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Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API.

Desvignes T, Loher P, Eilbeck K, Ma J, Urgese G, Fromm B, Sydes J, Aparicio-Puerta E, Barrera V, Espín R, Thibord F, Ros XB, Londin E, Telonis AG, Ficarra E, Friedländer MR, Postlethwait JH, Rigoutsos I, Hackenberg M, Vlachos IS, Halushka MK, Pantano L.

Bioinformatics. 2019 Aug 29. pii: btz675. doi: 10.1093/bioinformatics/btz675. [Epub ahead of print]


TRNA-derived fragments as sex-dependent circulating candidate biomarkers for Parkinson's disease.

Magee R, Londin E, Rigoutsos I.

Parkinsonism Relat Disord. 2019 May 25. pii: S1353-8020(19)30256-1. doi: 10.1016/j.parkreldis.2019.05.035. [Epub ahead of print]


Short RNA regulators: the past, the present, the future, and implications for precision medicine and health disparities.

Rigoutsos I, Londin E, Kirino Y.

Curr Opin Biotechnol. 2019 Aug;58:202-210. doi: 10.1016/j.copbio.2019.05.014. Epub 2019 Jul 16. Review.


IsomiRs and tRNA-derived fragments are associated with metastasis and patient survival in uveal melanoma.

Londin E, Magee R, Shields CL, Lally SE, Sato T, Rigoutsos I.

Pigment Cell Melanoma Res. 2019 Jul 8. doi: 10.1111/pcmr.12810. [Epub ahead of print]


The Sustained Induction of c-MYC Drives Nab-Paclitaxel Resistance in Primary Pancreatic Ductal Carcinoma Cells.

Parasido E, Avetian GS, Naeem A, Graham G, Pishvaian M, Glasgow E, Mudambi S, Lee Y, Ihemelandu C, Choudhry M, Peran I, Banerjee PP, Avantaggiati ML, Bryant K, Baldelli E, Pierobon M, Liotta L, Petricoin E, Fricke ST, Sebastian A, Cozzitorto J, Loots GG, Kumar D, Byers S, Londin E, DiFeo A, Narla G, Winter J, Brody JR, Rodriguez O, Albanese C.

Mol Cancer Res. 2019 Sep;17(9):1815-1827. doi: 10.1158/1541-7786.MCR-19-0191. Epub 2019 Jun 4.


tRNA Fragments Show Intertwining with mRNAs of Specific Repeat Content and Have Links to Disparities.

Telonis AG, Loher P, Magee R, Pliatsika V, Londin E, Kirino Y, Rigoutsos I.

Cancer Res. 2019 Jun 15;79(12):3034-3049. doi: 10.1158/0008-5472.CAN-19-0789. Epub 2019 Apr 17.


Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation.

Srinivasan S, Yeri A, Cheah PS, Chung A, Danielson K, De Hoff P, Filant J, Laurent CD, Laurent LD, Magee R, Moeller C, Murthy VL, Nejad P, Paul A, Rigoutsos I, Rodosthenous R, Shah RV, Simonson B, To C, Wong D, Yan IK, Zhang X, Balaj L, Breakefield XO, Daaboul G, Gandhi R, Lapidus J, Londin E, Patel T, Raffai RL, Sood AK, Alexander RP, Das S, Laurent LC.

Cell. 2019 Apr 4;177(2):446-462.e16. doi: 10.1016/j.cell.2019.03.024.


Single-Cell Genomics.

Paolillo C, Londin E, Fortina P.

Clin Chem. 2019 Aug;65(8):972-985. doi: 10.1373/clinchem.2017.283895. Epub 2019 Mar 14. Review.


Autosomal recessive congenital ichthyosis: Genomic landscape and phenotypic spectrum in a cohort of 125 consanguineous families.

