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: CEMiTool
https://packages.ecosyste.ms/registries/bioconductor.org/packages/CEMiTool
Co-expression Modules identification Tool
1 version
Latest release: 10 months ago
25,816 downloads total
Papers Mentioning CEMiTool 31
10.1186/s12859-021-04179-4
GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor packageCited by: 12
Author(s): Gwenaëlle G. Lemoine, Marie‐Pier Scott‐Boyer, Bathilde Ambroise, Olivier Périn, Arnaud Droit
Software Mentions: 10
Published: about 3 years ago
10.1172/jci.insight.147535
The relationship between cytokine and neutrophil gene network distinguishes SARS-CoV-2–infected patients by sex and ageCited by: 12
Author(s): Paula Paccielli Freire, Amélia Pasqual Marques, G. Baiocchi, Lena F. Schimke, Dennyson Leandro M. Fonseca, Ranieri Coelho Salgado, Igor Salerno Filgueiras, Sarah M.S. Napoleao, Desirée Rodrigues Plaça, Karen Tiemi Akashi, Thiago Dominguez Crespo Hirata, Nadia El Khawanky, Lasse Melvær Giil, Gustavo Cabral-Miranda, Robson Francisco Carvalho, Luís Carlos S. Ferreira, Antônio Condino‐Neto, Helder I. Nakaya, Igor Jurišica, Hans D. Ochs, Niels Olsen Saraiva Câmara, Vera Lúcia Garcia Calich, Otávio Cabral-Marques
Software Mentions: 10
Published: about 3 years ago
10.1186/s41065-021-00196-8
Dynamic co-expression modular network analysis in nonalcoholic fatty liver diseaseCited by: 4
Author(s): Jing Zheng, WU Hui-zhong, Zhiying Zhang, Songqiang Yao
Software Mentions: 9
Published: almost 3 years ago
10.3389/fonc.2021.597447
A Dynamic Transcription Factor Signature Along the Colorectal Adenoma-Carcinoma Sequence in Patients With Co-Occurrent Adenoma and CarcinomaCited by: 3
Author(s): Zongfu Pan, Ying He, Wei Zhu, Tao Xu, Xiaoping Hu, Ping Huang
Software Mentions: 8
Published: about 3 years ago
10.3389/fcimb.2018.00326
In Search of Biomarkers for Pathogenesis and Control of Leishmaniasis by Global Analyses of Leishmania-Infected MacrophagesCited by: 16
Author(s): Patrícia Sampaio Tavares Veras, Pablo Ivan Pereira Ramos, Juliana Perrone Bezerra de Menezes
Software Mentions: 8
Published: almost 6 years ago
10.1038/s41597-020-00659-z
lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNACited by: 35
Author(s): Fayaz Seifuddin, Komudi Singh, Abhilash Suresh, Jennifer Judy, Yun Ching Chen, Vijender Chaitankar, Ilker Tunc, Xiangbo Ruan, Ping Li, Yi Chen, Haiming Cao, Richard S. Lee, Fernando S. Goes, Peter P. Zandi, M. Saleet Jafri, Mehdi Pirooznia
Software Mentions: 7
Published: almost 4 years ago
10.1038/s41598-020-69905-z
A lncRNA landscape in breast cancer reveals a potential role for AC009283.1 in proliferation and apoptosis in HER2-enriched subtypeCited by: 20
Author(s): Alberto Cedro‐Tanda, Magdalena Ríos-Romero, Sandra Romero-Córdoba, Mireya Cisneros-Villanueva, Rosa Rebollar-Vega, Luis Alfaro-Ruiz, Silvia Jiménez-Morales, Carlos Alberto Domínguez-Reyes, Felipe Villegas-Carlos, Alberto Tenorio-Torres, Verónica Bautista-Piña, Fredy Omar Beltrán-Anaya, Alfredo Hidalgo‐Miranda
Software Mentions: 6
Published: almost 4 years ago
10.1073/pnas.1822046116
Long noncoding RNAs are involved in multiple immunological pathways in response to vaccinationCited by: 47
Author(s): Diógenes Saulo de Lima, Lucas Esteves Cardozo, Vinicius Maracaja‐Coutinho, Andreas Suhrbier, Karim Mane, David Jeffries, Eduardo Lani Volpe da Silveira, Paulo Amaral, Rino Rappuoli, Thushan I. de Silva, Helder I. Nakaya
Software Mentions: 5
Published: almost 5 years ago
10.1007/s10142-018-0639-3
Hotspots in the genomic architecture of field drought responses in wheat as breeding targetsCited by: 38
Author(s): Sergio Gálvez, Rosa Mérida-García, C. Camino, Philippa Borrill, Michaël Abrouk, Ricardo H. Ramírez-González, Sezgi Biyiklioglu, Francisco Amil-Ruíz, Gabriel Dorado, Hikmet Budak, Victoria González-Dugo, Pablo J. Zarco‐Tejada, R. Appels, Cristóbal Uauy, Pilar Hernández
Software Mentions: 5
Published: over 5 years ago
10.1038/s41598-020-63275-2
