I, Baranova A, Younossi AM. Gene expression profiles associated with depression in patients with chronic hepatitis C (CH-C). Brain and Behavior (Wiley) Article first published online: 6 JUL 2012; DOI: 10.1002/brb3.72. PMID: 23139898.

  19. Birerdinc A, Jarrar M, Stotish T, Randhawa M, Baranova A. Manipulating molecular switches in brown adipocytes and their precursors: a therapeutic potential. Prog Lipid Research, accepted. PMID: 22960032.

  20. Baranova A, Lal P, Birerdinc A, Younossi ZM. Non-Invasive markers for hepatic fibrosis. BMC Gastroenterol . 2011 Aug 17;11:9.1.PMID: 21849046.

  21. Estep M, Abawi M, Jarrar M, Wang L, Stepanova M, Elariny H, Moazez A, Goodman Z, Chandhoke V, Baranova A, Younossi ZM. Association of Obestatin, Ghrelin, and Inflammatory Cytokines in Obese Patients with Non-alcoholic Fatty Liver Disease. Obes Surg . 2011 Jul 9. PMID: 21744131.

  22. Vernon G, Baranova A, Younossi ZM. Systematic review: the epidemiology and natural history of non-alcoholic fatty liver disease and non-alcoholic steatohepatitis in adults. liment Pharmacol Ther. 2011 Aug;34(3):274-85. doi: 10.1111/j.1365-2036.2011.04724.x. PMID: 21623852

  23. Baranova A, Tran TP, Birerdinc A, Younossi ZM. Systematic review: association of polycystic ovary syndrome with metabolic syndrome and non-alcoholic fatty liver disease. Aliment Pharmacol Ther. 2011 Jan 20. doi: 10.1111/j.1365-2036.2011.04579.x. [Epub ahead of print] PubMed PMID: 21251033.

  24. Baranova A, Jarrar MH, Stepanova M, Johnson A, Rafiq N, Gramlich T, Chandhoke V, Younossi ZM. Association of serum adipocytokines with hepatic steatosis and fibrosis in patients with chronic hepatitis C. Digestion. 2011;83(1-2):32-40. Epub 2010 Sep 15. PubMed PMID: 20847561.

  25. Page S, Chandhoke V, Baranova A. Melanin and melanogenesis in adipose tissue: possible mechanisms for abating oxidative stress and inflammation? Obes Rev. 2010 Jun 22. [Epub ahead of print] PubMed PMID: 20576005.

  26. Younossi ZM, Page S, Rafiq N, Birerdinc A, Stepanova M, Hossain N, Afendy A, Younoszai Z, Goodman Z, Baranova A. A Biomarker Panel for Non-alcoholic Steatohepatitis (NASH) and NASH-Related Fibrosis. Obes Surg. 2010 Jun 8. [Epub ahead of print] PubMed PMID: 20532833.

  27. Younossi ZM, Limongi D, Stepanova M, Pierobon M, Afendy A, Mehta R, Baranova A, Liotta L, Petricoin E. Protein Pathway Activation Associated with Sustained Virologic Response in Patients with Chronic Hepatitis C Treated with Pegylated Interferon (PEG-IFN) and Ribavirin (RBV). J Proteome Res. 2011 Jan 4. [Epub ahead of print] PubMed PMID: 21204552.

  28. Estep M, Armistead D, Hossain N, Elarainy H, Goodman Z, Baranova A, Chandhoke V, Younossi ZM. Differential expression of miRNAs in the visceral adipose tissue of patients with non-alcoholic fatty liver disease. Aliment Pharmacol Ther. 2010 Aug;32(3):487-97. Epub 2010 May 22. PubMed PMID: 20497147.

  29. Mehta R, Birerdinc A, Hossain N, Afendy A, Chandhoke V, Younossi Z, Baranova A. Validation of endogenous reference genes for qRT-PCR analysis of human visceral adipose samples. BMC Mol Biol. 2010 May 21;11:39. PubMed PMID: 20492695; PubMed Central PMCID: PMC2886049.

  30. Younossi ZM, Baranova A, Stepanova M, Page S, Calvert VS, Afendy A, Goodman Z, Chandhoke V, Liotta L, Petricoin E. Phosphoproteomic biomarkers predicting histologic nonalcoholic steatohepatitis and fibrosis. J Proteome Res. 2010 Jun 4;9(6):3218-24. PubMed PMID: 20441224.

  31. Stepanova M, Hossain N, Afendy A, Perry K, Goodman ZD, Baranova A, Younossi Z. Hepatic gene expression of Caucasian and African-American patients with obesity-related non-alcoholic fatty liver disease. Obes Surg. 2010 May;20(5):640-50. Epub 2010 Jan 30. PubMed PMID: 20119733.

  32. Birerdinc A, Afendy A, Stepanova M, Younossi I, Manyam G, Baranova A, Younossi ZM. Functional pathway analysis of genes associated with response to treatment for chronic hepatitis C. J Viral Hepat. 2010 Oct;17(10):730-6. doi: 10.1111/j.1365-2893.2009.01235.x. PubMed PMID: 20002302.