Youssefian L, Vahidnezhad H, Saeidian AH, Touati A, Sotoudeh S, Mahmoudi H, Mansouri P, Daneshpazhooh M, Aghazadeh N, Hesari KK, Basiri M, Londin E, Kumar G, Zeinali S, Fortina P, Uitto J.

Hum Mutat. 2019 Mar;40(3):288-298. doi: 10.1002/humu.23695. Epub 2019 Jan 16.


Murine MPDZ-linked hydrocephalus is caused by hyperpermeability of the choroid plexus.

Yang J, Simonneau C, Kilker R, Oakley L, Byrne MD, Nichtova Z, Stefanescu I, Pardeep-Kumar F, Tripathi S, Londin E, Saugier-Veber P, Willard B, Thakur M, Pickup S, Ishikawa H, Schroten H, Smeyne R, Horowitz A.

EMBO Mol Med. 2019 Jan;11(1). pii: e9540. doi: 10.15252/emmm.201809540.


Evaluation of Post-transcriptional Gene Regulation in Pancreatic Cancer Cells: Studying RNA Binding Proteins and Their mRNA Targets.

Jain A, Brown SZ, Thomsett HL, Londin E, Brody JR.

Methods Mol Biol. 2019;1882:239-252. doi: 10.1007/978-1-4939-8879-2_22. Review.


Host IDO2 Gene Status Influences Tumor Progression and Radiotherapy Response in KRAS-Driven Sporadic Pancreatic Cancers.

Nevler A, Muller AJ, Sutanto-Ward E, DuHadaway JB, Nagatomo K, Londin E, O'Hayer K, Cozzitorto JA, Lavu H, Yeo TP, Curtis M, Villatoro T, Leiby BE, Mandik-Nayak L, Winter JM, Yeo CJ, Prendergast GC, Brody JR.

Clin Cancer Res. 2019 Jan 15;25(2):724-734. doi: 10.1158/1078-0432.CCR-18-0814. Epub 2018 Sep 28.


Profiles of miRNA Isoforms and tRNA Fragments in Prostate Cancer.

Magee RG, Telonis AG, Loher P, Londin E, Rigoutsos I.

Sci Rep. 2018 Mar 28;8(1):5314. doi: 10.1038/s41598-018-22488-2.


Whole exome sequencing identifies a germline MET mutation in two siblings with hereditary wild-type RET medullary thyroid cancer.

Sponziello M, Benvenuti S, Gentile A, Pecce V, Rosignolo F, Virzì AR, Milan M, Comoglio PM, Londin E, Fortina P, Barnabei A, Appetecchia M, Marandino F, Russo D, Filetti S, Durante C, Verrienti A.

Hum Mutat. 2018 Mar;39(3):371-377. doi: 10.1002/humu.23378. Epub 2017 Dec 20.


MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects.

Pliatsika V, Loher P, Magee R, Telonis AG, Londin E, Shigematsu M, Kirino Y, Rigoutsos I.

Nucleic Acids Res. 2018 Jan 4;46(D1):D152-D159. doi: 10.1093/nar/gkx1075.


Recessive mutation in tetraspanin CD151 causes Kindler syndrome-like epidermolysis bullosa with multi-systemic manifestations including nephropathy.

Vahidnezhad H, Youssefian L, Saeidian AH, Mahmoudi H, Touati A, Abiri M, Kajbafzadeh AM, Aristodemou S, Liu L, McGrath JA, Ertel A, Londin E, Kariminejad A, Zeinali S, Fortina P, Uitto J.

Matrix Biol. 2018 Mar;66:22-33. doi: 10.1016/j.matbio.2017.11.003. Epub 2017 Nov 11.


Assessment of isomiR Discrimination Using Commercial qPCR Methods.

Magee R, Telonis AG, Cherlin T, Rigoutsos I, Londin E.

Noncoding RNA. 2017 Jun;3(2). pii: 18. doi: 10.3390/ncrna3020018. Epub 2017 Mar 24.