Modulation of stress and immune response by Amblyomin-X results in tumor cell death in a horse melanoma modelCited by: 9
Author(s): Flávio Lichtenstein, Asif Iqbal, Sonia Elisabete Alves de Lima Will, Rosemary Viola Bösch, Carlos DeOcesano-Pereira, Maurício Barbugiani Goldfeder, Roger Chammas, Carlos Eduardo Madureira Trufen, Kátia L.P. Morais, Jean Gabriel de Souza, Renato José Mendonça Natalino, Inácio L.M. Junqueira-de-Azevedo, Milton Yutaka Nishiyama-Jr, Úrsula Castro de Oliveira, F Alves, Jaqueline Mayara Araujo, Aline Ramos Maia Lobba, Ana Marisa Chudzinski‐Tavassi
Software Mentions: 5
Published: over 4 years ago
10.1186/s12864-020-6545-9
Trait differentiation and modular toxin expression in palm-pitvipersCited by: 16
Author(s): Andrew J. Mason, Mark J. Margres, Jason L. Strickland, Darin R. Rokyta, Mahmood Sasa, Christopher L. Parkinson
Software Mentions: 5
Published: over 4 years ago
10.1038/s42003-021-02204-z
Random errors in protein synthesis activate an age-dependent program of muscle atrophy in miceCited by: 5
Author(s): James M. Moore, Rashid Akbergenov, Martina Nigri, Patricia Isnard-Petit, Amandine Grimm, Petra Seebeck, Lisa Michelle Restelli, Stephan Frank, Anne Eckert, Kader Thiam, David P Wolfer, Dimitri Shcherbakov, Erik C. Böttger
Software Mentions: 5
Published: about 3 years ago
10.3389/fmolb.2020.605623
Long Non-coding RNA BTG3-7:1 and JUND Co-regulate C21ORF91 to Promote Triple-Negative Breast Cancer ProgressCited by: 0
Author(s): Dan Zheng, Xiujing He, Ting Luo, Xiaorong Zhong, Hong Zheng, Jiqiao Yang, Yanchu Li, Jing Jing
Software Mentions: 4
Published: over 3 years ago
10.1186/s12859-018-2053-1
CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analysesCited by: 176
Author(s): Pedro Russo, Gustavo Rodrigues Ferreira, Lucas Esteves Cardozo, Matheus Carvalho Bürger, Raúl Arias‐Carrasco, Sandra Regina Maruyama, Thiago Dominguez Crespo Hirata, Diógenes Saulo de Lima, Fernando M. Passos, Kiyoshi F. Fukutani, Melissa Lever, João Silva, Vinicius Maracaja‐Coutinho, Hidehiko Nakaya
Software Mentions: 4
Published: over 6 years ago
10.1523/ENEURO.0263-20.2021
Intrauterine Growth Restriction Followed by Oxygen Support Uniquely Interferes with Genetic Regulators of MyelinationCited by: 2
Author(s): Jill Chang, Robert H. Lurie, Abhineet Sharma, Mirrah Bashir, Camille Fung, Robert W. Dettman, Maria L.V. Dizon
Software Mentions: 3
Published: about 3 years ago
10.1186/s13293-020-00288-6
Sex-specific and shared expression profiles of vulnerability and resilience to trauma in brain and bloodCited by: 11
Author(s): Grace S Kim, Monica Uddin
Software Mentions: 3
Published: over 4 years ago
10.3390/cells10092289
Comprehensive Characterization of Multitissue Expression Landscape, Co-Expression Networks and Positive Selection in PikeperchCited by: 1
Author(s): Julien Alban Nguinkal, Marieke Verleih, Lidia de los Ríos-Pérez, Ronald M. Brunner, Arne Sahm, Saptarshi Bej, Alexander Rebl, Tom Goldammer
Software Mentions: 3
Published: almost 3 years ago
10.3389/fphys.2020.567614
Long Non-coding RNAs Are Differentially Expressed After Different Exercise Training ProgramsCited by: 25
Author(s): Bernardo Bonilauri, Bruno Dallagiovanna
Software Mentions: 3
Published: almost 4 years ago
10.7150/jca.31435
Aberrant AFP expression characterizes a subset of hepatocellular carcinoma with distinct gene expression patterns and inferior prognosisCited by: 15
Author(s): Wei Chen, Jianjun Peng, Jinning Ye, Weigang Dai, Guanghua Li, Yulong He
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-019-41205-1
A Systems Vaccinology Approach Reveals the Mechanisms of Immunogenic Responses to Hantavax Vaccination in HumansCited by: 20
Author(s): Anzar Khan, Ok Sarah Shin, Jinhyuk Na, Jae Kwan Kim, Rak Kyun Seong, Man Seong Park, Ji Yun Noh, Joon Young Song, Hee Jin Cheong, Youngja Hwang Park, Woo Joo Kim
Software Mentions: 3
Published: over 5 years ago
10.1038/s41598-019-48741-w
SerpinB2 inhibits migration and promotes a resolution phase signature in large peritoneal macrophagesCited by: 24