  33. Younossi ZM, Afendy A, Stepanova M, Hossain N, Younossi I, Ankrah K, Gramlich T, Baranova A. Gene expression profile associated with superimposed non-alcoholic fatty liver disease and hepatic fibrosis in patients with chronic hepatitis C. Liver Int. 2009 Oct;29(9):1403-12. Epub 2009 Jun 3. PubMed PMID: 19515216.

  34. Estep JM, Baranova A, Hossain N, Elariny H, Ankrah K, Afendy A, Chandhoke V, Younossi ZM. Expression of Cytokine Signaling Genes in Morbidly Obese Patients with Non-Alcoholic Steatohepatitis and Hepatic Fibrosis. Obes Surg. 2009 Mar 12. [Epub ahead of print] PubMed PMID: 19280268.

  35. Younossi ZM, Baranova A, Afendy A, Collantes R, Stepanova M, Manyam G, Bakshi A, Sigua CL, Chan JP, Iverson AA, Santini CD, Chang SY. Early gene expression profiles of patients with chronic hepatitis C treated with pegylated interferon-alfa and ribavirin. Hepatology. 2009 Mar;49(3):763-74. PubMed PMID: 19140155.

  36. Baranova AV. [Adipokine genetics: unbalanced protein secretion by human adipose tissue as a cause of the metabolic syndrome]. Genetika. 2008 Oct;44(10):1338-55. Review. Russian. PubMed PMID: 19062531.

  37. Randhawa M, Huff T, Valencia JC, Younossi Z, Chandhoke V, Hearing VJ, Baranova A. Evidence for the ectopic synthesis of melanin in human adipose tissue. FASEB J. 2009 Mar;23(3):835-43. Epub 2008 Oct 29. PubMed PMID: 18971261; PubMed Central PMCID: PMC2653983.

  38. Younossi ZM, Jarrar M, Nugent C, Randhawa M, Afendy M, Stepanova M, Rafiq N, Goodman Z, Chandhoke V, Baranova A. A Novel Diagnostic Biomarker Panel for Obesity-related Nonalcoholic Steatohepatitis (NASH). Obes Surg. 2008 May 24.

  39. Baranova A, Younossi ZM. The future is around the corner: Noninvasive diagnosis of progressive nonalcoholic steatohepatitis. Hepatology. 2008 Feb;47(2):373-5.

  40. Jarrar MH, Baranova A, Collantes R, Ranard B, Stepanova M, Bennett C, Fang Y, Elariny H, Goodman Z, Chandhoke V, Younossi ZM. Adipokines and cytokines in non-alcoholic fatty liver disease. Aliment Pharmacol Ther. 2008 Mar 1;27(5):412-21.

  41. Baranova A, Schlauch K, Elariny H, Jarrar M, Bennett C, Nugent C, Gowder SJ, Younoszai Z, Collantes R, Chandhoke V, Younossi ZM. Gene expression patterns in hepatic tissue and visceral adipose tissue of patients with non-alcoholic fatty liver disease. Obes Surg. 2007 Aug;17(8):1111-8.

  42. Calvert VS, Collantes R, Elariny H, Afendy A, Baranova A, Mendoza M, Goodman Z, Liotta LA, Petricoin EF, Younossi ZM. A systems biology approach to the pathogenesis of obesity-related nonalcoholic fatty liver disease using reverse phase protein microarrays for multiplexed cell signaling analysis. Hepatology. 2007 Jul;46(1):166-72.

  43. Baranova A, Randhawa M, Jarrar M, Younossi ZM. Adipokines and melanocortins in the hepatic manifestation of metabolic syndrome: nonalcoholic fatty liver disease. Expert Rev Mol Diagn. 2007 Mar;7(2):195-205. Review.

  44. Younossi ZM, Gorreta F, Ong J, Schlauch K, Del Giacco L, Elariny H, Van Meter A, Younoszai A, Goodman Z, Baranova A, Christensen A, Grant G, Chandhoke V. Hepatic Gene Expression in Patients with Obesity-related Non-Alcoholic Steatohepatitis. Liver International, Liver Int. 2005 Aug;25(4):760-71

  45. Baranova A, Gowder SJ, Schlauch K, Elariny H, Collantes R, Afendy A, Ong JP, Goodman Z, Chandhoke V, Younossi ZM. Gene expression of leptin, resistin, and adiponectin in the white adipose tissue of obese patients with non-alcoholic Fatty liver disease and insulin resistance.Obes Surg. 2006 Sep;16(9):1118-25.

  46. A Baranova; R Collantes; S Gowder; H Elariny; K Schlauch; A Younoszai; S King; M Randhawa; S Pusulury; T Alsheddi; J Ong; L Martin; V Chandhoke; ZM Younossi. Obesity-related Differential Gene Expression in the Visceral Adipose Tissue, Obesity Surgery, 2005, V. 15, P. 58-65

  47. Younossi ZM, Baranova A, Ziegler K, Del Giacco L, Schlauch K, Born TL, Elariny H, Gorreta F, VanMeter A, Younoszai A, Ong JP, Goodman Z, Chandhoke V. A genomic and proteomic study of the spectrum of nonalcoholic fatty liver disease. Hepatology. 2005 Sep;42(3):665-74.