Posttranscriptional Regulation of PARG mRNA by HuR Facilitates DNA Repair and Resistance to PARP Inhibitors.

Chand SN, Zarei M, Schiewer MJ, Kamath AR, Romeo C, Lal S, Cozzitorto JA, Nevler A, Scolaro L, Londin E, Jiang W, Meisner-Kober N, Pishvaian MJ, Knudsen KE, Yeo CJ, Pascal JM, Winter JM, Brody JR.

Cancer Res. 2017 Sep 15;77(18):5011-5025. doi: 10.1158/0008-5472.CAN-16-2704. Epub 2017 Jul 7.


Posttranscriptional Upregulation of IDH1 by HuR Establishes a Powerful Survival Phenotype in Pancreatic Cancer Cells.

Zarei M, Lal S, Parker SJ, Nevler A, Vaziri-Gohar A, Dukleska K, Mambelli-Lisboa NC, Moffat C, Blanco FF, Chand SN, Jimbo M, Cozzitorto JA, Jiang W, Yeo CJ, Londin ER, Seifert EL, Metallo CM, Brody JR, Winter JM.

Cancer Res. 2017 Aug 15;77(16):4460-4471. doi: 10.1158/0008-5472.CAN-17-0015. Epub 2017 Jun 26.


CRISPR Knockout of the HuR Gene Causes a Xenograft Lethal Phenotype.

Lal S, Cheung EC, Zarei M, Preet R, Chand SN, Mambelli-Lisboa NC, Romeo C, Stout MC, Londin E, Goetz A, Lowder CY, Nevler A, Yeo CJ, Campbell PM, Winter JM, Dixon DA, Brody JR.

Mol Cancer Res. 2017 Jun;15(6):696-707. doi: 10.1158/1541-7786.MCR-16-0361. Epub 2017 Feb 27.


Knowledge about the presence or absence of miRNA isoforms (isomiRs) can successfully discriminate amongst 32 TCGA cancer types.

Telonis AG, Magee R, Loher P, Chervoneva I, Londin E, Rigoutsos I.

Nucleic Acids Res. 2017 Apr 7;45(6):2973-2985. doi: 10.1093/nar/gkx082.


Threshold-seq: a tool for determining the threshold in short RNA-seq datasets.

Magee R, Loher P, Londin E, Rigoutsos I.

Bioinformatics. 2017 Jul 1;33(13):2034-2036. doi: 10.1093/bioinformatics/btx073.


Post-transcriptional Regulation of BRCA2 through Interactions with miR-19a and miR-19b.

Mogilyansky E, Clark P, Quann K, Zhou H, Londin E, Jing Y, Rigoutsos I.

Front Genet. 2016 Aug 31;7:143. doi: 10.3389/fgene.2016.00143. eCollection 2016.


Next generation sequencing in cancer: opportunities and challenges for precision cancer medicine.

Paolillo C, Londin E, Fortina P.

Scand J Clin Lab Invest Suppl. 2016;245:S84-91. doi: 10.1080/00365513.2016.1210331. Epub 2016 Aug 17.


GPRC5A is a potential oncogene in pancreatic ductal adenocarcinoma cells that is upregulated by gemcitabine with help from HuR.

Zhou H, Telonis AG, Jing Y, Xia NL, Biederman L, Jimbo M, Blanco F, Londin E, Brody JR, Rigoutsos I.

Cell Death Dis. 2016 Jul 14;7:e2294. doi: 10.1038/cddis.2016.169.


High Concentration Capture Probes Enhance Massively Parallel Sequencing Assays.

Farooqi MS, Mitui M, Londin ER, Park JY.

Clin Chem. 2016 Jul;62(7):1032-4. doi: 10.1373/clinchem.2016.255026. Epub 2016 May 23. No abstract available.


What is translational bioinformatics?

Londin ER, Barash CI.

Appl Transl Genom. 2015 Aug 28;6:1-2. doi: 10.1016/j.atg.2015.08.003. eCollection 2015 Sep. No abstract available.


