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Items: 1 to 50 of 146

1.

Pisces: an accurate and versatile variant caller for somatic and germline next-generation sequencing data.

Dunn T, Berry G, Emig-Agius D, Jiang Y, Lei S, Iyer A, Udar N, Chuang HY, Hegarty J, Dickover M, Klotzle B, Robbins J, Bibikova M, Peeters M, Strömberg M.

Bioinformatics. 2019 May 1;35(9):1579-1581. doi: 10.1093/bioinformatics/bty849.

2.

Targeted methylation sequencing of plasma cell-free DNA for cancer detection and classification.

Liu L, Toung JM, Jassowicz AF, Vijayaraghavan R, Kang H, Zhang R, Kruglyak KM, Huang HJ, Hinoue T, Shen H, Salathia NS, Hong DS, Naing A, Subbiah V, Piha-Paul SA, Bibikova M, Granger G, Barnes B, Shen R, Gutekunst K, Fu S, Tsimberidou AM, Lu C, Eng C, Moulder SL, Kopetz ES, Amaria RN, Meric-Bernstam F, Laird PW, Fan JB, Janku F.

Ann Oncol. 2018 Jun 1;29(6):1445-1453. doi: 10.1093/annonc/mdy119.

3.

PTEN loss is associated with prostate cancer recurrence and alterations in tumor DNA methylation profiles.

Geybels MS, Fang M, Wright JL, Qu X, Bibikova M, Klotzle B, Fan JB, Feng Z, Ostrander EA, Nelson PS, Stanford JL.

Oncotarget. 2017 Sep 15;8(48):84338-84348. doi: 10.18632/oncotarget.20940. eCollection 2017 Oct 13.

4.

Lipoxygenase Inhibitors Nordihydroguaiaretic Acid and Fungus Lecanicillum lecanii Extract Induce Death of Lymphoid Leukemia Cells.

Bibikova MV, Spiridonova NA, Korystova AF, Kublik LN, Levitman MK, Shaposhnikova VV, Korystov YN.

Bull Exp Biol Med. 2017 Jul;163(3):330-333. doi: 10.1007/s10517-017-3796-9. Epub 2017 Jul 26.

PMID:
28744653
5.

Gene expression signature of Gleason score is associated with prostate cancer outcomes in a radical prostatectomy cohort.

Jhun MA, Geybels MS, Wright JL, Kolb S, April C, Bibikova M, Ostrander EA, Fan JB, Feng Z, Stanford JL.

Oncotarget. 2017 Jun 27;8(26):43035-43047. doi: 10.18632/oncotarget.17428.

6.

Gene expression panel predicts metastatic-lethal prostate cancer outcomes in men diagnosed with clinically localized prostate cancer.

Rubicz R, Zhao S, Wright JL, Coleman I, Grasso C, Geybels MS, Leonardson A, Kolb S, April C, Bibikova M, Troyer D, Lance R, Lin DW, Ostrander EA, Nelson PS, Fan JB, Feng Z, Stanford JL.

Mol Oncol. 2017 Feb;11(2):140-150. doi: 10.1002/1878-0261.12014. Epub 2016 Oct 19.

7.

Epigenetic signature of Gleason score and prostate cancer recurrence after radical prostatectomy.

Geybels MS, Wright JL, Bibikova M, Klotzle B, Fan JB, Zhao S, Feng Z, Ostrander EA, Lin DW, Nelson PS, Stanford JL.

Clin Epigenetics. 2016 Sep 15;8:97. doi: 10.1186/s13148-016-0260-z. eCollection 2016.

8.

[Apoptotic endonuclease EndoG induces alternative splicing of telomerase catalytic subunit hTERT and death of tumor cells].

Zhdanov DD, Vasina DA, Orlova VS, Gotovtseva VY, Bibikova MV, Pokrovsky VS, Pokrovskaya MV, Aleksandrova SS, Sokolov NN.