  48. Ancha Baranova, Karen Schlauch, Shobha Gowder, Rochelle Collantes, Vikas Chandhoke and Zobair M. Younossi. Microarray technology in the study of obesity and non-alcoholic fatty liver disease, Liver International, 2005 Dec;25(6):1091-6. Review
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Circulating DNA

  1. Ivanov M, Baranova A, Butler T, Spellman P, Mileyko V. Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation. BMC Genomics. 2015 Dec 16;16 Suppl 13:S1.PMID: 26693644.

  2. Vasilyeva I, Bespalov V, Baranova A. Radioprotective combination of ?-tocopherol and ascorbic acid promotes apoptosis that is evident by release of low-molecular weight DNA fragments into circulation. Int J Radiat Biol. 2015;91(11):872-7. doi: 10.3109/09553002.2015.1087066. Epub 2015 Oct 16. PubMed PMID: 26473391.

  3. Glebova K, Veiko N, Kostyuk S, Izhevskaya V, Baranova A. ROxidized extracellular DNA as a stress signal that may modify response to anticancer therapy. Cancer Lett. 2015 Jan 1;356(1):22-33.

  4. Kostyuk SV, Konkova MS, Ershova ES, Alekseeva AJ, Smirnova TD, Stukalov SV, Kozhina EA, Shilova NV, Zolotukhina TV, Markova ZG, Izhevskaya VL, Baranova A, Veiko NN. An exposure to the oxidized DNA enhances both instability of genome and survival in cancer cells. PLoS One. 2013 Oct 17;8(10):e77469. PMID: 24147001.

  5. Kostyuk SV, Tabakov VJ, Chestkov VV, Konkova MS, Glebova KV, Baydakova GV, Ershova ES, Izhevskaya VL, Baranova A, Veiko NN. Oxidized DNA induces an adaptive response in human fibroblasts. Mutat Res. 2013 May 1. [Epub ahead of print] PubMed
    PMID: 23644378.

  6. Ermakov AV, Konkova MS, Kostyuk SV, Izevskaya VL, Baranova A, Veiko NN.Oxidized extracellular DNA as a stress signal in human cells. Oxid Med Cell Longev. 2013;2013:649747. PubMed Central PMCID: PMC3606786.

  7. Kostjuk S, Loseva P, Chvartatskaya O, Ershova E, Smirnova T, Malinovskaya E, Roginko O, Kuzmin V, Izhevskaia V, Baranova A, Ginter E, Veiko N.Extracellular GC-rich DNA activates TLR9- and NF-kB-dependent signaling pathways in human adipose-derived mesenchymal stem cells (haMSCs). Expert Opin Biol Ther. 2012 Jun;12 Suppl 1:S99-111. doi: 10.1517/14712598.2012.690028. Epub 2012 May 18. PubMed PMID: 22594608.

  8. Loseva P, Kostyuk S, Malinovskaya E, Clement N, Dechesne CA, Dani C, Smirnova T, Glebova K, Baidakova G, Baranova A, Izhevskaia V, Ginter E, Veiko N. Extracellular DNA oxidation stimulates activation of NRF2 and reduces the production of ROS in human mesenchymal stem cells. Expert Opin Biol Ther. 2012 Jun;12 Suppl 1:S85-97. doi: 10.1517/14712598.2012.688948. Epub 2012 May 18.PubMed PMID: 22594577.

  9. Kostyuk SV, Ermakov AV, Alekseeva AY, Smirnova TD, Glebova KV, Efremova LV, Baranova A, Veiko NN. Role of extracellular DNA oxidative modification in radiation induced bystander effects in human endotheliocytes. Mutat Res. 2011 Oct 4. PMID: 22001237
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Ageing

  1. Velegzhaninov I, Mezenceva V, Shostal O, Baranova A, Moskalev A. Age dynamics of DNA damage and CpG methylation in the peripheral blood leukocytes of mice. Mutat Res. - Fundamental and Molecular Mechanisms of Mutagenesis. 2015 May;775:38-42. PMID: 25867117.

