Ecosyste.ms: Papers

10.1186/s12916-020-01686-8

In utero and childhood exposure to tobacco smoke and multi-layer molecular signatures in children
Cited by: 19
Author(s): Marta Vives-Usano, Carles Hernández-Ferrer, Léa Maitre, Carlos Ruiz‐Arenas, Sandra Andrušaitytė, Eva Borràs, Ángel Carracedo, Maribel Casas, Leda Chatzi, Muireann Coen, Xavier Estivill, Juan R. González, Kristine B. Gützkow, Hector C. Keun, Chung-Ho E Lau, Solène Cadiou, Johanna Lepeule, Dan Mason, Inés Quintela, Oliver Robinson, Eduard Sabidó, Gillian Santorelli, Per E. Schwarze, Alexandros P. Siskos, Rémy Slama, Marina Vafeiadi, Eulàlia Martı́, Martine Vrijheid, Mariona Bustamante
Software Mentions: 14
Published: over 4 years ago

10.1186/s12885-020-07695-3

Comprehensive analysis of prognostic gene signatures based on immune infiltration of ovarian cancer
Cited by: 18
Author(s): Shi-Bai Yan, Jinling Fang, Yongcai Chen, Yong Xie, Siyou Zhang, Xiaohui Zhu, Fang Fěng
Software Mentions: 13
Published: almost 4 years ago

10.18632/aging.102087

Identification of hub genes in prostate cancer using robust rank aggregation and weighted gene co-expression network analysis
Cited by: 71
Author(s): Zhenyu Song, Chongxi Fan, Zhiyuan Zhuo, Zhe Ma, Wenzhi Li, Gang Chen
Software Mentions: 10
Published: over 5 years ago

10.1186/s12859-016-1442-6

Unboxing cluster heatmaps
Cited by: 25
Author(s): Sophie Engle, Sean Whalen, Alark Joshi, Katherine S. Pollard
Software Mentions: 9
Published: almost 8 years ago

10.1371/journal.pone.0177276

Succinct workflows for circulating tumor cells after enrichment: From systematic counting to mutational profiling
Cited by: 11
Author(s): Vernon G. Wong, Josephine Mun Yee Ko, Chi-Tat Lam, Maria Li Lung
Software Mentions: 9
Published: over 7 years ago

10.1186/s12885-017-3726-2

Guanylate-binding protein-1 is a potential new therapeutic target for triple-negative breast cancer
Cited by: 26
Author(s): Melissa Quintero, Douglas Adamóski, Larissa Menezes dos Reis, Carolline Fernanda Rodrigues Ascenção, Krishina Ratna Sousa de Oliveira, Kaliandra de Almeida Gonçalves, Milton Dias, Marcelo Falsarella Carazzolle, Sandra Martha Gomes Dias
Software Mentions: 9
Published: about 7 years ago

10.1186/s13148-020-00996-1

Integrated analysis reveals the alterations that LMNA interacts with euchromatin in LMNA mutation-associated dilated cardiomyopathy
Cited by: 9
Author(s): Xiaolin Zhang, Xiuli Shao, Ruijia Zhang, Rongli Zhu, Rui Feng
Software Mentions: 8
Published: almost 4 years ago

10.18632/aging.203017

Identification of key transcriptome biomarkers based on a vital gene module associated with pathological changes in Alzheimer’s disease
Cited by: 11
Author(s): Tong Zhang, Yang Shen, Yiqing Guo, Junyan Yao
Software Mentions: 7
Published: over 3 years ago

10.18632/aging.103949

Analysis of DNA methylation-driven genes for predicting the prognosis of patients with colorectal cancer
Cited by: 3
Author(s): Boshi Fu, Du Cheng, Zhuona Wu, Mingwei Li, Yi Zhao, Xinli Liu, Huizhe Wu, Minjie Wei
Software Mentions: 7
Published: about 4 years ago

10.7717/peerj.4402

Comparative genomic analysis of a new tellurite-resistant<i>Psychrobacter</i>strain isolated from the Antarctic Peninsula
Cited by: 19
Author(s): Claudia Muñoz-Villagrán, Katterinne N. Mendez, Fabián A. Cornejo, Maximiliano Figueroa, Agustina Undabarrena, Eduardo Morales, Mauricio Arenas-Salinas, Felipe Arenas, Eduardo Castro-Nallar, Claudio C. Vásquez
Software Mentions: 6
Published: almost 7 years ago

