Jiang Y, Soong D, Wang L, Melnick A*, Elemento O*. 2012. Genome-wide Detection of Genes Targeted by Aberrant Somatic Hypermutation in Lymphoma. Submitted. Data @ GSE34316. * Joint corresponding authors
Rickman DS*, Soong D*, Moss B, Mosquera JM, Dlabal J, Terry S, MacDonald TY, Tripodi J, Bunting K, Najfeld V, Demichelis F, Melnick A, Elemento O*, Rubin MA*. 2012. Oncogene-Mediated Alterations in Chromatin Conformation, PNAS, accepted. * Joint first authors, Joint senior authors.
Mason CE and Elemento O. 2012. Faster sequencers, larger datasets, new challenges. Genome Biology, 13:314 PDF
Demichelis F, ..., Soong D, Rickman D, Elemento O, ..., Rubin M. 2012. Identification of functionally active, low frequency copy number variants at 15q21.3 and 12q21.31 associated with prostate cancer risk. PNAS Published online before print April 10, 2012, doi: 10.1073/pnas.1117405109
Meyer K, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey S. 2012. Comprehensive Analysis of mRNA Methylation Reveals Pervasive Adenosine Methylation in 3' UTRs. Cell, accepted
Gollamudi S, Johri A, Calingasan NY, Yang L, Elemento O, Beal MF. 2012. Concordant Signaling Pathways Produced by Pesticide Exposure in Mice Correspond to Pathways Identified in Human Parkinson’s Disease. PLoS ONE 7(5): e36191. doi:10.1371/journal.pone.0036191
Keutgen XM, Filicori F, Crowley M, Buitrago D, Scognamiglio T, Zarnegar R, Elemento O*, Fahey III TJ*. 2012. A panel of four microRNAs accurately differentiates benign from malignant indeterminate thyroid lesions on fine needle aspiration. Clinical Cancer Research 18; 2032; doi:10.1158/1078-0432.CCR-11-2487. * Joint corresponding authors
Patent pending (Filed March 2012).
Wacker SA, Houghtaling BR, Elemento O*, Kapoor TM*. 2012. Using transcriptome sequencing to identify mechanisms of drug action and resistance in human cells. Nature Chemical Biology. Published online: 12 February 2012 | doi:10.1038/nchembio.779 * Joint corresponding authors Supplementary data and software. PDF
Rated as Must Read (Factor 8.0) on Faculty of 1000.
Patent pending (filed February 2012).
Keutgen XM, Kundel A, Buitrago D. Zackson D, Elemento O, Fahey TJ III, Zarnegar R. 2012. Parathyroidectomy versus Calcimimetics for the treatment of Primary Hyperparathyroidism. Annals of Surgery, published online 30 March 2012, doi: 10.1097/SLA.0b013e31824c5252
Giannopoulou E, Elemento O. 2011. An integrated ChIP-seq analysis platform with customizable workflows (ChIPseeqer). BMC Bioinformatics 2011, 12:277. Supplementary Data: ChIPseeqer Installation and Tutorial
Shaknovich R, ..., Elemento O, Melnick A. 2011. DNA Methyltransferase 1 and DNA Methylation Patterning Contribute to Germinal Center B-Cell Differentiation. Blood. Published online before print August 9, 2011, doi: 10.1182/blood-2011-06-357996.
Velichutina I, Shaknovich R, Geng H, Johnson N, Gascoyne RD, Melnick A* and Elemento O*. 2010. EZH2 Mediates Epigenetic Silencing of a Germinal Center Specific Transcriptional Program That Contributes to Proliferation and Lymphomagenesis. Blood, 116 5247-5255.* Joint Corresponding Authors
Lieber DS, Elemento O*, Tavazoie S*. 2010. Large-scale discovery and characterization of protein regulatory motifs in eukaryotes. PLoS ONE, 5(12): e14444. doi:10.1371/journal.pone.0014444 * Joint Corresponding Authors
Campbell TL, De Silva EK, Olzewski KL, Elemento O, Llinas M. 2010. Identification and genome-wide mapping of DNA binding specificities for the ApiAP2 family of regulators from the malaria parasite. PLoS Pathogens, 6(10): e1001165. doi:10.1371/journal.ppat.1001165. Suppl Data/Programs .