Author(s): Wayne A. Schroder, Thiago Dominguez Crespo Hirata, Thuy T. Le, Joy Gardner, Glen M. Boyle, Jonathan Ellis, Eri Nakayama, Dilan Pathirana, Helder I. Nakaya, Andreas Suhrbier
Software Mentions: 3
Published: almost 5 years ago
10.1038/s41398-020-0730-0
Stress genomics revisited: gene co-expression analysis identifies molecular signatures associated with childhood adversityCited by: 19
Author(s): Linda Dieckmann, Steve W. Cole, Robert Kumsta
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.ppat.1007880
Systems analysis of subjects acutely infected with the Chikungunya virusCited by: 26
Author(s): Alessandra Soares‐Schanoski, Natália Baptista Cruz, Luíza Antunes de Castro-Jorge, Roberto Gameiro de Carvalho, Cliomar Alves dos Santos, Nancy da Rós, Ursula de Oliveira, Danuza Duarte Costa, Cecília Luiza Simões Santos, Marielton dos Passos Cunha, Maria Leonor S. Oliveira, Juliana Cardoso Alves, Regina Adalva de Lucena Couto Océa, Danielle Rodrigues Ribeiro, André Nicolau Aquime Gonçalves, Patrícia Gonzalez-Dias, Andreas Suhrbier, Paolo Marinho de Andrade Zanotto, Inácio L.M. Junqueira-de-Azevedo, Dario S. Zamboni, Roque Pacheco de Almeida, Paulo Lee Ho, Jorge Kalil, Milton Yutaka Nishiyama-Jr, Helder I. Nakaya
Software Mentions: 2
Published: about 5 years ago
10.3389/fgene.2019.00146
webCEMiTool: Co-expression Modular Analysis Made EasyCited by: 14
Author(s): Lucas Esteves Cardozo, Pedro Russo, Bruno Gomes-Correia, Mariana Araújo-Pereira, Gonzalo Sepúlveda-Hermosilla, Vinicius Maracaja‐Coutinho, Helder I. Nakaya
Software Mentions: 2
Published: over 5 years ago
10.3390/genes12071103
Classification of High-Grade Serous Ovarian Carcinoma by Epithelial-to-Mesenchymal Transition Signature and Homologous Recombination Repair GenesCited by: 9
Author(s): Min Hwan Sohn, Se Ik Kim, Jong Yeon Shin, Hee Seung Kim, Hyun Hoon Chung, Jae Weon Kim, Maria Lee, Jeong Sun Seo
Software Mentions: 2
Published: about 3 years ago
10.3389/fimmu.2019.01845
Neonatal T Follicular Helper Cells Are Lodged in a Pre-T Follicular Helper Stage Favoring Innate Over Adaptive Germinal Center ResponsesCited by: 12
Author(s): Béatris Mastelic-Gavillet, Maria Vono, Patrícia Gonzalez-Dias, Frederico Moraes Ferreira, Lucas Esteves Cardozo, Paul Henri Lambert, Helder I. Nakaya, Claire‐Anne Siegrist
Software Mentions: 2
Published: almost 5 years ago
10.3389/fimmu.2021.693074
Plasma Metabolomics Reveals Dysregulated Metabolic Signatures in HIV-Associated Immune Reconstitution Inflammatory SyndromeCited by: 9
Author(s): Luxin Pei, Kiyoshi F. Fukutani, Rafael Tibúrcio, Adam Rupert, Eric Dahlstrom, Frances Galindo, Elizabeth Laidlaw, Andrea Lisco, Maura Manion, Bruno B. Andrade, Irini Sereti
Software Mentions: 2
Published: about 3 years ago
10.1093/braincomms/fcab123
Transcriptomic analysis of human brains with Alzheimer’s disease reveals the altered expression of synaptic genes linked to cognitive deficitsCited by: 19
Author(s): Jamal B Williams, Qing Cao, Zhen Yan
Software Mentions: 2
Published: over 3 years ago
10.18632/aging.104091
Alteration of tumor-associated macrophage subtypes mediated by KRT6A in pancreatic ductal adenocarcinomaCited by: 8
Author(s): Junfeng Zhang, Hui Sun, Songsong Liu, Wenjie Huang, Jianyou Gu, Zhiping Zhao, Huan Qin, Liwen Luo, Jiali Yang, Yongfei Fang, Jiayun Ge, Bing Ni, Huaizhi Wang
Software Mentions: 1
Published: over 3 years ago
10.1590/1678-9199-JVATITD-2019-0061
São Paulo School of Advanced Sciences on Vaccines: an overviewCited by: 1
Author(s): Sara Sorgi, Vivian Bonezi, Mariana Ribeiro Dominguez, Alba Marina Gimenez, Irina Dobrescu, Sílvia Beatriz Boscardin, Helder I. Nakaya, Daniel Youssef Bargieri, Irene S. Soares, Eduardo Lani Volpe da Silveira
Software Mentions: 1
Published: over 4 years ago
10.1155/2021/8889986
GLI3 Promotes Invasion and Predicts Poor Prognosis in Colorectal CancerCited by: 10
Author(s): Mingyang Shen, Zhengyuan Zhang, Ping Wang
Software Mentions: 1
Published: over 3 years ago