10.1186/s13073-019-0644-8

Clinical utility of custom-designed NGS panel testing in pediatric tumors
Cited by: 77
Author(s): Lea F. Surrey, Suzanne P. MacFarland, Fengqi Chang, Ke Cao, Komal S. Rathi, Gozde Akgumus, Daniel Gallo, Fumin Lin, Adam Gleason, Pichai Raman, Richard Aplenc, Rochelle Bagatell, Jane E. Minturn, Yaël P. Mossé, Mariarita Santi, Sarah K. Tasian, Angela J. Waanders, Mahdi Sarmady, John M. Maris, Stephen P. Hunger, Marilyn M. Li
Software Mentions: 6
Published: over 5 years ago

10.3390/genes9010019

High Density Single Nucleotide Polymorphism (SNP) Mapping and Quantitative Trait Loci (QTL) Analysis in a Biparental Spring Triticale Population Localized Major and Minor Effect Fusarium Head Blight Resistance and Associated Traits QTL
Cited by: 28
Author(s): Raman Dhariwal, George Fedak, Yves Dion, Curtis Pozniak, André Laroche, François Eudes, H. S. Randhawa
Software Mentions: 6
Published: almost 7 years ago

10.1186/s12885-020-07724-1

Correction to: Comprehensive analysis of prognostic gene signatures based on immune infiltration of ovarian cancer
Cited by: 1
Author(s): Shi-Bai Yan, Jinling Fang, Yongcai Chen, Yong Xie, Siyou Zhang, Xiaohui Zhu, Fang Fěng
Software Mentions: 6
Published: almost 4 years ago

10.1155/2020/4908427

Comprehensive Analysis of mRNA Expression Profiles in Head and Neck Cancer by Using Robust Rank Aggregation and Weighted Gene Coexpression Network Analysis
Cited by: 4
Author(s): Zijian Cao, Yin-Jie Ao, Yu Guo, Shui‐Hong Zhou
Software Mentions: 4
Published: almost 4 years ago

10.1111/bpa.12595

Epigenomic signature of adrenoleukodystrophy predicts compromised oligodendrocyte differentiation
Cited by: 18
Author(s): Agatha Schlüter, Juan Sandoval, Stéphane Fourcade, Ángel Díaz‐Lagares, Montserrat Ruíz, Patrizia Casaccia, Manel Esteller, Aurora Pujol
Software Mentions: 4
Published: over 6 years ago

10.1002/cam4.2192

Immune microenvironments differ in immune characteristics and outcome of glioblastoma multiforme
Cited by: 21
Author(s): Botao Zhang, Rongfang Shen, Shujun Cheng, Feng Li
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2016.01519

Transcriptomic and Metabolomic Analysis Revealed Multifaceted Effects of Phage Protein Gp70.1 on Pseudomonas aeruginosa
Cited by: 11
Author(s): Xia Zhao, Canhuang Chen, Xingyu Jiang, Wei Shen, Guangtao Huang, Shuai Le, Shuguang Lu, Lingyun Zou, Qingshan Ni, Ming Li, Yan Zhao, Jing Wang, Xiancai Rao, Fuquan Hu, Yinling Tan
Software Mentions: 4
Published: about 8 years ago

10.1534/g3.119.400716

Whole Genome Sequencing and Comparative Genomics of Two Nematicidal <i>Bacillus</i> Strains Reveals a Wide Range of Possible Virulence Factors
Cited by: 9
Author(s): Nik Susič, Sandra Janežič, Maja Rupnik, Barbara Gerič Stare
Software Mentions: 4
Published: over 4 years ago

10.3390/ijms21114057

Embryonic Program Activated during Blast Crisis of Chronic Myelogenous Leukemia (CML) Implicates a TCF7L2 and MYC Cooperative Chromatin Binding
Cited by: 3
Author(s): Christophe Desterke, Patricia Hugues, Jin Wook Hwang, Annelise Bennaceur-Griscelli, Ali G. Turhan
Software Mentions: 3
Published: over 4 years ago

10.3389/fonc.2019.00314

Effect of Compound Kushen Injection, a Natural Compound Mixture, and Its Identified Chemical Components on Migration and Invasion of Colon, Brain, and Breast Cancer Cell Lines
Cited by: 41
Author(s): Saeed Nourmohammadi, Thazin Nwe Aung, Jingang Cui, Jinxin V. Pei, Michael L. De Ieso, Yuka Harata-Lee, Zhibo Qu, David L. Adelson, Andrea J. Yool
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0138782