Biomed Khim. 2016 Mar;62(3):239-50. doi: 10.18097/PBMC20166203239. Russian.

PMID:
27420614
9.

Epigenome-Wide Tumor DNA Methylation Profiling Identifies Novel Prognostic Biomarkers of Metastatic-Lethal Progression in Men Diagnosed with Clinically Localized Prostate Cancer.

Zhao S, Geybels MS, Leonardson A, Rubicz R, Kolb S, Yan Q, Klotzle B, Bibikova M, Hurtado-Coll A, Troyer D, Lance R, Lin DW, Wright JL, Ostrander EA, Fan JB, Feng Z, Stanford JL.

Clin Cancer Res. 2017 Jan 1;23(1):311-319. doi: 10.1158/1078-0432.CCR-16-0549. Epub 2016 Jun 29.

10.

Prostate tumor DNA methylation is associated with cigarette smoking and adverse prostate cancer outcomes.

Shui IM, Wong CJ, Zhao S, Kolb S, Ebot EM, Geybels MS, Rubicz R, Wright JL, Lin DW, Klotzle B, Bibikova M, Fan JB, Ostrander EA, Feng Z, Stanford JL.

Cancer. 2016 Jul 15;122(14):2168-77. doi: 10.1002/cncr.30045. Epub 2016 May 3.

11.

DNA methylation profiles in African American prostate cancer patients in relation to disease progression.

Rubicz R, Zhao S, Geybels M, Wright JL, Kolb S, Klotzle B, Bibikova M, Troyer D, Lance R, Ostrander EA, Feng Z, Fan JB, Stanford JL.

Genomics. 2019 Jan;111(1):10-16. doi: 10.1016/j.ygeno.2016.02.004. Epub 2016 Feb 21.

PMID:
26902887
12.

[Screening of Organisms Producing Inhibitors of 15-Lipoxygenase Among Micromycetes.]

Bibikova MV, Spiridonova IA, Danilenko AN, Kim YA, Korystova AF, Shaposhnikova VV, Korystov YN.

Antibiot Khimioter. 2016;61(7-8):3-9. Russian.

PMID:
29533554
13.

Epigenomic profiling of prostate cancer identifies differentially methylated genes in TMPRSS2:ERG fusion-positive versus fusion-negative tumors.

Geybels MS, Alumkal JJ, Luedeke M, Rinckleb A, Zhao S, Shui IM, Bibikova M, Klotzle B, van den Brandt PA, Ostrander EA, Fan JB, Feng Z, Maier C, Stanford JL.

Clin Epigenetics. 2015 Dec 12;7:128. doi: 10.1186/s13148-015-0161-6. eCollection 2015.

14.

Substantial DNA methylation differences between two major neuronal subtypes in human brain.

Kozlenkov A, Wang M, Roussos P, Rudchenko S, Barbu M, Bibikova M, Klotzle B, Dwork AJ, Zhang B, Hurd YL, Koonin EV, Wegner M, Dracheva S.

Nucleic Acids Res. 2016 Apr 7;44(6):2593-612. doi: 10.1093/nar/gkv1304. Epub 2015 Nov 26.

15.

Epigenomic profiling of DNA methylation in paired prostate cancer versus adjacent benign tissue.

Geybels MS, Zhao S, Wong CJ, Bibikova M, Klotzle B, Wu M, Ostrander EA, Fan JB, Feng Z, Stanford JL.

Prostate. 2015 Dec;75(16):1941-50. doi: 10.1002/pros.23093. Epub 2015 Sep 18.

16.

Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics.

Munchel S, Hoang Y, Zhao Y, Cottrell J, Klotzle B, Godwin AK, Koestler D, Beyerlein P, Fan JB, Bibikova M, Chien J.

Oncotarget. 2015 Sep 22;6(28):25943-61. doi: 10.18632/oncotarget.4671.

17.

DNA methylation fingerprint of neuroblastoma reveals new biological and clinical insights.