Beyond the one-locus-one-miRNA paradigm: microRNA isoforms enable deeper insights into breast cancer heterogeneity.

Telonis AG, Loher P, Jing Y, Londin E, Rigoutsos I.

Nucleic Acids Res. 2015 Oct 30;43(19):9158-75. doi: 10.1093/nar/gkv922. Epub 2015 Sep 22.


The mRNA-binding protein HuR promotes hypoxia-induced chemoresistance through posttranscriptional regulation of the proto-oncogene PIM1 in pancreatic cancer cells.

Blanco FF, Jimbo M, Wulfkuhle J, Gallagher I, Deng J, Enyenihi L, Meisner-Kober N, Londin E, Rigoutsos I, Sawicki JA, Risbud MV, Witkiewicz AK, McCue PA, Jiang W, Rui H, Yeo CJ, Petricoin E, Winter JM, Brody JR.

Oncogene. 2016 May;35(19):2529-41. doi: 10.1038/onc.2015.325. Epub 2015 Sep 21.


Reply to Backes and Keller: Identification of novel tissue-specific and primate-specific human microRNAs.

Londin E, Loher P, Rigoutsos I.

Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):E2851. doi: 10.1073/pnas.1505397112. Epub 2015 May 15. No abstract available.


Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs.

Londin E, Loher P, Telonis AG, Quann K, Clark P, Jing Y, Hatzimichael E, Kirino Y, Honda S, Lally M, Ramratnam B, Comstock CE, Knudsen KE, Gomella L, Spaeth GL, Hark L, Katz LJ, Witkiewicz A, Rostami A, Jimenez SA, Hollingsworth MA, Yeh JJ, Shaw CA, McKenzie SE, Bray P, Nelson PT, Zupo S, Van Roosbroeck K, Keating MJ, Calin GA, Yeo C, Jimbo M, Cozzitorto J, Brody JR, Delgrosso K, Mattick JS, Fortina P, Rigoutsos I.

Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):E1106-15. doi: 10.1073/pnas.1420955112. Epub 2015 Feb 23.


Clinical exome performance for reporting secondary genetic findings.

Park JY, Clark P, Londin E, Sponziello M, Kricka LJ, Fortina P.

Clin Chem. 2015 Jan;61(1):213-20. doi: 10.1373/clinchem.2014.231456. Epub 2014 Nov 20.


Clinical genomics: when whole genome sequencing is like a whole-body CT scan.

Park JY, Kricka LJ, Clark P, Londin E, Fortina P.

Clin Chem. 2014 Nov;60(11):1390-2. doi: 10.1373/clinchem.2014.230276. Epub 2014 Aug 11. No abstract available.


Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types.

Clark PM, Loher P, Quann K, Brody J, Londin ER, Rigoutsos I.

Sci Rep. 2014 Aug 8;4:5947. doi: 10.1038/srep05947.


Donor splice-site mutation in CUL4B is likely cause of X-linked intellectual disability.

Londin ER, Adijanto J, Philp N, Novelli A, Vitale E, Perria C, Serra G, Alesi V, Surrey S, Fortina P.

Am J Med Genet A. 2014 Sep;164A(9):2294-9. doi: 10.1002/ajmg.a.36629. Epub 2014 Jun 4.


HuR posttranscriptionally regulates WEE1: implications for the DNA damage response in pancreatic cancer cells.

Lal S, Burkhart RA, Beeharry N, Bhattacharjee V, Londin ER, Cozzitorto JA, Romeo C, Jimbo M, Norris ZA, Yeo CJ, Sawicki JA, Winter JM, Rigoutsos I, Yen TJ, Brody JR.

Cancer Res. 2014 Feb 15;74(4):1128-40. doi: 10.1158/0008-5472.CAN-13-1915.


The human platelet: strong transcriptome correlations among individuals associate weakly with the platelet proteome.