  2. Stepanova M, Rodriguez E, Birerdinc A, Baranova A.Age-independent rise of inflammatory scores may contribute to accelerated aging in multi-morbidity. Oncotarget. 2015 Jan 30;6(3):1414-21.PMID: 25638154

  3. Baranova A, Willett JD. Anti-aging dilemma: to restore the hardware or to reinstall the software?Front Genet. 2015 Apr 14;6:129. PMID: 25926845.
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Chronic lymphocytic leukemia and 13q14 related papers

  1. Biderman B, Marakhonov A, Skoblov M, Birerdinc A, Nohelty E, Page S, Khomenkov V, Chandhoke V, Sudarikov A, Nikitin E, Baranova A., Inhibition of potassium currents as a pharmacologic target for investigation in chronic lymphocytic leukemia. Drug News Perspect. 2010 Dec;23(10):625-31. PubMed PMID: 21180648

  2. Birerdinc A, Nohelty E, Marakhonov A, Manyam G, Panov I, Coon S, Nikitin E, Skoblov M, Chandhoke V, Baranova A., Pro-apoptotic and antiproliferative activity of human KCNRG, a putative tumor suppressor in 13q14 region. Tumour Biol. 2010 Jan;31(1):33-45. Epub 2009 Dec 18. PubMed PMID: 20237900; PubMed Central PMCID: PMC2803748.

  3. Nikitin EA, Malakho SG, Biderman BV, Baranova AV, Lorie YY, Shevelev AY, Peklo MM, Vlasik TN, Moskalev EA, Zingerman BV, Vorob'ev IA, Poltaraus B, Sudarikov AB, Vorobjev AI. Expression level of lipoprotein lipase and dystrophin genes predict survival in B-cell chronic lymphocytic leukemia. Leuk Lymphoma. 2007 May;48(5):912-22.

  4. Skoblov M, Shakhbazov K, Oshchepkov D, Ivanov D, Guskova A, Ivanov D, Rubtsov P, Prasolov V, Yankovsky N, Baranova A. Human RFP2 gene promoter: Unique structure and unusual strength. Biochem Biophys Res Commun. 2006 Apr 14;342(3):859-66

  5. Tiazhelova TV, Ivanov DV, Baranova AV, Yankovsky NK. Search for transcribed segments in the region of q14.3 of human chromosome 13 in silico. Genetika. 2004 Mar;40(3):422-6.

  6. van Everdink WJ, Baranova A, Lummen C, Tyazhelova T, Looman MWG, Ivanov D, Verlind E, Pestova A, Faber H, van der Veen AY, Yankovsky N, Vellenga E, Buys CHCM. RFP2, c13ORF1 and FAM10aaA4 are the most likely tumor suppressor gene candidates for B-cell chronic lymphocytic leukemia. Cancer Genetics and Cytogenetics, 2003 Oct 1; 146 ( 1 ): 48-57 .

  7. Baranova A, Hammarsund M, Ivanov D, Skoblov M, Sangfelt O, Corcoran M, Borodina T, Makeeva N, Pestova A, Tyazhelova T, Nazarenko S, Gorreta F, Alsheddi T, Schlauch K, Nikitin E, Kapanadze B, Shagin D, Poltaraus A, Ivanovich Vorobiev A, Zabarovsky E, Lukianov S, Chandhoke V, Ibbotson R, Oscier D, Einhorn S, Grander D, Yankovsky N. Distinct organization of the candidate tumor supperssor gene RFP2 in human and mouse: multiple mRNA isoforms in both species and human-specific antisense transcript RFP2OS. Gene. 2003 Dec 4;321:103-12.

  8. Ivanov DV, Tyazhelova TV, Lemonnier L, Kononenko N, Pestova AA, Prevarskaya N, Skryma R, Panchin YV, Yankovsky NK, Baranova AV. A new human gene KCNRG encoding potassium channel regulating protein is a cancer suppressor gene candidate located in 13q14.3 FEBS Letters 2003 Mar 27;539(1-3):156-60.

  9. Baranova AV, Ivanov DV, Tiazhelova TV, Iankovskii NK. Structural-functional characteristics of the 13q14 region of the human genome in the search for potential tumor suppressor genes. Mol Biol (Mosk). 2004 Mar-Apr;38(2):203-12. Review.

  10. Tiazhelova TV, Ivanov DV, Makeeva NV, Kapanadze BI, Nikitin EA, Semov AB, Sangfeldt O, Grander D, Vorob'ev AI, Einhorn S, Iankovskii NK, Baranova AV. Transcription map of the 13q14 region, frequently deleted in B-cell chronic lymphocytic leukemia patients. Genetika. 2001 Nov;37(11):1530-7.

  11. Nikitin EA, Baranova AV, Aseeva EA, Domracheva EV. Molecular and cytogenetic aberrations in chronic lymphocytic leukaemia. Haematology and transfusiology, 2000, 45 (3): 61-63.