Gómez S, Castellano G, Mayol G, Suñol M, Queiros A, Bibikova M, Nazor KL, Loring JF, Lemos I, Rodríguez E, de Torres C, Mora J, Martín-Subero JI, Lavarino C.

Epigenomics. 2015 Oct;7(7):1137-53. doi: 10.2217/epi.15.49. Epub 2015 Jun 12.

18.

TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer.

Chien J, Sicotte H, Fan JB, Humphray S, Cunningham JM, Kalli KR, Oberg AL, Hart SN, Li Y, Davila JI, Baheti S, Wang C, Dietmann S, Atkinson EJ, Asmann YW, Bell DA, Ota T, Tarabishy Y, Kuang R, Bibikova M, Cheetham RK, Grocock RJ, Swisher EM, Peden J, Bentley D, Kocher JP, Kaufmann SH, Hartmann LC, Shridhar V, Goode EL.

Nucleic Acids Res. 2015 Aug 18;43(14):6945-58. doi: 10.1093/nar/gkv111. Epub 2015 Apr 27.

19.

[Change of Tumor Cell Multiple Drug Resistance Inhibitory Activity of Oligomycins in Complexes with Lithium and Zinc].

Bibikova MV, Danilenko AN, Katlinsky AV, Korystova AF, Kublik LN, Levitman MKh, Shaposhnikova VV, Korystov YN.

Antibiot Khimioter. 2015;60(11-12):9-14. Russian.

PMID:
27141641
20.

[Determination of oligomycins hydrophobicity parameters].

Danilenko AN, Bibikova MV, Spiridonova IA.

Antibiot Khimioter. 2014;59(3-4):3-6. Russian.

PMID:
25300113
21.

Application of a low cost array-based technique - TAB-Array - for quantifying and mapping both 5mC and 5hmC at single base resolution in human pluripotent stem cells.

Nazor KL, Boland MJ, Bibikova M, Klotzle B, Yu M, Glenn-Pratola VL, Schell JP, Coleman RL, Cabral-da-Silva MC, Schmidt U, Peterson SE, He C, Loring JF, Fan JB.

Genomics. 2014 Nov;104(5):358-67. doi: 10.1016/j.ygeno.2014.08.014. Epub 2014 Aug 29.

22.

Tumor hypomethylation at 6p21.3 associates with longer time to recurrence of high-grade serous epithelial ovarian cancer.

Wang C, Cicek MS, Charbonneau B, Kalli KR, Armasu SM, Larson MC, Konecny GE, Winterhoff B, Fan JB, Bibikova M, Chien J, Shridhar V, Block MS, Hartmann LC, Visscher DW, Cunningham JM, Knutson KL, Fridley BL, Goode EL.

Cancer Res. 2014 Jun 1;74(11):3084-91. doi: 10.1158/0008-5472.CAN-13-3198. Epub 2014 Apr 11.

23.

Validation study of genes with hypermethylated promoter regions associated with prostate cancer recurrence.

Stott-Miller M, Zhao S, Wright JL, Kolb S, Bibikova M, Klotzle B, Ostrander EA, Fan JB, Feng Z, Stanford JL.

Cancer Epidemiol Biomarkers Prev. 2014 Jul;23(7):1331-9. doi: 10.1158/1055-9965.EPI-13-1000. Epub 2014 Apr 9.

24.

A panel of CpG methylation sites distinguishes human embryonic stem cells and induced pluripotent stem cells.

Huang K, Shen Y, Xue Z, Bibikova M, April C, Liu Z, Cheng L, Nagy A, Pellegrini M, Fan JB, Fan G.

Stem Cell Reports. 2013 Dec 26;2(1):36-43. doi: 10.1016/j.stemcr.2013.11.003. eCollection 2014 Jan 14.

25.

Clinical characteristics of ovarian cancer classified by BRCA1, BRCA2, and RAD51C status.

