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1

Long non-coding RNAs discriminate the stages and gene regulatory states of human humoral immune response

Agirre, Xabier, Meydan, Cem, Jiang, Yanwen, Garate, Leire, Doane, Ashley S., Li, Zhuoning, Verma, Akanksha, Paiva, Bruno, Martín-Subero, José I., Elemento, Olivier, Mason, Christopher E., Prosper, Fel

Journal:

Nature Communications

Year:

2019

Language:

english

File:

PDF, 3.49 MB

english, 2019

2

Graph convolutional networks for computational drug development and discovery

Sun, Mengying, Zhao, Sendong, Gilvary, Coryandar, Elemento, Olivier, Zhou, Jiayu, Wang, Fei

Journal:

Briefings in Bioinformatics

Year:

2019

Language:

english

File:

PDF, 438 KB

english, 2019

3

The aging skin microenvironment dictates stem cell behavior

Ge, Yejing, Miao, Yuxuan, Gur-Cohen, Shiri, Gomez, Nicholas, Yang, Hanseul, Nikolova, Maria, Polak, Lisa, Hu, Yang, Verma, Akanksha, Elemento, Olivier, Krueger, James G., Fuchs, Elaine

Journal:

Proceedings of the National Academy of Sciences

Year:

2020

Language:

english

File:

PDF, 3.79 MB

english, 2020

4

Prédiction de la réponse au cisplatine des tumeurs de la vessie infiltrant le muscle : HOXA9 un nouveau biomarqueur épigénétique

Xylinas, E., Clozel, T., De La Taille, A., Elemento, O., Shariat, S.

Journal:

Progrès en Urologie

Year:

2013

Language:

french

File:

PDF, 187 KB

french, 2013

5

Cancer systems biology: embracing complexity to develop better anticancer therapeutic strategies

Du, W, Elemento, O

Journal:

Year:

2015

Language:

english

File:

PDF, 1.63 MB

english, 2015

6

Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition

Lu, X., Li, J. M., Elemento, O., Tavazoie, S., Wieschaus, E. F.

Journal:

Development (The Company of Biologists)

Year:

2009

Language:

english

File:

PDF, 1.78 MB

english, 2009

7

A Data-Driven Approach to Predicting Successes and Failures of Clinical Trials

Gayvert, Kaitlyn M., Madhukar, Neel S., Elemento, Olivier

Journal:

Cell Chemical Biology

Year:

2016

Language:

english

File:

PDF, 1.23 MB

english, 2016

8

Reversible methylation of m6Am in the 5′ cap controls mRNA stability

Mauer, Jan, Luo, Xiaobing, Blanjoie, Alexandre, Jiao, Xinfu, Grozhik, Anya V., Patil, Deepak P., Linder, Bastian, Pickering, Brian F., Vasseur, Jean-Jacques, Chen, Qiuying, Gross, Steven S., Elemento,

Journal:

Year:

2016

Language:

english

File:

PDF, 4.62 MB

english, 2016

9

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

Jiang, Yanwen, Nie, Kui, Redmond, David, Melnick, Ari M., Tam, Wayne, Elemento, Olivier

Journal:

Journal of Visualized Experiments

Year:

2015

Language:

english

File:

PDF, 812 KB

english, 2015

10

Deep Convolutional Neural Networks Enable Discrimination of Heterogeneous Digital Pathology Images

Khosravi, Pegah, Kazemi, Ehsan, Imielinski, Marcin, Elemento, Olivier, Hajirasouliha, Iman

Journal:

Year:

2017

Language:

english

File:

PDF, 2.30 MB

english, 2017

11

Comprehensive characterization of the mutational landscape in multiple myeloma cell lines reveals potential drivers and pathways associated with tumor progression and drug resistance

Vikova, Veronika, Jourdan, Michel, Robert, Nicolas, Requirand, Guilhem, Boireau, Stéphanie, Bruyer, Angélique, Vincent, Laure, Cartron, Guillaume, Klein, Bernard, Elemento, Olivier, Kassambara, Albouk

Journal:

Year:

2019

Language:

english

File:

PDF, 2.76 MB

english, 2019

12

Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing

Grive, Kathryn J., Hu, Yang, Shu, Eileen, Grimson, Andrew, Elemento, Olivier, Grenier, Jennifer K., Cohen, Paula E., Copenhaver, Gregory P.