  12. Kapanadze B, Kashuba V, Baranova A, Rasool O, van Everdink W, Liu Y, Syomov A, Corcoran M, Poltaraus A, Brodyansky V, Syomova N, Kazakov A, Ibbotson R, van den Berg A, Gizatullin R, Fedorova L, Sulimova G, Zelenin A, Deaven L, Lehrach H, Grander D, Buys C, Oscier D, Zabarovsky ER, Yankovsky N. A cosmid and cDNA fine physical map of a human chromosome 13q14 region frequently lost in B-cell chronic lymphocytic leukemia and identification of a new putative tumor suppressor gene, Leu5. FEBS Lett 1998 Apr 17; 426(2):266-270. pdf

  13. Yie Liu, Martin Corcoran, Omid Rasool, Ganka Ivanova, Rachel Ibbotson, Dan Grander, Arati Iyengar, Anna Baranova, Vladimir Kashuba, Mats Merup, Xiushan Wu, Anne Gardiner, Roman Mullenbach, Andrew Poltaraus, Anna Linda Hultstrom, Gunnar Julisson, Robert Chapman, Mary Tiller, Gosta Gahrton, Nick Yankovsky, Eugene Zabarovsky, Stefan Einhorn, David Oscier. Cloning of two candidate tumor suppressor genes within a 10 kb region on chromosome 13q14, frequently deleted in chronic lymphocytic leukemia. Oncogene 1997 15, 2463-2473

  14. Baranova AV, Ivanov DV, Makeeva NV, Nikitin EA, Sangfelt O, Borodina TA, Kapanadze BI, Tyazhelova TV, Corcoran M, Fyodorova LI, Shagin DV, Nemtsova MV, Polataraus AB, Zelenin AV, Zaletaev DV, Lukyanov SA, Grander D, Einhorn S, Yankovsky NK. Modern strategy of a search for putative tumor suppressor genes: cloning of Leu5 gene involved in CLL as an example. Haematology and transfusiology, 2000, 45 (3): 15-19.

  15. Kapanadze BI, Brodianskii VM, Semov AB, Baranova AV, Sulimova GE, Aitova SS, Udina IG, Ptitsyna SN, Sal'nikova LE, Chudinov OS, Borbiev TE, Kashuba VV, Gizatullin R, Zabarovskaia V, Zabarovskii ER, Fedorova LI, Zelenin AV, L'iu I, Rasul O, Einkhorn S, van Everdink W, van den Berg A, Buys C, Corcoran M, Iankovskii NK, et al. Cosmid contig and cDNA map of the 13q14 region is frequently deleted in human B-cell chronic lymphocytic leukemia. Mol Biol (Mosk). 1997 May-Jun; 31(3):515-9.

  16. Kapanadze BI, Brodianskii VM, Baranova AV, Sevat'ianov SIu, Fedorova ND, Kurskov MM, Kostina MA, Mironov AA, Sineokii SP, Zakhar'ev VM, Grafodatskii AS, Modianov NN, Iankovskii NK. Cosmid libraries containing DNA from human chromosome 13. Genetika 1996 Mar;32(3):331-40
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Tumorigenesis related papers (non-CLL)

  1. Kazubskaia TP, Kozlova VM, Kondrat'eva TT, Pavlovskaia AI, Marakhonov AV, Baranova AV, Ivanova NI, Stepanova AA, Poliakov AV, Belev NF, Brzhezovskii VZh.Follicular cell (papillary and follicular) thyroid carcinoma, genetic inheritance, and molecular diagnostic markers. Arkh Patol. 2014 Sep-Oct;76(5):3-12. PMID: 25543402

  2. Marakhonov AV, Baranova AV, Skoblov MIu. Antisense regulation of human gene MAP3K13: true phenomenon or artifact. Mol Biol (Mosk). 2008 Jul-Aug;42(4):581-7.

  3. Baranova A, Gowder S, Naouar S, King S, Schlauch K, Jarrar M, Ding Y, Cook B, Chandhoke V, Christensen A. Expression profile of ovarian tumors: distinct signature of Sertoli-Leydig cell tumor, Int J Gynecol Cancer. 2006 Nov-Dec;16(6):1963-72.

  4. Semova N, Kapanadze B, Corcoran M, Kutsenko A, Baranova A, Kisselev L, Semov A. Molecular cloning, structural analysis, and expression of human IRLB, MYC promoter-binding protein: new DENN domain containing protein family emerges. Genomics, 2003 Genomics. 2003 Sep;82(3):343-54.

  5. Borodina TA, Ivanov DV, Khusnutdinova EK, Spitsyn VA, Baranova AV, Iankovskii NK. A new pentanucleotide STR-marker, located in the intron of the ING1 tumor suppressor gene and its allelic polymorphism. Genetika. 2001 Jan;37(1):117-9.

  6. Baranova AV, Ivanov DV, Makeeva NV, Corcoran M, Nikitin EA, Borodina TA, Poltaraus AB, Glinshchikova OA, Sudarikov AB, Oscier D, Iankovskii NK. Genomic organization of the suppressor gene for tumor growth ING1. Mol Biol (Mosk). 2000 Mar-Apr;34(2):263-9.

  7. Udina IG, Baranova AV, Kompaniitsev AA, Sulimova GE. Evolutionarily-conserved gene CKAP2, located in region 13q14.3 of the human genome, is frequently rearranged in various tumors. Genetika. 2001 Jan;37(1):120-3.

  8. Baranova AV, Iankovskii NK. Tumor suppressor genes. Mol Biol (Mosk). 1998 Mar-Apr;32(2):206-18. Review.
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TUMOR MARKERS

  1. Sikaroodi M, Galachiantz Y, Baranova A., Tumor markers: the potential of "omics" approach. Curr Mol Med. 2010 Mar;10(2):249-57. Review. PubMed PMID: 20196723.