Rajadhyaksha AM*, Elemento O*, ..., and Higgins JJ. 2010. Targeted DNA capture and high-throughput sequencing identifies mutation in FLVCR1 that causes Posterior Column Ataxia and Retinitis Pigmentosa. American Journal of Human Genetics, Volume 87, Issue 5, 643-654 * Equal Contribution
Keutgen XM, ..., Elemento O, ..., Fahey TJ III. 2010. Low Dicer Expression Correlates with Aggressive Features in Thyroid Cancer. Submitted.
Shaknovich R*, Geng H*, Johnson N, Tsikitas L, Cerchietti L, Greally JM , Gascoyne RD*, Elemento O*, Melnick A*. 2010. DNA methylation signatures define molecular subtypes of Diffuse Large B Cell Lymphoma. Blood, Published Online July 2010, DOI 10.1182/blood-2010-05-285320 * Equal Contribution or * Joint Corresponding Authors
Goodarzi H*, Elemento O*, Tavazoie S. Revealing global regulatory perturbations across human cancers. 2009. Molecular Cell, 36(5):900-911. *Equal Contribution
Accompanying preview article by Prensner and Chinnaiyan
Highlighted in Nature Reviews Cancer
da Piedade I, Tang MH, Elemento O. DISPARE: A DIScriminative PAttern REfinement algorithm for Position Weight Matrices. 2009. BMC Bioinformatics, 10:388
Ci W, Polo JM, Cerchietti L, Shaknovich R, Wang L, Yang N, Ye K, Farinha P, Horsman DE, Gascoyne RD, Elemento O*, Melnick A*. 2009. The BCL6 transcriptional program features repression of multiple oncogenes in primary B-cells and is deregulated in DLBCL, 2009. Blood, 113(22):5536-5548, * Joint Corresponding Authors
Lu X, Li J, Elemento O, Tavazoie S, Wieschaus E. 2009. Revealing nucleocytoplasmic ratio regulated zygotic transcription during Mid Blastula Transition using a genomic approach. 2009. Development 136(12):2101-10
Highlighted in Nature Reviews Genetics
Legesse-Miller A, Elemento O, Pfau S, Forman J, Tavazoie S, Coller H. let-7 overexpression leads to an increased fraction of cells in G2/M, direct down-regulation of Cdc34 and stabilization of Wee1 kinase in primary fibroblasts. 2009. Journal of Biological Chemistry (JBC)
Elemento O*, Slonim N* and Tavazoie S. 2007. A universal framework for regulatory element discovery across all genomes and data-types (FIRE), Molecular Cell 28(2). Web site. *Equal Contribution
Rated as 'Must Read' (Factor 6.0) by Faculty of 1000 Biology.
Highlighted in Nature Reviews Genetics
Elemento O. 2007. Developing a systems-level understanding of gene expression (Meeting Report, CSHL Systems Biology 2007) Genome Biology, 8:304
, PDF (local copy)
De Renzis S, Elemento O, Tavazoie S and Wieschaus E. 2007. Unmasking the activation of the zygotic genome using chromosomal deletions in the Drosophila embryo, PLoS Biology, 5(5): e117
Full Text Suppl Material.