Journal:

Year:

2019

Language:

english

File:

PDF, 55.85 MB

english, 2019

13

Supplemental estrogen and caloric restriction reduce obesity-induced periprostatic white adipose inflammation in mice

Bhardwaj, Priya, Ikeda, Takahiro, Zhou, Xi Kathy, Wang, Hanhan, Zheng, Xi Emily, Giri, Dilip D, Elemento, Olivier, Verma, Akanksha, Miyazawa, Miki, Mukherjee, Sushmita, Falcone, Domenick J, Wendel, Ni

Journal:

Year:

2019

Language:

english

File:

PDF, 1.92 MB

english, 2019

14

The Missing Pieces of Artificial Intelligence in Medicine

Gilvary, Coryandar, Madhukar, Neel, Elkhader, Jamal, Elemento, Olivier

Journal:

Trends in Pharmacological Sciences

Year:

2019

Language:

english

File:

PDF, 539 KB

english, 2019

15

Clinical features of neuroendocrine prostate cancer

Conteduca, Vincenza, Oromendia, Clara, Eng, Kenneth W., Bareja, Rohan, Sigouros, Michael, Molina, Ana, Faltas, Bishoy M., Sboner, Andrea, Mosquera, Juan Miguel, Elemento, Olivier, Nanus, David M., Tag

Journal:

European Journal of Cancer

Year:

2019

File:

PDF, 1.39 MB

2019

16

A Bayesian machine learning approach for drug target identification using diverse data types

Madhukar, Neel S., Khade, Prashant K., Huang, Linda, Gayvert, Kaitlyn, Galletti, Giuseppe, Stogniew, Martin, Allen, Joshua E., Giannakakou, Paraskevi, Elemento, Olivier

Journal:

Nature Communications

Year:

2019

Language:

english

File:

PDF, 3.83 MB

english, 2019

17

Inhibition of EZH2 Catalytic Activity Selectively Targets a Metastatic Subpopulation in Triple-Negative Breast Cancer

Yomtoubian, Shira, Lee, Sharrell B., Verma, Akanksha, Izzo, Franco, Markowitz, Geoffrey, Choi, Hyejin, Cerchietti, Leandro, Vahdat, Linda, Brown, Kristy A., Andreopoulou, Eleni, Elemento, Olivier, Cha

Journal:

Year:

2020

Language:

english

File:

PDF, 5.90 MB

english, 2020

18

Molecular Profiles of Mixed Endometrial Carcinoma

Matrai, Cathleen, Motanagh, Samaneh, Mirabelli, Susanna, Ma, Lucy, He, Bing, Chapman-Davis, Eloise, Kurtis, Boaz, Elemento, Olivier, Mosquera, Juan Miguel, Ellenson, Lora H.

Journal:

American Journal of Surgical Pathology

Year:

2020

File:

PDF, 538 KB

2020

19

The posssible role of enantiodiscrimination in bilirubin toxicity

Carlotta Bernardini, Paola D'Arrigo, Gioia Elemento, Giovanna Mancini, Stefano Servi, Alessandro Sorrenti

Journal:

Year:

2009

Language:

english

File:

PDF, 198 KB

english, 2009

20

An exact and polynomial distance-based algorithm to reconstruct single copy tandem duplication trees

Olivier Elemento, Olivier Gascuel

Journal:

Journal of Discrete Algorithms

Year:

2005

Language:

english

File:

PDF, 162 KB

english, 2005

21

An integrated ChIP-seq analysis platform with customizable workflows

Eugenia G Giannopoulou, Olivier Elemento

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 2.48 MB

english, 2011

22

Mutations in FLVCR1 Cause Posterior Column Ataxia and Retinitis Pigmentosa

Anjali M. Rajadhyaksha, Olivier Elemento, Erik G. Puffenberger, Kathryn C. Schierberl, Jenny Z. Xiang, Maria L. Putorti, José Berciano, Chantal Poulin, Bernard Brais, Michel Michaelides, Richard G. We

Journal:

The American Journal of Human Genetics

Year:

2010

Language:

english

File:

PDF, 1.36 MB

english, 2010

23

A panel of four microRNAs accurately differentiates benign from malignant indeterminate thyroid lesions on fine needle aspiration

Xavier M. Keutgen, Filippo Filicori, Michael Crowley, Daniel Buitrago, Theresa Scognamiglio, Rasa Zarnegar, Olivier Elemento, Thomas J. Fahey III

Journal:

Journal of the American College of Surgeons

Year:

2011

Language:

english

File:

PDF, 111 KB

english, 2011

24

DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices

Isabelle da Piedade, Man-Hung Eric Tang, Olivier Elemento

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 1.74 MB

english, 2009

25

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

Kate D. Meyer, Yogesh Saletore, Paul Zumbo, Olivier Elemento, Christopher E. Mason, Samie R. Jaffrey

Journal:

Year:

2012

Language:

english

File:

PDF, 887 KB

english, 2012

26

A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types

Olivier Elemento, Noam Slonim, Saeed Tavazoie

Journal:

Year:

2007

Language:

english

File:

PDF, 2.01 MB

english, 2007

27

Revealing Global Regulatory Perturbations across Human Cancers

Hani Goodarzi, Olivier Elemento, Saeed Tavazoie

Journal:

Year:

2009

Language:

english

File:

PDF, 1.24 MB

english, 2009

28

IMGT/PhyloGene: an on-line tool for comparative analysis of immunoglobulin and T cell receptor genes

Olivier Elemento, Marie-Paule Lefranc

Journal:

Developmental & Comparative Immunology

Year:

2003

Language:

english

File:

PDF, 1.04 MB

english, 2003

29

Variation of water exchange dynamics with ligand structure and stereochemistry in lanthanide complexes based on 1,4-diazepine derivatives

Elemento, Elisa M., Parker, David, Aime, Silvio, Gianolio, Eliana, Lattuada, Luciano

Journal:

Organic & Biomolecular Chemistry

Year:

2009

Language:

english

File:

PDF, 420 KB

english, 2009

30

Faster sequencers, larger datasets, new challenges

Christopher E Mason, Olivier Elemento

Journal:

Year:

2012

Language:

english

File:

PDF, 67 KB

english, 2012

31

Antagonistic Function of the RNA-binding Protein HuR and miR-200b in Post-transcriptional Regulation of Vascular Endothelial Growth Factor-A Expression and Angiogenesis

Chang, S.-H., Lu, Y.-C., Li, X., Hsieh, W.-Y., Xiong, Y., Ghosh, M., Evans, T., Elemento, O., Hla, T.

Journal:

Journal of Biological Chemistry

Year:

2013

Language:

english

File:

PDF, 4.23 MB

english, 2013

32

A Panel of Four miRNAs Accurately Differentiates Malignant from Benign Indeterminate Thyroid Lesions on Fine Needle Aspiration

Keutgen, X. M., Filicori, F., Crowley, M. J., Wang, Y., Scognamiglio, T., Hoda, R., Buitrago, D., Cooper, D., Zeiger, M. A., Zarnegar, R., Elemento, O., Fahey, T. J.

Journal:

Clinical Cancer Research

Year:

2012

Language:

english

File:

PDF, 307 KB

english, 2012

33

NFIB is a governor of epithelial–melanocyte stem cell behaviour in a shared niche

Chang, Chiung-Ying, Pasolli, H. Amalia, Giannopoulou, Eugenia G., Guasch, Géraldine, Gronostajski, Richard M., Elemento, Olivier, Fuchs, Elaine

Journal:

Year:

2013

Language:

english

File:

PDF, 1.86 MB

english, 2013

34

AID stabilizes stem-cell phenotype by removing epigenetic memory of pluripotency genes

Kumar, Ritu, DiMenna, Lauren, Schrode, Nadine, Liu, Ting-Chun, Franck, Philipp, Muñoz-Descalzo, Silvia, Hadjantonakis, Anna-Katerina, Zarrin, Ali A., Chaudhuri, Jayanta, Elemento, Olivier, Evans, Todd

Journal:

Year:

2013

Language:

english

File:

PDF, 1.67 MB

english, 2013

35

Oncogenic transcription factors as master regulators of chromatin topology

Elemento, Olivier, Rubin, Mark A., Rickman, David S.

Journal:

Year:

2012

Language:

english

File:

PDF, 722 KB

english, 2012

36

The fat mass and obesity associated gene (Fto) regulates activity of the dopaminergic midbrain circuitry

Hess, Martin E, Hess, Simon, Meyer, Kate D, Verhagen, Linda A W, Koch, Linda, Brönneke, Hella S, Dietrich, Marcelo O, Jordan, Sabine D, Saletore, Yogesh, Elemento, Olivier, Belgardt, Bengt F, Franz, T

Journal:

Nature Neuroscience

Year:

2013

Language:

english

File:

PDF, 1.87 MB

english, 2013

37

Concentration as the Switch for Chiral Recognition in Biomembrane Models

Bombelli, Cecilia, Bernardini, Carlotta, Elemento, Gioia, Mancini, Giovanna, Sorrenti, Alessandro, Villani, Claudio

Journal:

Journal of the American Chemical Society

Year:

2008

Language:

english

File:

PDF, 70 KB

english, 2008

38

A stable transcription factor complex nucleated by oligomeric AML1–ETO controls leukaemogenesis

Sun, Xiao-Jian, Wang, Zhanxin, Wang, Lan, Jiang, Yanwen, Kost, Nils, Soong, T. David, Chen, Wei-Yi, Tang, Zhanyun, Nakadai, Tomoyoshi, Elemento, Olivier, Fischle, Wolfgang, Melnick, Ari, Patel, Dinsha

Journal:

Year:

2013

Language:

english

File:

PDF, 1.08 MB

english, 2013

39

Developing a systems-level understanding of gene expression

Olivier Elemento

Journal:

Year:

2007

Language:

english

File:

PDF, 57 KB

english, 2007

40

Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach

Olivier Elemento, Saeed Tavazoie

Journal:

Year:

2005

Language:

english

File:

PDF, 1007 KB

english, 2005

41

Synergistic Activation of Inflammatory Cytokine Genes by Interferon-γ-Induced Chromatin Remodeling and Toll-like Receptor Signaling

Qiao, Yu, Giannopoulou, Eugenia G., Chan, Chun Hin, Park, Sung-ho, Gong, Shiaoching, Chen, Janice, Hu, Xiaoyu, Elemento, Olivier, Ivashkiv, Lionel B.