  2. Krukovskaia LL, Polev DE, Nosova IuK, Baranova AV, Koliubaeva SN, Kozlov AP. Investigation of transcription factor Brachyury (T) expression in human normal and tumor tissues. Vopr Onkol. 2008;54(6):739-43. Russian.

  3. Deigner HP, Baranova AV. Current methods and perspectives in biomarker discovery. Curr Mol Med. 2010 Mar;10(2):113-4. PubMed PMID: 20230374.

  4. Palena C, Polev DE, Tsang KY, Fernando RI, Litzinger M, Krukovskaya LL, Baranova AV, Kozlov AP, Schlom J. The human T-box mesodermal transcription factor Brachyury is a candidate target for T-cell-mediated cancer immunotherapy. Clin Cancer Res. 2007 Apr 15;13(8):2471-8.

  5. Krukovskaja L, Baranova A, Tyazhelova T, Polev D, Kozlov A.P. Experimental Study of Human Expressed Sequences Identified In Silico as Tumor Specific. Tumor Biology, 2005. Jan-Feb;26(1):17-24

  6. Baranova AV, Lobashev A.V., Ivanov D.V., Krukovskaya L.L., Zinchenko V.V., Shestakov S.V., Kozlov A.P., Yankovsky N.K. A computer differential display reveals genes with with specific expression patterns: from potential human tumor markers down to plant stress-resistance genes. // In Proc. Third International conference on bioinformatics of genome regulation and structure. (BGRS 2002), vol. 3, July 14-20, Novosibirsk 2002 P.80-81.

  7. V Baranova, A.V.Lobashev, D.V. Ivanov, L.L. Krukovskaya, N.K. Yankovsky, A.P. Kozlov. In silico screening for tumour-specific expressed sequences in human genome. FEBS Letters, 2001, V. 508 (1) P. 143-148. pdf
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Biosensors

  1. Konopleva MN, Khrulnova SA, Baranova A, Ekimov LV, Bazhenov SV, Goryanin II, Manukhov IV. A combination of luxR1 and luxR2 genes activates Pr-promoters of psychrophilic Aliivibrio logei lux-operon independently of chaperonin GroEL/ES and protease Lon at high concentrations of autoinducer. Biochem Biophys Res Commun. 2016 May 13;473(4):1158-62. doi: 10.1016/j.bbrc.2016.04.032. Epub 2016 Apr 9. PubMed PMID: 27067048.

  2. Khrulnova SA, Baranova A, Bazhenov SV, Goryanin II, Konopleva MN, Maryshev IV, Salykhova AI, Vasilyeva AV, Manukhov IV, Zavilgelsky GB. Lux-operon of the Marine Psychrophilic Bacteria Aliivibrio logei: a Comparative Analysis of the LuxR1/LuxR2 Regulatory Activity in Escherichia coli cells. Microbiology. 2016 Feb 3. doi: 10.1099/mic.0.000253. [Epub ahead of print] PubMed PMID: 26847185.

  3. Melkina OE, Goryanin II, Manukhov IV, Baranova AV, Kolb VA, Svetlov MS,Zavilgelsky GB. Trigger factor assists the refolding of heterodimeric but not monomeric luciferases. Biochemistry (Mosc). 2014 Jan;79(1):62-8. doi:10.1134/S000629791401009X.PubMed PMID: 24512665.

  4. Manukhov IV, Khrul'nova SA, Baranova A, Zavilgelsky GB. Comparative analysis of the lux operons in Aliivibrio logei KCh1 (a Kamchatka Isolate) and Aliivibrio salmonicida. J Bacteriol. 2011 Aug;193(15): 3998-4001. PMID: 21665974

  5. Manukhov IV, Melkina OE, Goryanin II, Baranova AV, Zavilgelsky GB. The N-terminal domain of Aliivibrio fischeri LuxR is a target of the GroEL chaperonin. J Bacteriol. 2010 Oct;192(20):5549-51. Epub 2010 Aug 20. PubMed PMID: 20729362; PubMed Central PMCID: PMC2950498.
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Bioinformatics and Comparative Genomics

  1. Manyam G, Birerdinc A, Baranova A. KPP: KEGG Pathway Painter. BMC Syst Biol. 2015; 9 Suppl 2:S3.PMID: 25879163.

  2. Veytsman B, Wang L, Cui T, Bruskin S, Baranova A. Distance-based classifiers as potential diagnostic and prediction tools for human diseases. BMC Genomics. 2014;15 Suppl 12:S10.PMID: 25563076.

  3. Baranova A. PLRRC8s revisited: and now they SWELL! Bioessays. 2014 Nov;36(11):1017-8.PMID: 25257378.

  4. Marakhonov A, Sadovskaya N, Antonov I, Baranova A, Skoblov M. PAnalysis of discordant Affymetrix probesets casts serious doubt on idea of microarray data reutilization. BMC Genomics. 2014;15 Suppl 12:S8. PubMed PMID: 25563078.