Londin ER, Hatzimichael E, Loher P, Edelstein L, Shaw C, Delgrosso K, Fortina P, Bray PF, McKenzie SE, Rigoutsos I.

Biol Direct. 2014 Feb 14;9:3. doi: 10.1186/1745-6150-9-3.


Performance of exome sequencing for pharmacogenomics.

Londin ER, Clark P, Sponziello M, Kricka LJ, Fortina P, Park JY.

Per Med. 2014;12(2):109-115.


Use of linkage analysis, genome-wide association studies, and next-generation sequencing in the identification of disease-causing mutations.

Londin E, Yadav P, Surrey S, Kricka LJ, Fortina P.

Methods Mol Biol. 2013;1015:127-46. doi: 10.1007/978-1-62703-435-7_8.


HuR is a post-transcriptional regulator of core metabolic enzymes in pancreatic cancer.

Burkhart RA, Pineda DM, Chand SN, Romeo C, Londin ER, Karoly ED, Cozzitorto JA, Rigoutsos I, Yeo CJ, Brody JR, Winter JM.

RNA Biol. 2013 Aug;10(8):1312-23. doi: 10.4161/rna.25274. Epub 2013 Jun 13.


The complex transcriptional landscape of the anucleate human platelet.

Bray PF, McKenzie SE, Edelstein LC, Nagalla S, Delgrosso K, Ertel A, Kupper J, Jing Y, Londin E, Loher P, Chen HW, Fortina P, Rigoutsos I.

BMC Genomics. 2013 Jan 16;14:1. doi: 10.1186/1471-2164-14-1.


The microRNAs within the DLK1-DIO3 genomic region: involvement in disease pathogenesis.

Benetatos L, Hatzimichael E, Londin E, Vartholomatos G, Loher P, Rigoutsos I, Briasoulis E.

Cell Mol Life Sci. 2013 Mar;70(5):795-814. doi: 10.1007/s00018-012-1080-8. Epub 2012 Jul 24. Review.


HuR's post-transcriptional regulation of Death Receptor 5 in pancreatic cancer cells.

Pineda DM, Rittenhouse DW, Valley CC, Cozzitorto JA, Burkhart RA, Leiby B, Winter JM, Weber MC, Londin ER, Rigoutsos I, Yeo CJ, Gorospe M, Witkiewicz AK, Sachs JN, Brody JR.

Cancer Biol Ther. 2012 Aug;13(10):946-55. doi: 10.4161/cbt.20952. Epub 2012 Aug 1.


Whole-exome sequencing of DNA from peripheral blood mononuclear cells (PBMC) and EBV-transformed lymphocytes from the same donor.

Londin ER, Keller MA, D'Andrea MR, Delgrosso K, Ertel A, Surrey S, Fortina P.

BMC Genomics. 2011 Sep 26;12:464. doi: 10.1186/1471-2164-12-464.


CoAIMs: a cost-effective panel of ancestry informative markers for determining continental origins.

Londin ER, Keller MA, Maista C, Smith G, Mamounas LA, Zhang R, Madore SJ, Gwinn K, Corriveau RA.

PLoS One. 2010 Oct 15;5(10):e13443. doi: 10.1371/journal.pone.0013443.


Expression and regulation of the zinc finger transcription factor Churchill during zebrafish development.

Londin ER, Mentzer L, Gates KP, Sirotkin HI.

Gene Expr Patterns. 2007 Jun;7(6):645-50. Epub 2007 May 4.


Chordin, FGF signaling, and mesodermal factors cooperate in zebrafish neural induction.

Londin ER, Niemiec J, Sirotkin HI.

Dev Biol. 2005 Mar 1;279(1):1-19.


Altered gating properties of functional Cx26 mutants associated with recessive non-syndromic hearing loss.

Meşe G, Londin E, Mui R, Brink PR, White TW.

Hum Genet. 2004 Aug;115(3):191-9. Epub 2004 Jul 7.


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