Transcriptome Profiling of Pediatric Core Binding Factor AML
Cited by: 13
Author(s): Chih Hao Hsu, Cu Nguyen, Chunhua Yan, Rhonda E. Ries, Qing Rong Chen, Ying Hu, Fabiana Ostronoff, Derek L. Stirewalt, George A. Komatsoulis, Shawn Levy, Daoud Meerzaman, Soheil Meshinchi
Software Mentions: 3
Published: about 9 years ago

10.1111/jcmm.14664

The non‐coding RNome after splenectomy
Cited by: 12
Author(s): Mihnea P. Dragomir, Ștefan Tudor, Kan Okubo, Masayoshi Shimizu, Meng Chen, Dana Elena Giza, Weixiang He, Cristina Ivan, C Vasilescu
Software Mentions: 3
Published: about 5 years ago

10.3390/cancers12010064

RNA Sequencing of Collecting Duct Renal Cell Carcinoma Suggests an Interaction between miRNA and Target Genes and a Predominance of Deregulated Solute Carrier Genes
Cited by: 15
Author(s): Sven Wach, Helge Täubert, Katrin Weigelt, Nora Hase, Marcel Köhn, Danny Misiak, Stefan Hüttelmaier, Christine Stöhr, Andreas Kahlmeyer, Florian Haller, Julio Vera, Arndt Hartmann, Bernd Wullich, Xin Lai
Software Mentions: 3
Published: almost 5 years ago

10.3390/cells9092092

An Evolutionary Cancer Epigenetic Approach Revealed DNA Hypermethylation of Ultra-Conserved Non-Coding Elements in Squamous Cell Carcinoma of Different Mammalian Species
Cited by: 2
Author(s): Luca Morandi, Silvia Sabattini, Andrea Renzi, Antonella Rigillo, Giuliano Bettini, Eva Dervas, A Schauer, M. Morandi, Davide Bartolomeo Gissi, Achille Tarsitano, Stefania Evangelisti, Caterina Tonon
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2017.00456

Comparative Genomics Analysis of a New Exiguobacterium Strain from Salar de Huasco Reveals a Repertoire of Stress-Related Genes and Arsenic Resistance
Cited by: 30
Author(s): Juan Castro‐Severyn, Francisco Remonsellez, Sandro L. Valenzuela, Cesar Salinas, Jonathan Fortt, Pablo S. Aguilar, Coral Pardo-Esté, Cristina Dorador, Raquel Quatrini, Franck Molina, Daniel Aguayo, Eduardo Castro-Nallar, Claudia P. Saavedra
Software Mentions: 3
Published: over 7 years ago

10.1093/g3journal/jkaa026

<i>De novo</i> assembly of a chromosome-scale reference genome for the northern flicker <i>Colaptes auratus</i>
Cited by: 3
Author(s): Jack P. Hruska, Joseph D. Manthey
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12859-018-2440-7

Comparing the performance of selected variant callers using synthetic data and genome segmentation
Cited by: 35
Author(s): Xiaopeng Bian, Bin Zhu, Mingyi Wang, Ying Hu, Qingrong Chen, Cu Nguyen, Belynda Hicks, Daoud Meerzaman
Software Mentions: 3
Published: about 6 years ago

10.18632/oncotarget.26029

Identification of a novel gene fusion in ALT positive osteosarcoma
Cited by: 27
Author(s): Emily Mason-Osann, Anqi Dai, Jess Floro, Ying Jie Lock, Matthew Reiss, Himabindu Gali, Adeline Matschulat, Adam Labadorf, Rachel Litman Flynn
Software Mentions: 3
Published: about 6 years ago

10.1155/2021/4664955

Systematic Profiling of mRNA Splicing Reveals the Prognostic Predictor and Potential Therapeutic Target for Glioblastoma Multiforme
Cited by: 5
Author(s): Botao Zhang, Quanyou Wu, Shujun Cheng, Wenbin Li
Software Mentions: 3
Published: over 3 years ago

