bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3389/fgene.2020.00091

Genome-Wide Identification and Characterization of DNA Methylation and Long Non-Coding RNA Expression in Gastric Cancer
Cited by: 14
Author(s): Peng Song, Lei Wu, Wenxian Guan
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-019-6397-3

Host plant adaptation in the polyphagous whitefly, Trialeurodes vaporariorum, is associated with transcriptional plasticity and altered sensitivity to insecticides
Cited by: 25
Author(s): Adam Pym, Kumar Saurabh Singh, A. Nordgren, T.G. Emyr Davies, Christoph Zimmer, Jan Eliáš, Russell Slater, Chris Bass
Software Mentions: 4
Published: about 5 years ago

10.1534/g3.114.016238

A Survey of Imprinted Gene Expression in Mouse Trophoblast Stem Cells
Cited by: 27
Author(s): J. Mauro Calabrese, Joshua Starmer, Megan D. Schertzer, Della Yee, Terry Magnuson
Software Mentions: 4
Published: over 9 years ago

10.1186/1471-2164-15-982

Retinal transcriptome profiling at transcription start sites: a cap analysis of gene expression early after axonal injury
Cited by: 19
Author(s): Masayuki Yasuda, Yuji Tanaka, Koji M. Nishiguchi, Morin Ryu, S. Tsuda, Kouichi Maruyama, Toru Nakazawa
Software Mentions: 4
Published: about 10 years ago

10.1186/1471-2164-14-665

Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation
Cited by: 23
Author(s): Matthias Harbers, Sachi Kato, Michiel de Hoon, Yoshihide Hayashizaki, Piero Carninci, Charles Plessy
Software Mentions: 4
Published: about 11 years ago

10.1186/s12864-018-4499-y

Transcripts within rod photoreceptors of the Zebrafish retina
Cited by: 28
Author(s): Chi Sun, Carlos Galicia, Deborah L. Stenkamp
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12864-015-1706-y

Systematically dissecting the global mechanism of miRNA functions in mouse pluripotent stem cells
Cited by: 3
Author(s): Anyou Wang, Qianchuan He, Yan Zhong
Software Mentions: 4
Published: over 9 years ago

10.1186/s12859-021-04061-3

ProgPerm: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries
Cited by: 2
Author(s): Liangliang Zhang, Yushu Shi, Kim Anh, Christine B. Peterson, Robert R. Jenq
Software Mentions: 4
Published: almost 4 years ago

10.3389/fgene.2020.00877

Muscle Transcriptome Analysis Reveals Potential Candidate Genes and Pathways Affecting Intramuscular Fat Content in Pigs
Cited by: 25
Author(s): Xueyan Zhao, Hongmei Hu, Haichao Lin, Wang Cheng, Yanping Wang, Jiying Wang
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-021-81689-4

Polycomb represses a gene network controlling puberty via modulation of histone demethylase Kdm6b expression
Cited by: 19
Author(s): Hollis Wright, Carlos F. Aylwin, Carlos A. Toro, Sergio R. Ojeda, Alejandro Lomniczi
Software Mentions: 4
Published: almost 4 years ago

10.3390/cancers13061421

Efficacy of Targeted Radionuclide Therapy Using [131I]ICF01012 in 3D Pigmented BRAF- and NRAS-Mutant Melanoma Models and In Vivo NRAS-Mutant Melanoma
Cited by: 5
Author(s): Hussein Akil, Mercédès Quintana, J. Raymond, Tommy Billoux, Valentin Benboubker, Sophie Besse, Philippe Auzeloux, Véronique Delmas, Valérie Petit, Lionel Larue, M. D’Incan, Françoise Degoul, Jacques Rouanet
Software Mentions: 4
Published: almost 4 years ago

10.1186/1471-2164-14-S8-S1

Interdisciplinary dialogue for education, collaboration, and innovation: Intelligent Biology and Medicine in and beyond 2013
Cited by: 49
Author(s): Bing Zhang, Yufei Huang, Jason McDermott, Rebecca H Posey, Hua Xu, Zhongming Zhao
Software Mentions: 4
Published: almost 12 years ago

10.3389/fgene.2020.594569

Contributions of Adaptive Plant Architecture to Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice: Molecular Mechanisms Based on Transcriptional Networks
Cited by: 6
Author(s): Isaiah Catalino M. Pabuayon, Ai Kitazumi, Glenn B. Gregorio, Rakesh Kumar Singh, Benildo G. de los Reyes
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-017-3967-0

