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Articles (75)
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1

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

Mathelier, Anthony, Fornes, Oriol, Arenillas, David J., Chen, Chih-yu, Denay, Grégoire, Lee, Jessica, Shi, Wenqiang, Shyr, Casper, Tan, Ge, Worsley-Hunt, Rebecca, Zhang, Allen W., Parcy, François, Len

Journal:

Nucleic Acids Research

Année:

2016

Langue:

english

Fichier:

PDF, 1.82 MB

english, 2016

2

CMF-Impute: An accurate imputation tool for single cell RNA-seq data

Xu, Junlin, Cai, Lijun, Liao, Bo, Zhu, Wen, Yang, JiaLiang, Mathelier, Anthony

Journal:

Année:

2020

Langue:

english

Fichier:

PDF, 1.43 MB

english, 2020

3

Joint learning dimension reduction and clustering of single-cell RNA-sequencing data

Wu, Wenming, Ma, Xiaoke, Mathelier, Anthony

Journal:

Année:

2020

Fichier:

PDF, 731 KB

2020

4

DNA Features Viewer, a sequence annotation formatting and plotting library for Python

Zulkower, Valentin, Rosser, Susan, Mathelier, Anthony

Journal:

Année:

2020

Fichier:

PDF, 316 KB

2020

5

Scirpy: A Scanpy extension for analyzing single-cell T-cell receptor sequencing data

Sturm, Gregor, Szabo, Tamas, Fotakis, Georgios, Haider, Marlene, Rieder, Dietmar, Trajanoski, Zlatko, Finotello, Francesca, Mathelier, Anthony

Journal:

Année:

2020

Fichier:

PDF, 1.76 MB

2020

6

Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment

Rebecca Worsley Hunt,Anthony Mathelier,Luis del Peso,Wyeth W Wasserman

Journal:

Année:

2014

Langue:

english

Fichier:

PDF, 1.60 MB

english, 2014

7

Identification of altered cis-regulatory elements in human disease

Mathelier, Anthony, Shi, Wenqiang, Wasserman, Wyeth W.

Journal:

Trends in Genetics

Année:

2015

Langue:

english

Fichier:

PDF, 9.21 MB

english, 2015

8

The Potential of MicroRNAs in Personalized Medicine against Cancers

Saumet, Anne, Mathelier, Anthony, Lecellier, Charles-Henri

Journal:

BioMed Research International

Année:

2014

Langue:

english

Fichier:

PDF, 232 KB

english, 2014

9

The Next Generation of Transcription Factor Binding Site Prediction

Mathelier, Anthony, Wasserman, Wyeth W., Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2013

Langue:

english

Fichier:

PDF, 1.34 MB

english, 2013

10

15 TFBSshape: a motif database for DNA shape features of transcription factor binding sites

Yang, Lin, Dror, Iris, Zhou, Tianyin, Mathelier, Anthony, Wasserman, Wyeth W., Gordân, Raluca, Rohs, Remo

Journal:

Journal of Biomolecular Structure and Dynamics

Année:

2015

Langue:

english

Fichier:

PDF, 412 KB

english, 2015

11

DNA Methylation Profiling in Human Huntington's Disease Brain

De Souza, Rebecca A.G., Islam, Sumaiya A., McEwen, Lisa M., Mathelier, Anthony, Hill, Austin, Mah, Sarah M., Wasserman, Wyeth W., Kobor, Michael S., Leavitt, Blair R.

Journal:

Human Molecular Genetics

Année:

2016

Langue:

english

Fichier:

PDF, 639 KB

english, 2016

12

DeepCAGE transcriptomics identify HOXD10 as transcription factor regulating lymphatic endothelial responses to VEGF-C

Klein, Sarah, Dieterich, Lothar C., Mathelier, Anthony, Chong, Chloé, Sliwa-Primorac, Adriana, Hong, Young-Kwon, Shin, Jay W., Lizio, Marina, Itoh, Masayoshi, Kawaji, Hideya, Lassmann, Timo, Daub, Car

Journal:

Journal of Cell Science

Année:

2016

Langue:

english

Fichier:

PDF, 3.05 MB

english, 2016

13

DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium

Dieterich, Lothar C., Klein, Sarah, Mathelier, Anthony, Sliwa-Primorac, Adriana, Ma, Qiaoli, Hong, Young-Kwon, Shin, Jay W., Hamada, Michito, Lizio, Marina, Itoh, Masayoshi, Kawaji, Hideya, Lassmann,

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 4.01 MB

english, 2015

14

Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas

Mathelier, Anthony, Lefebvre, Calvin, Zhang, Allen W, Arenillas, David J, Ding, Jiarui, Wasserman, Wyeth W, Shah, Sohrab P

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 4.15 MB

english, 2015

15

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs

Arenillas, David J., Forrest, Alistair R. R., Kawaji, Hideya, Lassmann, Timo, Wasserman, Wyeth W., Mathelier, Anthony

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 286 KB

english, 2016

16

DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo

Mathelier, Anthony, Xin, Beibei, Chiu, Tsu-Pei, Yang, Lin, Rohs, Remo, Wasserman, Wyeth W.

