Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: ELMER

https://packages.ecosyste.ms/registries/bioconductor.org/packages/ELMER

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
1 version
Latest release: about 1 year ago
35,302 downloads total

Papers Mentioning ELMER 19

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
Cited by: 105
Author(s): Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Fulvio D’Angelo, Gianluca Bontempi, Michele Ceccarelli, Houtan Noushmehr
Software Mentions: 17
Published: almost 8 years ago

10.3389/fgene.2020.522125

Identification of Prognostic Markers in Cholangiocarcinoma Using Altered DNA Methylation and Gene Expression Profiles
Cited by: 11
Author(s): Nitish K. Mishra, Meng Niu, Siddesh Southekal, Prachi Bajpai, Amr Elkholy, Upender Manne, Chittibabu Guda
Software Mentions: 14
Published: about 4 years ago

10.1186/s12964-021-00728-9

Multi-omics analysis of tumor angiogenesis characteristics and potential epigenetic regulation mechanisms in renal clear cell carcinoma
Cited by: 28
Author(s): Wenzhong Zheng, Shiqiang Zhang, Huan Guo, Xiaobao Chen, Zhangcheng Huang, Shaoqin Jiang, Mengqiang Li
Software Mentions: 8
Published: over 3 years ago

10.18632/oncotarget.15993

Genome-wide DNA methylation analysis reveals molecular subtypes of pancreatic cancer
Cited by: 67
Author(s): Nitish K. Mishra, Chittibabu Guda
Software Mentions: 7
Published: over 7 years ago

10.1089/cmb.2020.0081

GeneDMRs: An R Package for Gene-Based Differentially Methylated Regions Analysis
Cited by: 5
Author(s): Xiao Wang, Dan Hao, Haja N. Kadarmideen
Software Mentions: 6
Published: over 3 years ago

10.1093/gigascience/giaa064

Integrative computational epigenomics to build data-driven gene regulation hypotheses
Cited by: 10
Author(s): Tyrone Chen, Sonika Tyagi
Software Mentions: 6
Published: over 4 years ago

10.1186/s12885-020-06784-7

Right and left-sided colon cancers - specificity of molecular mechanisms in tumorigenesis and progression
Cited by: 45
Author(s): Kavitha Mukund, Natalia Syulyukina, Sonia Ramamoorthy, Shankar Subramaniam
Software Mentions: 5
Published: over 4 years ago

10.1186/s13073-020-00749-y

Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford progeria syndrome
Cited by: 36
Author(s): Florian Köhler, Felix Bormann, Günter Raddatz, Julian Gutekunst, Nick Gilbert, Tanja Musch, Anke S. Lonsdorf, Sylvia Erhardt, Frank Lyko, Manuel Rodríguez-Paredes
Software Mentions: 5
Published: over 4 years ago

10.3390/cancers12030680

Global RNA Expression and DNA Methylation Patterns in Primary Anaplastic Thyroid Cancer
Cited by: 14
Author(s): Naveen Ravi, Minjun Yang, Nektaria Mylona, Johan Wennerberg, Kajsa Paulsson
Software Mentions: 4
Published: over 4 years ago

10.3389/fgene.2021.563051

Epigenetic Age Acceleration of Stomach Adenocarcinoma Associated With Tumor Stemness Features, Immunoactivation, and Favorable Prognosis
Cited by: 7
Author(s): Chunhong Hong, Shaohua Yang, Qiaojin Wang, Shiqiang Zhang, Wenhui Wu, Jinyao Chen, Danhui Zhong, Mingzhe Li, Liang Li, Jianfeng Li, Hong Yu, Hong Chen, Qianlin Zeng, Changhua Zhang
Software Mentions: 4
Published: over 3 years ago

10.3389/fncel.2019.00352

Beyond the Exome: The Non-coding Genome and Enhancers in Neurodevelopmental Disorders and Malformations of Cortical Development
Cited by: 48
Author(s): Elena Perenthaler, Soheil Yousefi, Eva Niggl, Tahsin Stefan Barakat
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-017-1266-3

Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network
Cited by: 30
Author(s): Priyanka Dhingra, Alexander Martínez-Fundichely, Adeline Berger, Franklin W. Huang, Andre Neil Forbes, Eric Minwei Liu, De Li Liu, Andrea Sboner, Pablo Tamayo, David S. Rickman, Mark A. Rubin, Ekta Khurana
Software Mentions: 2
Published: over 7 years ago

10.1186/s13059-018-1442-0

MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis
Cited by: 20
Author(s): Yin Tong, Jie Sun, Chi Fat Wong, Qianjin Kang, Beibei Ru, Ching Ngar Wong, Alexander C.L. Chan, Suet Yi Leung, Jiangwen Zhang
Software Mentions: 2
Published: over 6 years ago

10.3390/ma9080668

Micro-Tomographic Investigation of Ice and Clathrate Formation and Decomposition under Thermodynamic Monitoring
Cited by: 4
Author(s): Stefan Arzbacher, Joerg Petrasch, Alexander Ostermann, Thomas Loerting
Software Mentions: 2
Published: over 8 years ago

10.1186/s13059-015-0668-3

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes
Cited by: 163
Author(s): Lijing Yao, Hui Shen, Peter W. Laird, Peggy J. Farnham, Benjamin P. Berman
Software Mentions: 2
Published: over 9 years ago

10.3390/md7040816

Isolation of C11 Cyclopentenones from Two Didemnid Species, Lissoclinum sp. and Diplosoma sp.
Cited by: 24
Author(s): Takayuki Ogi, Palupi Margiastuti, Toshiaki Teruya, Junsei Taira, Kiyotake Suenaga, Katsuhiro Ueda
Software Mentions: 1
Published: almost 15 years ago

10.1038/s41598-020-60845-2

Collective effects of long-range DNA methylations predict gene expressions and estimate phenotypes in cancer
Cited by: 11
Author(s): Soyeon Kim, Hyun Jung Park, Xiangqin Cui, Degui Zhi
Software Mentions: 1
Published: over 4 years ago

10.1093/bioinformatics/bty902

ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles
Cited by: 74
Author(s): Tiago C. Silva, Simon Coetzee, Nicole Gull, Lijing Yao, Dennis J. Hazelett, Houtan Noushmehr, De–Chen Lin, Benjamin P. Berman
Software Mentions: 1
Published: about 6 years ago

10.3390/s20010266

Modelling the Characteristics of Ring-Shaped Magnetoelastic Force Sensor in Mohri’s Configuration
Cited by: 6
Author(s): Anna Ostaszewska-Liżewska, Roman Szewczyk, Peter Råback, Mika Malinen
Software Mentions: 1
Published: almost 5 years ago