Highlighted in Nature Reviews Genetics, Highlighted in Nature
Elemento O, Tavazoie S. 2007. Fastcompare: a non-alignment approach for genome-scale discovery of DNA and mRNA regulatory elements using network-level conservation, Methods Mol Biol, 395:349-66
Full Text Suppl Material
Slonim N*, Elemento O*, Tavazoie S. 2006. Genotype-phenotype association reveals intrinsic modularity in genetic networks. Molecular Systems Biology 2:2006.0005
Full Text Suppl Material
*Equal Contribution
Chan CS*, Elemento O*, Tavazoie S. 2005. Revealing post-transcriptional regulatory interactions through network-level conservation. PLOS Computational Biology 1(7): e69
Full Text Suppl Material
*Equal Contribution
Elemento O, Tavazoie S. 2005. Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biology, 6:R18
Full Text Suppl Material
Gascuel O, Bertrand D, Elemento O. 2005. Recontructing the duplication history of tandemly repeated sequences. Book chapter (novel results, peer-reviewed) in: Mathematics of Evolution and Phylogeny, Oxford University Press.
Elemento O, Gascuel O. 2005. An exact and polynomial distance-based algorithm to reconstruct single copy tandem duplication trees, Journal of Discrete Algorithms 3:362–374 (extended version of CPM03, re-peer-reviewed)
Full Text
Elemento O, Lefranc M-P. 2003. IMGT/PhyloGene : an online tool for comparative analysis of IG and TR genes. Developmental Comparative Immunology. 27(9):763-79
Elemento O, Gascuel O. An exact and polynomial distance-based algorithm to reconstruct single copy tandem duplication trees. Proceedings of the Fourteenth Annual Symposium on Combinatorial Pattern Matching (CPM 2003), volume 2676 of Lecture Notes in Computer Science. Springer Verlag, 2003.
Elemento O. 2003. Phylogenetic analyses of tandemly repeated gene families and application to immunoglobulin and T cell receptor genes in IMGT. PhD Thesis, University of Montpellier/CNRS PDF (in French).
Elemento O, Gascuel O. Lefranc M.P. 2002. Reconstructing the duplication history of tandemly repeated genes. Molecular Biology and Evolution 19 :278-288. Full Text
Elemento O, Gascuel O. 2002. A fast and accurate distance-based algorithm for reconstructing tandem duplication histories. Bioinformatics. 2002, 18, S2:S92-S99. Full Text
Elemento O. 1999. Using Principal Component Analysis to initialize and validate Kohonen maps (in French). Proceedings of the Annual French Classification Society Conference (SFC'99), pp325-331.
Rickman DS*, Soong D*, Moss B, Mosquera JM, Dlabal J, Terry S, MacDonald TY, Tripodi J, Bunting K, Najfeld V, Demichelis F, Melnick A, Elemento O*, Rubin MA*. 2012. Oncogene-Mediated Alterations in Chromatin Conformation, PNAS, accepted. * Joint first authors, Joint senior authors.
Mason CE and Elemento O. 2012. Faster sequencers, larger datasets, new challenges. Genome Biology, 13:314 PDF
Demichelis F, ..., Soong D, Rickman D, Elemento O, ..., Rubin M. 2012. Identification of functionally active, low frequency copy number variants at 15q21.3 and 12q21.31 associated with prostate cancer risk. PNAS Published online before print April 10, 2012, doi: 10.1073/pnas.1117405109
Meyer K, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey S. 2012. Comprehensive Analysis of mRNA Methylation Reveals Pervasive Adenosine Methylation in 3' UTRs. Cell, accepted
Gollamudi S, Johri A, Calingasan NY, Yang L, Elemento O, Beal MF. 2012. Concordant Signaling Pathways Produced by Pesticide Exposure in Mice Correspond to Pathways Identified in Human Parkinson’s Disease. PLoS ONE 7(5): e36191. doi:10.1371/journal.pone.0036191
Keutgen XM, Filicori F, Crowley M, Buitrago D, Scognamiglio T, Zarnegar R, Elemento O*, Fahey III TJ*. 2012. A panel of four microRNAs accurately differentiates benign from malignant indeterminate thyroid lesions on fine needle aspiration. Clinical Cancer Research 18; 2032; doi:10.1158/1078-0432.CCR-11-2487. * Joint corresponding authors
Patent pending (Filed March 2012).