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 2.20 MB

english, 2016

17

Evaluating the impact of single nucleotide variants on transcription factor binding

Shi, Wenqiang, Fornes, Oriol, Mathelier, Anthony, Wasserman, Wyeth W.

Journal:

Nucleic Acids Research

Année:

2016

Langue:

english

Fichier:

PDF, 2.57 MB

english, 2016

18

PAX6 MiniPromoters drive restricted expression from rAAV in the adult mouse retina

Hickmott, Jack W, Chen, Chih-yu, Arenillas, David J, Korecki, Andrea J, Lam, Siu Ling, Molday, Laurie L, Bonaguro, Russell J, Zhou, Michelle, Chou, Alice Y, Mathelier, Anthony, Boye, Sanford L, Hauswi

Journal:

Molecular Therapy — Methods & Clinical Development

Année:

2016

Langue:

english

Fichier:

PDF, 5.57 MB

english, 2016

19

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

Lizio, Marina, Harshbarger, Jayson, Abugessaisa, Imad, Noguchi, Shuei, Kondo, Atsushi, Severin, Jessica, Mungall, Chris, Arenillas, David, Mathelier, Anthony, Medvedeva, Yulia A., Lennartsson, Andreas

Journal:

Nucleic Acids Research

Année:

2016

Langue:

english

Fichier:

PDF, 517 KB

english, 2016

20

YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses

Chen, Chih-yu, Shi, Wenqiang, Balaton, Bradley P., Matthews, Allison M., Li, Yifeng, Arenillas, David J., Mathelier, Anthony, Itoh, Masayoshi, Kawaji, Hideya, Lassmann, Timo, Hayashizaki, Yoshihide, C

Journal:

Scientific Reports

Année:

2016

Langue:

english

Fichier:

PDF, 5.20 MB

english, 2016

21

Chromosomal periodicity and positional networks of genes in Escherichia coli

Mathelier, Anthony, Carbone, Alessandra

Journal:

Molecular Systems Biology

Année:

2010

Langue:

english

Fichier:

PDF, 948 KB

english, 2010

22

Intervene: a tool for intersection and visualization of multiple gene or genomic region sets

Aziz Khan,Anthony Mathelier

Journal:

BMC Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.59 MB

english, 2017

23

DNA methylation at enhancers identifies distinct breast cancer lineages

Fleischer, Thomas, Tekpli, Xavier, Mathelier, Anthony, Wang, Shixiong, Nebdal, Daniel, Dhakal, Hari P., Sahlberg, Kristine Kleivi, Schlichting, Ellen, Børresen-Dale, Anne-Lise, Borgen, Elin, Naume, Bj

Journal:

Nature Communications

Année:

2017

Langue:

english

Fichier:

PDF, 4.64 MB

english, 2017

24

JASPAR RESTful API: accessing JASPAR data from any programming language

Khan, Aziz, Mathelier, Anthony

Journal:

Année:

2017

Langue:

english

Fichier:

PDF, 78 KB

english, 2017

25

ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments

Chèneby, Jeanne, Gheorghe, Marius, Artufel, Marie, Mathelier, Anthony, Ballester, Benoit

Journal:

Nucleic Acids Research

Année:

2018

Langue:

english

Fichier:

PDF, 1.00 MB

english, 2018

26

Characterization of the human RFX transcription factor family by regulatory and target gene analysis

Sugiaman-Trapman, Debora, Vitezic, Morana, Jouhilahti, Eeva-Mari, Mathelier, Anthony, Lauter, Gilbert, Misra, Sougat, Daub, Carsten O., Kere, Juha, Swoboda, Peter

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 1.71 MB

english, 2018

27

Human Enhancers Harboring Specific Sequence Composition, Activity, and Genome Organization Are Linked to the Immune Response