Cunningham JM, Cicek MS, Larson NB, Davila J, Wang C, Larson MC, Song H, Dicks EM, Harrington P, Wick M, Winterhoff BJ, Hamidi H, Konecny GE, Chien J, Bibikova M, Fan JB, Kalli KR, Lindor NM, Fridley BL, Pharoah PP, Goode EL.

Sci Rep. 2014 Feb 7;4:4026. doi: 10.1038/srep04026.

26.

APOBEC3B upregulation and genomic mutation patterns in serous ovarian carcinoma.

Leonard B, Hart SN, Burns MB, Carpenter MA, Temiz NA, Rathore A, Vogel RI, Nikas JB, Law EK, Brown WL, Li Y, Zhang Y, Maurer MJ, Oberg AL, Cunningham JM, Shridhar V, Bell DA, April C, Bentley D, Bibikova M, Cheetham RK, Fan JB, Grocock R, Humphray S, Kingsbury Z, Peden J, Chien J, Swisher EM, Hartmann LC, Kalli KR, Goode EL, Sicotte H, Kaufmann SH, Harris RS.

Cancer Res. 2013 Dec 15;73(24):7222-31. doi: 10.1158/0008-5472.CAN-13-1753. Epub 2013 Oct 23.

27.

Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites.

Kozlenkov A, Roussos P, Timashpolsky A, Barbu M, Rudchenko S, Bibikova M, Klotzle B, Byne W, Lyddon R, Di Narzo AF, Hurd YL, Koonin EV, Dracheva S.

Nucleic Acids Res. 2014 Jan;42(1):109-27. doi: 10.1093/nar/gkt838. Epub 2013 Sep 20.

28.

Epigenome-wide ovarian cancer analysis identifies a methylation profile differentiating clear-cell histology with epigenetic silencing of the HERG K+ channel.

Cicek MS, Koestler DC, Fridley BL, Kalli KR, Armasu SM, Larson MC, Wang C, Winham SJ, Vierkant RA, Rider DN, Block MS, Klotzle B, Konecny G, Winterhoff BJ, Hamidi H, Shridhar V, Fan JB, Visscher DW, Olson JE, Hartmann LC, Bibikova M, Chien J, Cunningham JM, Goode EL.

Hum Mol Genet. 2013 Aug 1;22(15):3038-47. doi: 10.1093/hmg/ddt160. Epub 2013 Apr 9.

29.

Succinate dehydrogenase mutation underlies global epigenomic divergence in gastrointestinal stromal tumor.

Killian JK, Kim SY, Miettinen M, Smith C, Merino M, Tsokos M, Quezado M, Smith WI Jr, Jahromi MS, Xekouki P, Szarek E, Walker RL, Lasota J, Raffeld M, Klotzle B, Wang Z, Jones L, Zhu Y, Wang Y, Waterfall JJ, O'Sullivan MJ, Bibikova M, Pacak K, Stratakis C, Janeway KA, Schiffman JD, Fan JB, Helman L, Meltzer PS.

Cancer Discov. 2013 Jun;3(6):648-57. doi: 10.1158/2159-8290.CD-13-0092. Epub 2013 Apr 2.

30.

Whole-genome haplotyping by dilution, amplification, and sequencing.

Kaper F, Swamy S, Klotzle B, Munchel S, Cottrell J, Bibikova M, Chuang HY, Kruglyak S, Ronaghi M, Eberle MA, Fan JB.

Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5552-7. doi: 10.1073/pnas.1218696110. Epub 2013 Mar 18.

31.

[Streptomyces sp. 17, an organism producing oligomycin SC-iI (culture characteristics and antibiotic biological properties)].

Bibikova MV, Grammatikova NE, Spiridonova IA, Danilenko AN, Katlinskiĭ AV.

Antibiot Khimioter. 2012;57(7-8):3-6. Russian.

PMID:
23350188
32.

Genome-wide methylation profiles reveal quantitative views of human aging rates.

Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, Klotzle B, Bibikova M, Fan JB, Gao Y, Deconde R, Chen M, Rajapakse I, Friend S, Ideker T, Zhang K.

Mol Cell. 2013 Jan 24;49(2):359-367. doi: 10.1016/j.molcel.2012.10.016. Epub 2012 Nov 21.

33.

Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia.

Kulis M, Heath S, Bibikova M, Queirós AC, Navarro A, Clot G, Martínez-Trillos A, Castellano G, Brun-Heath I, Pinyol M, Barberán-Soler S, Papasaikas P, Jares P, Beà S, Rico D, Ecker S, Rubio M, Royo R, Ho V, Klotzle B, Hernández L, Conde L, López-Guerra M, Colomer D, Villamor N, Aymerich M, Rozman M, Bayes M, Gut M, Gelpí JL, Orozco M, Fan JB, Quesada V, Puente XS, Pisano DG, Valencia A, López-Guillermo A, Gut I, López-Otín C, Campo E, Martín-Subero JI.

Nat Genet. 2012 Nov;44(11):1236-42. doi: 10.1038/ng.2443. Epub 2012 Oct 14.

PMID:
23064414
34.

[The influence of compound aITEL1296 on telomerase activity and the growth of cancer cells].

Kovalenko NA, Zhdanov DD, Bibikova MV, Gotovtseva VIu.

Biomed Khim. 2011 Sep-Oct;57(5):501-10. Russian.

PMID:
22629600
35.

[Influence of natural complex compounds with hipolipidemic activity on expression of bacteria virulence factors].

Gotovtseva VIu, Grammatikova NÉ, Bibikova MV, Katlinskiĭ AV.

Antibiot Khimioter. 2011;56(7-8):3-6. Russian.

PMID:
22359861
36.

Highly parallel genome-wide expression analysis of single mammalian cells.

Fan JB, Chen J, April CS, Fisher JS, Klotzle B, Bibikova M, Kaper F, Ronaghi M, Linnarsson S, Ota T, Chien J, Laurent LC, Loring JF, Nisperos SV, Chen GY, Zhong JF.

PLoS One. 2012;7(2):e30794. doi: 10.1371/journal.pone.0030794. Epub 2012 Feb 8. Erratum in: PLoS One. 2012;7(2). doi: 10.1371/annotation/3f0ddf41-2e7a-4b56-93c2-2731f2890b19. Loring, Jeanne F [added].

37.

[Physico-chemical properties and structure of oligomycin SC-II, produced by Streptomyces virginiae 17].

Danilenko AN, Bibikova MV, Spiridonova IA, Grammatikova NE, Katlinskiĭ AV.

Antibiot Khimioter. 2012;57(11-12):3-7. Russian.

PMID:
23700929
38.

High density DNA methylation array with single CpG site resolution.

Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, Delano D, Zhang L, Schroth GP, Gunderson KL, Fan JB, Shen R.

Genomics. 2011 Oct;98(4):288-95. doi: 10.1016/j.ygeno.2011.07.007. Epub 2011 Aug 2.

39.

Array-based DNA methylation analysis in classical Hodgkin lymphoma reveals new insights into the mechanisms underlying silencing of B cell-specific genes.

Ammerpohl O, Haake A, Pellissery S, Giefing M, Richter J, Balint B, Kulis M, Le J, Bibikova M, Drexler HG, Seifert M, Shaknovic R, Korn B, Küppers R, Martín-Subero JI, Siebert R.

Leukemia. 2012 Jan;26(1):185-8. doi: 10.1038/leu.2011.194. Epub 2011 Aug 5. No abstract available.

PMID:
21818115
40.

A methyl-deviator epigenotype of estrogen receptor-positive breast carcinoma is associated with malignant biology.

Killian JK, Bilke S, Davis S, Walker RL, Jaeger E, Killian MS, Waterfall JJ, Bibikova M, Fan JB, Smith WI Jr, Meltzer PS.