Journal:

Year:

2013

Language:

english

File:

PDF, 2.64 MB

english, 2013

42

Epigenomic Alterations in Localized and Advanced Prostate Cancer

Lin, Pei-Chun, Giannopoulou, Eugenia G., Park, Kyung, Mosquera, Juan Miguel, Sboner, Andrea, Tewari, Ashutosh K., Garraway, Levi A., Beltran, Himisha, Rubin, Mark A., Elemento, Olivier

Journal:

Year:

2013

Language:

english

File:

PDF, 1.98 MB

english, 2013

43

Contemporary PBSB: Modular Graduate Education in Cells, Systems, and Quantitative Methods

Gardner, Daniel, Accardi, Alessio, Aksay, Emre R.F., Andersen, Olaf S., Banfelder, Jason R., Boudker, Olga, Christini, David J., Elemento, Olivier, Grafstein, Bernice, Krogh-Madsen, Trine

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 65 KB

english, 2013

44

156 Prediction and reversibility of cisplatin-resistance in bladder cancer: HOXA9 a novel epigenetic biomarker

Xylinas, E.N., Clozel, T., Zhuang, D., Crivelli, J.J., Kluth, L.A., Robinson, B.D., Scherr, D.S., Elemento, O., Shariat, S.F.

Journal:

European Urology Supplements

Year:

2013

Language:

english

File:

PDF, 72 KB

english, 2013

45

Loss of ubiquitin carboxyl-terminal hydrolase isoenzyme-1 expression is associated with local and distant metastases of gastrointestinal well-differentiated neuroendocrine (carcinoid) tumors

Kleiman, David A., Beninato, Toni, Crowley, Michael J., Panarelli, Nicole, Liu, Yi-Fang, Lieberman, Michael D., Elemento, Olivier, Zarnegar, Raza, Fahey, Thomas J.

Journal:

Journal of the American College of Surgeons

Year:

2013

Language:

english

File:

PDF, 143 KB

english, 2013

46

Molecular Diagnosis of Autosomal Dominant Polycystic Kidney Disease Using Next-Generation Sequencing

Tan, Adrian Y., Michaeel, Alber, Liu, Genyan, Elemento, Olivier, Blumenfeld, Jon, Donahue, Stephanie, Parker, Tom, Levine, Daniel, Rennert, Hanna

Journal:

The Journal of Molecular Diagnostics

Year:

2014

Language:

english

File:

PDF, 1.83 MB

english, 2014

47

Histone variant H3.3 is an essential maternal factor for oocyte reprogramming

Wen, D., Banaszynski, L. A., Liu, Y., Geng, F., Noh, K.-M., Xiang, J., Elemento, O., Rosenwaks, Z., Allis, C. D., Rafii, S.

Journal:

Proceedings of the National Academy of Sciences

Year:

2014

Language:

english

File:

PDF, 970 KB

english, 2014

48

Reprogramming human endothelial cells to haematopoietic cells requires vascular induction

Sandler, Vladislav M., Lis, Raphael, Liu, Ying, Kedem, Alon, James, Daylon, Elemento, Olivier, Butler, Jason M., Scandura, Joseph M., Rafii, Shahin

Journal:

Year:

2014

Language:

english

File:

PDF, 10.67 MB

english, 2014

49

Characterization of the human cumulus cell transcriptome during final follicular maturation and ovulation

Yerushalmi, G. M., Salmon-Divon, M., Yung, Y., Maman, E., Kedem, A., Ophir, L., Elemento, O., Coticchio, G., Dal Canto, M., Mignini Renzinu, M., Fadini, R., Hourvitz, A.

Journal:

Molecular Human Reproduction

Year:

2014

Language:

english

File:

PDF, 1.08 MB

english, 2014

50

Cell-Cycle Reprogramming for PI3K Inhibition Overrides a Relapse-Specific C481S BTK Mutation Revealed by Longitudinal Functional Genomics in Mantle Cell Lymphoma

Chiron, D., Di Liberto, M., Martin, P., Huang, X., Sharman, J., Blecua, P., Mathew, S., Vijay, P., Eng, K., Ali, S., Johnson, A., Chang, B., Ely, S., Elemento, O., Mason, C. E., Leonard, J. P., Chen-K

Journal:

Cancer Discovery

Year:

2014

Language:

english

File:

PDF, 4.18 MB

english, 2014