Regulation of gene expression in roots of the pH-sensitive Vaccinium corymbosum and the pH-tolerant Vaccinium arboreum in response to near neutral pH stress using RNA-Seq
Cited by: 15
Author(s): Miriam Payá‐Milans, Gerardo H. Nunez, James W. Olmstead, Timothy A. Rinehart, Margaret Staton
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-018-5089-8

Impact of energy restriction during late gestation on the muscle and blood transcriptome of beef calves after preconditioning
Cited by: 19
Author(s): Letícia P Sanglard, Moysés Nascimento, Philipe Moriel, Jeffrey R. Sommer, M.S. Ashwell, M. H. Poore, Márcio de Souza Duarte, Nick V. L. Serão
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-021-07790-0

A scaling-free minimum enclosing ball method to detect differentially expressed genes for RNA-seq data
Cited by: 4
Author(s): Yan Zhou, Bin Yang, Junhui Wang, Jiadi Zhu, Guo‐Liang Tian
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-016-2618-1

Transcriptome analysis of highly purified mouse spermatogenic cell populations: gene expression signatures switch from meiotic-to postmeiotic-related processes at pachytene stage
Cited by: 107
Author(s): Irene da Cruz, Rosana Rodríguez-Casuriaga, Federico F. Santiñaque, Joaquina Farías, Gianni Curti, Carlos A. Capoano, Gustavo A. Folle, Ricardo Benavente, José Sotelo‐Silveira, Adriana Geisinger
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2164-15-899

Characterization and comparative profiling of ovarian microRNAs during ovine anestrus and the breeding season
Cited by: 40
Author(s): Ran Di, Jianning He, Shuhui Song, Dongmei Tian, Qiuyue Liu, Xiaojun Liang, Qing Ma, Min Sun, Jiandong Wang, Wenming Zhao, G. L. Cao, Jinxin Wang, Ziyin Yang, Ying Ge, Mingxing Chu
Software Mentions: 4
Published: about 10 years ago

10.1038/s41598-020-80682-7

TIM29 is required for enhanced stem cell activity during regeneration in the flatworm Macrostomum lignano
Cited by: 2
Author(s): Stijn Mouton, Kirill Ustyantsev, Frank W. Beltman, Lisa Glazenburg, Eugène Berezikov
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12865-021-00428-6

Transcriptomics of type 2 diabetic and healthy human neutrophils
Cited by: 8
Author(s): Sarah E. Kleinstein, Jamison McCorrison, A. Razzaque Ahmed, Hatice Hastürk, Thomas E. Van Dyke, Marcelo Freire
Software Mentions: 4
Published: over 3 years ago

10.1186/s12916-021-01925-6

Glycolysis-associated lncRNAs identify a subgroup of cancer patients with poor prognoses and a high-infiltration immune microenvironment
Cited by: 17
Author(s): Kuo Hao Ho, Tzu Wen Huang, Chwen Ming Shih, Yi Ting Lee, Ann Jeng Liu, Peng Hsu Chen, Ku Chung Chen
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12916-020-01605-x

Circulating mRNAs are differentially expressed in pregnancies with severe placental insufficiency and at high risk of stillbirth
Cited by: 23
Author(s): Natalie J. Hannan, Owen Stock, Rebecca Spencer, Clare Whitehead, Anna L. David, Katie Groom, Scott Petersen, Amanda Henry, Joanne Said, Sean Seeho, Stefan C. Kane, Lavinia Gordon, Sally Beard, Kantaraja Chindera, Smita T. Karegodar, Richard Hiscock, Natasha Pritchard, Tu’uhevaha J Kaitu’u-Lino, Susan Walker, Stephen Tong
Software Mentions: 4
Published: over 4 years ago

10.1093/gigascience/giy080

A workflow for simplified analysis of ATAC-cap-seq data in R
Cited by: 5
Author(s): Ram Krishna Shrestha, Pingtao Ding, Jonathan D. G. Jones, Dan MacLean
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-015-1767-y

Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq
Cited by: 132
Author(s): Anto P. Rajkumar, Per Qvist, Ross Lazarus, Francesco Lescai, Jia Ju, Mette Nyegaard, Ole Mors, Anders D. Børglum, Qibin Li, Jane H. Christensen
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0211491

A five-gene signature predicts overall survival of patients with papillary renal cell carcinoma
Cited by: 29
Author(s): Zhe Gao, Dong Zhang, Yi Duan, Lei Yan, Yi‐Ming Fan, Zhiqing Fang, Zhaoxu Liu
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12870-019-1968-7