Am J Pathol. 2011 Jul;179(1):55-65. doi: 10.1016/j.ajpath.2011.03.022. Epub 2011 May 13.

41.

Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome.

Sandoval J, Heyn H, Moran S, Serra-Musach J, Pujana MA, Bibikova M, Esteller M.

Epigenetics. 2011 Jun;6(6):692-702. Epub 2011 Jun 1.

PMID:
21593595
42.

Genome-wide DNA methylation profiling.

Bibikova M, Fan JB.

Wiley Interdiscip Rev Syst Biol Med. 2010 Mar-Apr;2(2):210-223. doi: 10.1002/wsbm.35. Review.

PMID:
20836023
43.

[Hyphomycetes as organisms producing cyclodepsipeptides].

Bibikova MV, Puzhevskaia TO, Katlinskiĭ AV.

Antibiot Khimioter. 2010;55(3-4):35-44. Review. Russian.

PMID:
20695207
44.

Identification and functional relevance of de novo DNA methylation in cancerous B-cell populations.

Wang XM, Greiner TC, Bibikova M, Pike BL, Siegmund KD, Sinha UK, Müschen M, Jaeger EB, Weisenburger DD, Chan WC, Shibata D, Fan JB, Hacia JG.

J Cell Biochem. 2010 Mar 1;109(4):818-27. doi: 10.1002/jcb.22461.

45.

[Production of destruxins by coprotrophic Beauveria feline no. 7 strain].

Bibikova MV, Puzhevskaya TO, Danilenko AN, Spiridonova IA, Zatonsky GV, Alexandrova AV, Katlinsky AV.

Antibiot Khimioter. 2010;55(11-12):11-6. Russian.

PMID:
21574419
46.

Array-based DNA methylation profiling of primary lymphomas of the central nervous system.

Richter J, Ammerpohl O, Martín-Subero JI, Montesinos-Rongen M, Bibikova M, Wickham-Garcia E, Wiestler OD, Deckert M, Siebert R.

BMC Cancer. 2009 Dec 21;9:455. doi: 10.1186/1471-2407-9-455.

47.

Genome-wide DNA methylation profiling using Infinium® assay.

Bibikova M, Le J, Barnes B, Saedinia-Melnyk S, Zhou L, Shen R, Gunderson KL.

Epigenomics. 2009 Oct;1(1):177-200. doi: 10.2217/epi.09.14.

48.

A comprehensive microarray-based DNA methylation study of 367 hematological neoplasms.

Martin-Subero JI, Ammerpohl O, Bibikova M, Wickham-Garcia E, Agirre X, Alvarez S, Brüggemann M, Bug S, Calasanz MJ, Deckert M, Dreyling M, Du MQ, Dürig J, Dyer MJ, Fan JB, Gesk S, Hansmann ML, Harder L, Hartmann S, Klapper W, Küppers R, Montesinos-Rongen M, Nagel I, Pott C, Richter J, Román-Gómez J, Seifert M, Stein H, Suela J, Trümper L, Vater I, Prosper F, Haferlach C, Cruz Cigudosa J, Siebert R.

PLoS One. 2009 Sep 11;4(9):e6986. doi: 10.1371/journal.pone.0006986.

49.

DNA methylation and gene expression differences in children conceived in vitro or in vivo.

Katari S, Turan N, Bibikova M, Erinle O, Chalian R, Foster M, Gaughan JP, Coutifaris C, Sapienza C.

Hum Mol Genet. 2009 Oct 15;18(20):3769-78. doi: 10.1093/hmg/ddp319. Epub 2009 Jul 15.

50.

[Influence of natural hypolipidemic compounds on biofilm formation by Pseudomonas strains].

Puzhevskaia TO, Bibikova MV, Grammatikova NE, Mikhaĭlova NA, Katlinskiĭ AV.

Antibiot Khimioter. 2009;54(1-2):10-3. Russian.

PMID:
19499710

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