Lecellier, Charles-Henri, Wasserman, Wyeth W., Mathelier, Anthony

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 2.73 MB

english, 2018

28

New MiniPromoter Ple345 (NEFL) Drives Strong and Specific Expression in Retinal Ganglion Cells of Mouse and Primate Retina

Simpson, Elizabeth, Korecki, Andrea J, Fornes, Oriol, McGill, Trevor J, Cueva-Vargas, Jorge Luis, Agostinone, Jessica, Farkas, Rachelle A, Hickmott, Jack W, Lam, Siu Ling, Mathelier, Anthony, Renner,

Journal:

Human Gene Therapy

Année:

2018

Fichier:

PDF, 9.47 MB

2018

29

Computational Analysis of Transcriptional Regulation Sites at the HTT Gene Locus

De Souza, Rebecca A.G., Kosior, Natalia, Thomson, Sarah B., Mathelier, Anthony, Zhang, Allen W., Bečanović, Kristina, Wasserman, Wyeth W., Leavitt, Blair R.

Journal:

Journal of Huntington's Disease

Année:

2018

Langue:

english

Fichier:

PDF, 1.12 MB

english, 2018

30

New MiniPromoter Ple345 (NEFL) Drives Strong and Specific Expression in Retinal Ganglion Cells of Mouse and Primate Retina

Simpson, Elizabeth, Korecki, Andrea J, Fornes, Oriol, McGill, Trevor J, Cueva-Vargas, Jorge Luis, Agostinone, Jessica, Farkas, Rachelle A, Hickmott, Jack W, Lam, Siu Ling, Mathelier, Anthony, Renner,

Journal:

Human Gene Therapy

Année:

2018

Langue:

english

Fichier:

PDF, 9.47 MB

english, 2018

31

Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers

Khan, Aziz, Mathelier, Anthony, Zhang, Xuegong

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 13.83 MB

english, 2018

32

A map of direct TF–DNA interactions in the human genome

Gheorghe, Marius, Sandve, Geir Kjetil, Khan, Aziz, Chèneby, Jeanne, Ballester, Benoit, Mathelier, Anthony

Journal:

Nucleic Acids Research

Année:

2018

Langue:

english

Fichier:

PDF, 2.42 MB

english, 2018

33

Twenty-Seven Tamoxifen-Inducible iCre-Driver Mouse Strains for Eye and Brain; Including Seventeen Carrying a New Inducible-First Constitutive-Ready Allele

Korecki, Andrea J., Hickmott, Jack W., Lam, Siu Ling, Dreolini, Lisa, Mathelier, Anthony, Baker, Oliver, Kuehne, Claudia, Bonaguro, Russell J., Smith, Jillian, Tan, Chin-Vern, Zhou, Michelle, Goldowit

Journal:

Année:

2019

Fichier:

PDF, 2.32 MB

2019

34

Twenty-Seven Tamoxifen-Inducible iCre-Driver Mouse Strains for Eye and Brain; Including Seventeen Carrying a New Inducible-First Constitutive-Ready Allele

Korecki, Andrea J., Hickmott, Jack W., Lam, Siu Ling, Dreolini, Lisa, Mathelier, Anthony, Baker, Oliver, Kuehne, Claudia, Bonaguro, Russell J., Smith, Jillian, Tan, Chin-Vern, Zhou, Michelle, Goldowit

Journal:

Année:

2019

Langue:

english

Fichier:

PDF, 2.32 MB

english, 2019

35

High OGT activity is essential for MYC-driven proliferation of prostate cancer cells

Itkonen, Harri M, Urbanucci, Alfonso, Martin, Sara ES, Khan, Aziz, Mathelier, Anthony, Thiede, Bernd, Walker, Suzanne, Mills, Ian G

Journal:

Année:

2019

Langue:

english

Fichier:

PDF, 1.99 MB

english, 2019

36

High OGT activity is essential for MYC-driven proliferation of prostate cancer cells

Itkonen, Harri M, Urbanucci, Alfonso, Martin, Sara ES, Khan, Aziz, Mathelier, Anthony, Thiede, Bernd, Walker, Suzanne, Mills, Ian G

Journal:

Année:

2019

Fichier:

PDF, 1.99 MB

2019

37

A map of direct TF–DNA interactions in the human genome

Gheorghe, Marius, Sandve, Geir Kjetil, Khan, Aziz, Chèneby, Jeanne, Ballester, Benoit, Mathelier, Anthony

Journal:

Nucleic Acids Research

Année:

2019

Langue:

english

Fichier:

PDF, 69 KB

english, 2019

38

Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis

Ha, Thomas J., Zhang, Peter G. Y., Robert, Remi, Yeung, Joanna, Swanson, Douglas J., Mathelier, Anthony, Wasserman, Wyeth W., Im, Sujin, Itoh, Masayoshi, Kawaji, Hideya, Lassmann, Timo, Daub, Carsten

Journal:

Année:

2019

Langue:

english

Fichier:

PDF, 7.12 MB

english, 2019

39

MirGeneDB 2.0: the metazoan microRNA complement

Fromm, Bastian, Domanska, Diana, Høye, Eirik, Ovchinnikov, Vladimir, Kang, Wenjing, Aparicio-Puerta, Ernesto, Johansen, Morten, Flatmark, Kjersti, Mathelier, Anthony, Hovig, Eivind, Hackenberg, Michae

Journal:

Nucleic Acids Research

Année:

2019

Langue:

english

Fichier:

PDF, 2.72 MB

english, 2019

40

MirGeneDB 2.0: the metazoan microRNA complement

Fromm, Bastian, Domanska, Diana, Høye, Eirik, Ovchinnikov, Vladimir, Kang, Wenjing, Aparicio-Puerta, Ernesto, Johansen, Morten, Flatmark, Kjersti, Mathelier, Anthony, Hovig, Eivind, Hackenberg, Michae

Journal:

Nucleic Acids Research

Année:

2019

Langue:

english

Fichier:

PDF, 67 KB

english, 2019

41

Kalign 3: multiple sequence alignment of large data sets

Lassmann, Timo, Mathelier, Anthony

Journal:

Année:

2019

Langue:

english

Fichier:

PDF, 483 KB

english, 2019

42

SpaCell: integrating tissue morphology and spatial gene expression to predict disease cells

Tan, Xiao, Su, Andrew, Tran, Minh, Nguyen, Quan, Mathelier, Anthony

Journal:

Année:

2019

Fichier:

PDF, 2.73 MB

2019

43

Neural Inductive Matrix Completion with Graph Convolutional Networks for miRNA-disease Association Prediction

Li, Jin, Zhang, Sai, Liu, Tao, Ning, Chenxi, Zhang, Zhuoxuan, Zhou, Wei, Mathelier, Anthony

Journal:

Année:

2020

Fichier:

PDF, 1.34 MB

2020

44

RiboFlow, RiboR and RiboPy: An ecosystem for analyzing ribosome profiling data at read length resolution

Ozadam, Hakan, Geng, Michael, Cenik, Can, Mathelier, Anthony

Journal:

Année:

2020

Langue:

english

Fichier:

PDF, 319 KB

english, 2020

45

Visualization of circular RNAs and their internal splicing events from transcriptomic data

Zheng, Yi, Zhao, Fangqing, Mathelier, Anthony

Journal:

Année:

2020

Langue:

english

Fichier:

PDF, 395 KB

english, 2020

46

Nearest-neighbor Projected-Distance Regression (NPDR) for detecting network interactions with adjustments for multiple tests and confounding

Le, Trang T, Dawkins, Bryan A, McKinney, Brett A, Mathelier, Anthony

Journal:

Année:

2020

Langue:

english

Fichier:

PDF, 466 KB

english, 2020

47

Joint reconstruction of multiple gene networks by simultaneously capturing inter-tumor and intra-tumor heterogeneity

Tu, Jia-Juan, Ou-Yang, Le, Yan, Hong, Zhang, Xiao-Fei, Qin, Hong, Mathelier, Anthony

Journal:

Année:

2020

Langue:

english

Fichier:

PDF, 1.74 MB

english, 2020

48

DRIMC: an improved drug repositioning approach using Bayesian inductive matrix completion

Zhang, Wenjuan, Xu, Hunan, Li, Xiaozhong, Gao, Qiang, Wang, Lin, Mathelier, Anthony

Journal:

Année:

2020

Langue:

english

Fichier:

PDF, 1.55 MB

english, 2020

49

DEEPrior: a deep learning tool for the prioritization of gene fusions

Lovino, Marta, Ciaburri, Maria Serena, Urgese, Gianvito, Di Cataldo, Santa, Ficarra, Elisa, Mathelier, Anthony

Journal:

Année:

2020

Fichier:

PDF, 174 KB

2020

50

GeneSwitches: Ordering gene-expression and functional events in single-cell experiments

Cao, Elaine Y, Ouyang, John F, Rackham, Owen J L, Mathelier, Anthony

Journal:

Année:

2020

Fichier:

PDF, 321 KB

2020