10.1155/2017/6870614

Are Fusion Transcripts in Relapsed/Metastatic Head and Neck Cancer Patients Predictive of Response to Anti-EGFR Therapies?
Cited by: 2
Author(s): Paolo Bossi, Marco Siano, Cristiana Bergamini, Maria Cossu Rocca, Andrea Pietro Sponghini, Marco Giannoccaro, Luca Tonella, Alessandro Paolì, Edoardo Marchesi, Federica Perrone, Silvana Pilotti, Laura D. Locati, Silvana Canevari, Lisa Licitra, Loris De Cecco
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-020-60120-4

Systematic analysis of the Hippo pathway organization and oncogenic alteration in evolution
Cited by: 13
Author(s): Yuxuan Chen, Han Han, Gayoung Seo, Rebecca Vargas, Bing Yang, Kimberly Chuc, Huabin Zhao, Wenqi Wang
Software Mentions: 2
Published: over 4 years ago

10.1186/s13068-017-0743-y

Systematic and functional identification of small non-coding RNAs associated with exogenous biofuel stress in cyanobacterium Synechocystis sp. PCC 6803
Cited by: 22
Author(s): Guangsheng Pei, Tao Sun, Shawn Chen, Lei Chen, Weiwen Zhang
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2020.00860

Insights Into the Resistome of Bovine Clinical Mastitis Microbiome, a Key Factor in Disease Complication
Cited by: 52
Author(s): M. Nazmul Hoque, Arif Istiaq, Rebecca Clement, Keylie M. Gibson, Otun Saha, Ovinu Kibria Islam, Ruhshan Ahmed Abir, Munawar Sultana, Amam Zonaed Siddiki, Keith A. Crandall, M. Anwar Hossain
Software Mentions: 1
Published: over 4 years ago

10.3390/metabo9100241

Characterization of Lipid Profiles after Dietary Intake of Polyunsaturated Fatty Acids Using Integrated Untargeted and Targeted Lipidomics
Cited by: 45
Author(s): Satoko Naoe, Hiroshi Tsugawa, Mikiko Takahashi, Kazutaka Ikeda, Makoto Arita
Software Mentions: 1
Published: about 5 years ago

10.3390/microorganisms8081135

Multidrug-Resistant Avian Pathogenic Escherichia coli Strains and Association of Their Virulence Genes in Bangladesh
Cited by: 25
Author(s): Otun Saha, M. Nazmul Hoque, Ovinu Kibria Islam, Munawar Sultana, Mohammad Anwar Hossain
Software Mentions: 1
Published: over 4 years ago

10.3390/jcm8091284

Next-Generation Sequencing Profiles of the Methylome and Transcriptome in Peripheral Blood Mononuclear Cells of Rheumatoid Arthritis
Cited by: 7
Author(s): Chia‐Chun Tseng, Yuan‐Zhao Lin, Chia‐Hui Lin, Ruei‐Nian Li, Chang-Yi Yen, Hua‐Chen Chan, Wen‐Chan Tsai, Tsan‐Teng Ou, Cheng‐Chin Wu, Wan‐Yu Sung, Jeng-Hsien Yen
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-019-5711-4

Chromosomal imbalance in pigs showing a syndromic form of cleft palate
Cited by: 13
Author(s): Alexander Grahofer, Anna Letko, Irene M. Häfliger, Vidya Jagannathan, Alain Ducos, Olivia K. Richard, Vanessa G. Peter, Heiko Nathues, Cord Drögemüller
Software Mentions: 1
Published: over 5 years ago

10.3390/genes10050362

A Missense Variant in SCN8A in Alpine Dachsbracke Dogs Affected by Spinocerebellar Ataxia
Cited by: 7
Author(s): Anna Letko, Elisabeth Dietschi, Marco Nieburg, Vidhya Jagannathan, Corinne Gurtner, Anna Oevermann, Cord Drögemüller
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0188914

Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence
Cited by: 4
Author(s): A. F. Yassin, Stefan Langenberg, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Supratim Mukherjee, T. B. K. Reddy, Chris Daum, Nicole Shapiro, Natalia Ivanova, Tanja Woyke, Nikos C. Kyrpides
Software Mentions: 1
Published: almost 7 years ago

10.7554/eLife.20214

Blood transcriptome based biomarkers for human circadian phase
Cited by: 109
Author(s): Emma Laing, Carla S. Möller-Levet, Norman Poh, Nayantara Santhi, Simon N. Archer, Derk‐Jan Dijk
Software Mentions: 1
Published: almost 8 years ago