Wacker SA, Houghtaling BR, Elemento O*, Kapoor TM*. 2012. Using transcriptome sequencing to identify mechanisms of drug action and resistance in human cells. Nature Chemical Biology. Published online: 12 February 2012 | doi:10.1038/nchembio.779 * Joint corresponding authors Supplementary data and software. PDF
Rated as Must Read (Factor 8.0) on Faculty of 1000.
Patent pending (filed February 2012).
Keutgen XM, Kundel A, Buitrago D. Zackson D, Elemento O, Fahey TJ III, Zarnegar R. 2012. Parathyroidectomy versus Calcimimetics for the treatment of Primary Hyperparathyroidism. Annals of Surgery, published online 30 March 2012, doi: 10.1097/SLA.0b013e31824c5252
Giannopoulou E, Elemento O. 2011. An integrated ChIP-seq analysis platform with customizable workflows (ChIPseeqer). BMC Bioinformatics 2011, 12:277. Supplementary Data: ChIPseeqer Installation and Tutorial
Shaknovich R, ..., Elemento O, Melnick A. 2011. DNA Methyltransferase 1 and DNA Methylation Patterning Contribute to Germinal Center B-Cell Differentiation. Blood. Published online before print August 9, 2011, doi: 10.1182/blood-2011-06-357996.
Velichutina I, Shaknovich R, Geng H, Johnson N, Gascoyne RD, Melnick A* and Elemento O*. 2010. EZH2 Mediates Epigenetic Silencing of a Germinal Center Specific Transcriptional Program That Contributes to Proliferation and Lymphomagenesis. Blood, 116 5247-5255.* Joint Corresponding Authors
Lieber DS, Elemento O*, Tavazoie S*. 2010. Large-scale discovery and characterization of protein regulatory motifs in eukaryotes. PLoS ONE, 5(12): e14444. doi:10.1371/journal.pone.0014444 * Joint Corresponding Authors
Campbell TL, De Silva EK, Olzewski KL, Elemento O, Llinas M. 2010. Identification and genome-wide mapping of DNA binding specificities for the ApiAP2 family of regulators from the malaria parasite. PLoS Pathogens, 6(10): e1001165. doi:10.1371/journal.ppat.1001165. Suppl Data/Programs .
Rajadhyaksha AM*, Elemento O*, ..., and Higgins JJ. 2010. Targeted DNA capture and high-throughput sequencing identifies mutation in FLVCR1 that causes Posterior Column Ataxia and Retinitis Pigmentosa. American Journal of Human Genetics, Volume 87, Issue 5, 643-654 * Equal Contribution
Keutgen XM, ..., Elemento O, ..., Fahey TJ III. 2010. Low Dicer Expression Correlates with Aggressive Features in Thyroid Cancer. Submitted.
Shaknovich R*, Geng H*, Johnson N, Tsikitas L, Cerchietti L, Greally JM , Gascoyne RD*, Elemento O*, Melnick A*. 2010. DNA methylation signatures define molecular subtypes of Diffuse Large B Cell Lymphoma. Blood, Published Online July 2010, DOI 10.1182/blood-2010-05-285320 * Equal Contribution or * Joint Corresponding Authors
Goodarzi H*, Elemento O*, Tavazoie S. Revealing global regulatory perturbations across human cancers. 2009. Molecular Cell, 36(5):900-911. *Equal Contribution
Accompanying preview article by Prensner and Chinnaiyan
Highlighted in Nature Reviews Cancer
da Piedade I, Tang MH, Elemento O. DISPARE: A DIScriminative PAttern REfinement algorithm for Position Weight Matrices. 2009. BMC Bioinformatics, 10:388
Ci W, Polo JM, Cerchietti L, Shaknovich R, Wang L, Yang N, Ye K, Farinha P, Horsman DE, Gascoyne RD, Elemento O*, Melnick A*. 2009. The BCL6 transcriptional program features repression of multiple oncogenes in primary B-cells and is deregulated in DLBCL, 2009. Blood, 113(22):5536-5548, * Joint Corresponding Authors
Lu X, Li J, Elemento O, Tavazoie S, Wieschaus E. 2009. Revealing nucleocytoplasmic ratio regulated zygotic transcription during Mid Blastula Transition using a genomic approach. 2009. Development 136(12):2101-10
Highlighted in Nature Reviews Genetics
Legesse-Miller A, Elemento O, Pfau S, Forman J, Tavazoie S, Coller H. let-7 overexpression leads to an increased fraction of cells in G2/M, direct down-regulation of Cdc34 and stabilization of Wee1 kinase in primary fibroblasts. 2009. Journal of Biological Chemistry (JBC)
Elemento O*, Slonim N* and Tavazoie S. 2007. A universal framework for regulatory element discovery across all genomes and data-types (FIRE), Molecular Cell 28(2). Web site. *Equal Contribution
Rated as 'Must Read' (Factor 6.0) by Faculty of 1000 Biology.