  5. Ponomarenko E, Baranova A, Lisitsa A, Albar JP, Archakov A. The chromosome-centric human proteome project at FEBS Congress. Proteomics. 2014 Feb;14(2-3):147-52. PubMed PMID: 24285571 (Editorial)

  6. Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, Frishman D, Grossman R, Heath A, Higdon R, Hutz MH, Janko I, Jiang L,oshi S, Kel A, Kemnitz JW, Kohane IS, Kolker N, Lancet D, Lee E, Li W, Lisitsa A, Llerena A, Macnealy-Koch C, Marshall JC, Masuzzo P, May A, Mias G, Monroe M, Montague E, Mooney S, Nesvizhskii A, Noronha S, Omenn G, Rajasimha H, Ramamoorthy P, Sheehan J, Smarr L, Smith CV, Smith T, Snyder M, Rapole S, Srivastava S, Stanberry L, Stewart E, Toppo S, Uetz P, Verheggen K, Voy BH, Warnich L, Wilhelm SW, Yandl G. Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. OMICS. 2014 Jan;18(1):10-4. PMID: 24456465.

  7. Borzov EA, Marakhonov AV, Ivanov MV, Drozdova PB, Baranova AV, Skoblov MIu. RANDTRAN: random transcriptome sequence generator that accounts for partition specific features in eukaryotic mRNA datasets. Mol Biol (Mosk). 2014 Sep-Oct;48(5):859-67. PMID: 25842872.

  8. Skoblov M, Marakhonov A, Marakasova E, Guskova A, Chandhoke V, Birerdinc A, Baranova A. Protein partners of KCTD proteins provide insights about their functional roles in cell differentiation and vertebrate development. Bioessays. 2013 Apr 17. doi: 10.1002/bies.201300002. [Epub ahead of print] PubMed PMID: 23592240.

  9. Sherbakov D, Panchin Y, Baranova A. Extracting evolutionary insights using bioinformatics. Int J Genomics. 2013;2013:376235. PMID: 24324950. (Editorial Note to Special Issue)

  10. Akula N, Baranova A, Seto D, Solka J, Nalls MA, Singleton A, Ferrucci L, Tanaka T, Bandinelli S, Cho YS, Kim YJ, Lee JY, Han BG; Bipolar Disorder Genome Study (BiGS) Consortium; The Wellcome Trust Case-Control Consortium, McMahon FJ. A Network-Based Approach to Prioritize Results from Genome-Wide Association Studies. PLoS One. 2011; 6(9):e24220. PMID: 21915301

  11. Baranova A, Bode J, Manyam G, Emelianenko M. An efficient algorithm for systematic analysis of nucleotide strings suitable for siRNA design. BMC Res Notes. 2011 May 27;4:168. PMID: 21619643

  12. Wojtusiak J, Michalski RS, Simanivanh T, Baranova AV. Towards application of rule learning to the meta-analysis of clinical data: an example of the metabolic syndrome. Int J Med Inform. 2009 Dec;78(12):e104-11. Epub 2009 May 22. PubMed PMID: 19464941.

  13. Alsheddi T, Vasin L, Meduri R, Randhawa M, Glazko G, Baranova A. siRNAs with high specificity to the target: a systematic design by CRM algorithm Mol Biol (Mosk). 2008 Jan-Feb;42(1):163-71.

  14. Stepanova M, Tiazhelova T, Skoblov M, Baranova A. Potential regulatory SNPs in promoters of human genes: A systematic approach. Molecular and Cellular Probes, 2006, Dec; 20 ( 6 ): 348-58 .

  15. Klimov D, Skoblov M, Ryazantsev A, Tyazhelova T, Baranova A. In silico search for natural antisense transcripts reveals their differential expression in human tumors. J Bioinform Comput Biol. 2006 Apr;4(2):515-21.

  16. Stepanova M, Tiazhelova T, Skoblov M, Baranova A. A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas. Bioinformatics, 2005 May 1; 21 ( 9 ): 1789-96 .

  17. Andrei Lobashev, Mikhail Skoblov, Maria Stepanova, Igor Moiseev, Linda Dickerson, Ancha Baranova, Andrei Mironov, Nick Yankovsky. Single nucleotide polymorphism density distribution in the human genome as seen in public databases: possibility of gene set comparisons but not comparisons of genomic regions. Biophysics (Moscow). Vol. 48, Suppl. 1, 2003. 81-84.

