bioconductor: CEMiTool | Projects

10.1186/s12859-021-04179-4

GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package
Cited by: 12
Author(s): Gwenaëlle G. Lemoine, Marie‐Pier Scott‐Boyer, Bathilde Ambroise, Olivier Périn, Arnaud Droit
Software Mentions: 10
Published: over 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 age
Cited 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: over 3 years ago

10.1186/s41065-021-00196-8

Dynamic co-expression modular network analysis in nonalcoholic fatty liver disease
Cited by: 4
Author(s): Jing Zheng, WU Hui-zhong, Zhiying Zhang, Songqiang Yao
Software Mentions: 9
Published: over 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 Carcinoma
Cited by: 3
Author(s): Zongfu Pan, Ying He, Wei Zhu, Tao Xu, Xiaoping Hu, Ping Huang
Software Mentions: 8
Published: over 3 years ago

10.3389/fcimb.2018.00326

In Search of Biomarkers for Pathogenesis and Control of Leishmaniasis by Global Analyses of Leishmania-Infected Macrophages
Cited by: 16
Author(s): Patrícia Sampaio Tavares Veras, Pablo Ivan Pereira Ramos, Juliana Perrone Bezerra de Menezes
Software Mentions: 8
Published: about 6 years ago

10.1038/s41597-020-00659-z

lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA
Cited 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: about 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 subtype
Cited 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: over 4 years ago

10.1073/pnas.1822046116

Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination
Cited 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: over 5 years ago

10.1007/s10142-018-0639-3

Hotspots in the genomic architecture of field drought responses in wheat as breeding targets
Cited 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: about 6 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 model
Cited 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-pitvipers
Cited 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: almost 5 years ago

10.1038/s42003-021-02204-z

Random errors in protein synthesis activate an age-dependent program of muscle atrophy in mice
Cited 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: over 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 Progress
Cited by: 0
Author(s): Dan Zheng, Xiujing He, Ting Luo, Xiaorong Zhong, Hong Zheng, Jiqiao Yang, Yanchu Li, Jing Jing
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12859-018-2053-1

CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses
Cited 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: almost 7 years ago

10.1523/ENEURO.0263-20.2021

Intrauterine Growth Restriction Followed by Oxygen Support Uniquely Interferes with Genetic Regulators of Myelination
Cited 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: over 3 years ago

10.1186/s13293-020-00288-6

Sex-specific and shared expression profiles of vulnerability and resilience to trauma in brain and blood
Cited 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 Pikeperch
Cited 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: about 3 years ago

10.3389/fphys.2020.567614

Long Non-coding RNAs Are Differentially Expressed After Different Exercise Training Programs
Cited by: 25
Author(s): Bernardo Bonilauri, Bruno Dallagiovanna
Software Mentions: 3
Published: about 4 years ago

10.7150/jca.31435

Aberrant AFP expression characterizes a subset of hepatocellular carcinoma with distinct gene expression patterns and inferior prognosis
Cited by: 15
Author(s): Wei Chen, Jianjun Peng, Jinning Ye, Weigang Dai, Guanghua Li, Yulong He
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-019-41205-1

A Systems Vaccinology Approach Reveals the Mechanisms of Immunogenic Responses to Hantavax Vaccination in Humans
Cited 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 macrophages
Cited 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: about 5 years ago

10.1038/s41398-020-0730-0

Stress genomics revisited: gene co-expression analysis identifies molecular signatures associated with childhood adversity
Cited by: 19
Author(s): Linda Dieckmann, Steve W. Cole, Robert Kumsta
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.ppat.1007880

Systems analysis of subjects acutely infected with the Chikungunya virus
Cited 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: over 5 years ago

10.3389/fgene.2019.00146

webCEMiTool: Co-expression Modular Analysis Made Easy
Cited 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 Genes
Cited 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: over 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 Responses
Cited 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: over 5 years ago

10.3389/fimmu.2021.693074

Plasma Metabolomics Reveals Dysregulated Metabolic Signatures in HIV-Associated Immune Reconstitution Inflammatory Syndrome
Cited 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: over 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 deficits
Cited by: 19
Author(s): Jamal B Williams, Qing Cao, Zhen Yan
Software Mentions: 2
Published: almost 4 years ago

10.18632/aging.104091

Alteration of tumor-associated macrophage subtypes mediated by KRT6A in pancreatic ductal adenocarcinoma
Cited 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: about 4 years ago

10.1590/1678-9199-JVATITD-2019-0061

São Paulo School of Advanced Sciences on Vaccines: an overview
Cited 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: almost 5 years ago

10.1155/2021/8889986

GLI3 Promotes Invasion and Predicts Poor Prognosis in Colorectal Cancer
Cited by: 10
Author(s): Mingyang Shen, Zhengyuan Zhang, Ping Wang
Software Mentions: 1
Published: almost 4 years ago

Ecosyste.ms: Papers

Projects: bioconductor: CEMiTool

Papers Mentioning CEMiTool 31