Highlighted in Nature Reviews Genetics
Elemento O. 2007. Developing a systems-level understanding of gene expression (Meeting Report, CSHL Systems Biology 2007) Genome Biology, 8:304
, PDF (local copy)
De Renzis S, Elemento O, Tavazoie S and Wieschaus E. 2007. Unmasking the activation of the zygotic genome using chromosomal deletions in the Drosophila embryo, PLoS Biology, 5(5): e117
Full Text Suppl Material.
Highlighted in Nature Reviews Genetics, Highlighted in Nature
Elemento O, Tavazoie S. 2007. Fastcompare: a non-alignment approach for genome-scale discovery of DNA and mRNA regulatory elements using network-level conservation, Methods Mol Biol, 395:349-66
Full Text Suppl Material
Slonim N*, Elemento O*, Tavazoie S. 2006. Genotype-phenotype association reveals intrinsic modularity in genetic networks. Molecular Systems Biology 2:2006.0005
Full Text Suppl Material
*Equal Contribution
Chan CS*, Elemento O*, Tavazoie S. 2005. Revealing post-transcriptional regulatory interactions through network-level conservation. PLOS Computational Biology 1(7): e69
Full Text Suppl Material
*Equal Contribution
Elemento O, Tavazoie S. 2005. Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biology, 6:R18
Full Text Suppl Material
Gascuel O, Bertrand D, Elemento O. 2005. Recontructing the duplication history of tandemly repeated sequences. Book chapter (novel results, peer-reviewed) in: Mathematics of Evolution and Phylogeny, Oxford University Press.
Elemento O, Gascuel O. 2005. An exact and polynomial distance-based algorithm to reconstruct single copy tandem duplication trees, Journal of Discrete Algorithms 3:362–374 (extended version of CPM03, re-peer-reviewed)
Full Text
Elemento O, Lefranc M-P. 2003. IMGT/PhyloGene : an online tool for comparative analysis of IG and TR genes. Developmental Comparative Immunology. 27(9):763-79
Elemento O, Gascuel O. An exact and polynomial distance-based algorithm to reconstruct single copy tandem duplication trees. Proceedings of the Fourteenth Annual Symposium on Combinatorial Pattern Matching (CPM 2003), volume 2676 of Lecture Notes in Computer Science. Springer Verlag, 2003.
Elemento O. 2003. Phylogenetic analyses of tandemly repeated gene families and application to immunoglobulin and T cell receptor genes in IMGT. PhD Thesis, University of Montpellier/CNRS PDF (in French).
Elemento O, Gascuel O. Lefranc M.P. 2002. Reconstructing the duplication history of tandemly repeated genes. Molecular Biology and Evolution 19 :278-288. Full Text
Elemento O, Gascuel O. 2002. A fast and accurate distance-based algorithm for reconstructing tandem duplication histories. Bioinformatics. 2002, 18, S2:S92-S99. Full Text
Elemento O. 1999. Using Principal Component Analysis to initialize and validate Kohonen maps (in French). Proceedings of the Annual French Classification Society Conference (SFC'99), pp325-331.