  18. Makeeva NV, Pestova AA, Borodina TA, Madera DA, Ivanov DV, Stepanova EV, Baranova AV. Fundamental and applied aspects of vertebrate comparative genomics. Genetika, 2003, Review

  19. Tyazhelova TV, Ivanov DV, Baranova AV, Yankovsky NK. In silico search for transcribed sequences in human chromosome 13 area q14.3 Genetika, 2003,

  20. Kapanadze B, Makeeva N, Corcoran M, Jareborg N, Hammarsund M, Baranova A, Zabarovsky E, Vorontsova O, Merup M, Gahrton G, Jansson M, Yankovsky N, Einhorn S, Oscier D, Grandér D, Sangfelt O. Comparative sequence analysis of a region on human chromosome 13q14, frequently deleted in B-cell chronic lymphocytic leukemia and its homologous region on mouse chromosome 14. Genomics, 2000, V. 70., P. 327-334. pdf

  21. Makeeva NV, Pestova AA, Borodina TA, Madera DA, Ivanov DV, Stepanova EV, Baranova AV. Fundamental and applied aspects of vertebrate comparative genomics. Russian Journal of Genetics, 2003, 39 (9): 973-985 SEP 2003 Review
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Pannexins

  1. Baranova A. The more the merrier: the pannexin family just got a new branch. Bioessays. 2012 Jul;34(7):530-1. PubMed PMID:
    22696111.

  2. Oxana Litvin, Anya Tiunova, Yvette Connell-Alberts, Yury Panchin and Ancha Baranova. What is hidden in the pannexin treasure trove: the sneak peek and the guesswork. Journal of Cellular and Molecular Medicine, J Cell Mol Med. 2006 Jul-Sep;10(3):613-34.

  3. Abeele FV, Bidaux G, Gordienko D, Beck B, Panchin YV, Baranova A, Ivanov DV, Skryma R, Prevarskaya N. Functional implications of calcium permeability of the channel formed by Pannexin 1. Journal of Cell Biology, J Cell Biol. 2006 Aug 14;174(4):535-46.

  4. Baranova A, Ivanov D, Petrash N, Pestova A, Skoblov M, Kelmanson I, Shagin D, Nazarenko S, Geraymovych E, Litvin O, Tiunova A, Born TL, Usman N, Staroverov D, Lukyanov S, Panchin Y. The mammalian pannexin family is homologous to the invertebrate innexin gap junction proteins. Genomics. 2004 Apr;83(4):706-16. Top 10 Cited in Genomics in Year 2004
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Thiazolidinediones AND breast carcinoma

  1. A. Baranova. PPAR Ligands as Potential Modifiers of Breast Carcinoma
    Outcomes.     PPAR research, 2008.

  2. Jarrar MH, Baranova A. PPARgamma activation by thiazolidinediones (TZDs) may modulate breast carcinoma outcome: the importance of interplay with TGFbeta signalling. J Cell Mol Med. 2007 Jan-Feb;11(1):71-87. Review.
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MISCELLANEOUS

  1. Jacobsen KH, Aguirre AA, Bailey CL, Baranova AV, Crooks AT, Croitoru A, Delamater PL, Gupta J, Kehn-Hall K, Narayanan A, Pierobon M, Rowan KE, Schwebach JR, Seshaiyer P, Sklarew DM, Stefanidis A, Agouris P. Lessons from the Ebola Outbreak: Action Items for Emerging Infectious Disease Preparedness and Response. Ecohealth. 2016 Feb 25. PMID: 26915507.

  2. Myakishev-Rempel M, Stadler I, Polesskaya O, Motiwala AS, Nardia FB, Mintz B, Baranova A, Zavislan J, Lanzafame RJ. Red Light Modulates Ultraviolet-Induced Gene Expression in the Epidermis of Hairless Mice. Photomed Laser Surg. 2015 Oct;33(10):498-503.PMID: 26398729.

  3. Glebova K, Reznik ON, Reznik AO, Mehta R, Galkin A, Baranova A, Skoblov M. siRNA technology in kidney transplantation: current status and future potential. BioDrugs. 2014 Aug;28(4):345-61. PMID: 24573958.

  4. Marakasova ES, Akhmatova NK, Amaya M, Eisenhaber B, Eisenhaber F, van Hoek ML, Baranova AV.Prenylation: from bacteria to eukaryotes. Mol Biol (Mosk). 2013 Sep-Oct;47(5):717-30. PMID: 25509344.

  5. Petrenko AA, Korolenkova LI, Skvortsov DA, Fedorova MD, Skoblov MU, Baranova AV, Zvereva ME, Rubtsova MP, Kisseljov FL. Cervical intraepithelial neoplasia: Telomerase activity and splice pattern of hTERT mRNA. Biochimie. 2010 Dec;92(12):1827-31. Epub 2010 Aug 5. PubMed PMID: 20691751.

  6. Myakishev M, Polesskaya O, Kulichkova V, Baranova A, Gause L, Konstantinova I. PCR-based detection of Pol III-transcribed transposons and its application to the rodent model of ultraviolet response. Cell Stress Chaperones. 2008 Spring;13(1):111-6.

  7. A.A. Guskova, A.V. Zagurny, M. Skoblov, A. Baranova, V. Andronova, N.Yankovsky, G.Galegov, Yu. Skoblov. Molecular analysis of HPV type I thymidine kinase. 2006 Mol Biol (Mosk). Jan-Feb;39(1):155-8.
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