Reconstruction of the full-length transcriptome atlas using PacBio Iso-Seq provides insight into the alternative splicing in Gossypium australe
Cited by: 40
Author(s): Shouli Feng, Min Xu, Fujie Liu, Changjiang Cui, Baoliang Zhou
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-79704-1

Data-driven detection of subtype-specific differentially expressed genes
Cited by: 9
Author(s): Lulu Chen, Yingzhou Lu, Chiung Ting Wu, Robert Clarke, Guoqiang Yu, Jennifer E. Van Eyk, David M. Herrington, Yue Wang
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12870-018-1602-0

Dual RNA-seq analysis provides new insights into interactions between Norway spruce and necrotrophic pathogen Heterobasidion annosum s.l.
Cited by: 31
Author(s): Andriy Kovalchuk, Zhen Zeng, Rajendra P. Ghimire, Minna Kivimäenpää, Tommaso Raffaello, Mengxia Liu, Mukrimin Mukrimin, Risto Kasanen, Hui Sun, Riitta Julkunen‐Tiitto, Jarmo K. Holopainen, Fred O. Asiegbu
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-78364-5

Hdac3 deletion in myeloid progenitor cells enhances bone healing in females and limits osteoclast fusion via Pmepa1
Cited by: 7
Author(s): David H. H. Molstad, Elizabeth L. Zars, Andrew Norton, Kim C. Mansky, Jennifer J. Westendorf, Elizabeth W. Bradley
Software Mentions: 4
Published: about 4 years ago

10.1186/s12859-015-0859-7

Effects of Mecp2 loss of function in embryonic cortical neurons: a bioinformatics strategy to sort out non-neuronal cells variability from transcriptome profiling
Cited by: 9
Author(s): Marcella Vacca, Kumar Parijat Tripathi, Luisa Speranza, Riccardo Aiese Cigliano, Francesco Scalabrì, Federico Marracino, Michele Madonna, Walter Sanseverino, Carla Perrone-Capano, Mario Rosario Guarracino, Maurizio D’Esposito
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12870-016-0926-x

Identification of nuclear genes controlling chlorophyll synthesis in barley by RNA-seq
Cited by: 9
Author(s): Nikolay A. Shmakov, Gennady V. Vasiliev, Natalya V. Shatskaya, А. В. Дорошков, Е. И. Гордеева, D. A. Afonnikov, Е. К. Хлесткина
Software Mentions: 4
Published: about 8 years ago

10.3390/cancers12092543

CeRNA Network Analysis Representing Characteristics of Different Tumor Environments Based on 1p/19q Codeletion in Oligodendrogliomas
Cited by: 4
Author(s): Ju Won Ahn, Young Joon Park, Su Jung Kang, So Jung Hwang, Kyung Gi Cho, Jaejoon Lim, KyuBum Kwack
Software Mentions: 4
Published: over 4 years ago

10.1038/s41419-021-03727-3

Interrogation of gender disparity uncovers androgen receptor as the transcriptional activator for oncogenic miR-125b in gastric cancer
Cited by: 14
Author(s): Ben Liu, Meng Zhou, Xiangchun Li, Xining Zhang, Qinghua Wang, Luyang Liu, Meng Yang, Da Yang, Yan Guo, Qiang Zhang, Hong Zheng, Qiong Wang, Lian Li, Xinlei Chu, Wei Wang, Haixin Li, Fengju Song, Yuan Pan, Wei Zhang, Kexin Chen
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2021.642759

The Analysis of Gene Expression Data Incorporating Tumor Purity Information
Cited by: 1
Author(s): Seungjun Ahn, Tyler Grimes, Somnath Datta
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2105-15-91

Differential meta-analysis of RNA-seq data from multiple studies
Cited by: 88
Author(s): Andrea Rau, Guillemette Marot, Florence Jaffrézic
Software Mentions: 4
Published: over 10 years ago

10.1186/s12918-019-0693-z

Identification of Hürthle cell cancers: solving a clinical challenge with genomic sequencing and a trio of machine learning algorithms
Cited by: 22
Author(s): Yangyang Hao, Quan‐Yang Duh, Richard T. Kloos, Joshua E. Babiarz, R. Mack Harrell, S. Thomas Traweek, Su Yeon Kim, Grazyna Fedorowicz, P. Sean Walsh, Peter M. Sadow, Jing Huang, Giulia C. Kennedy
Software Mentions: 4
Published: over 5 years ago

10.18632/oncotarget.15807

Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease
Cited by: 39
Author(s): Magnus Tobiasson, Hani Abdulkadir, Andreas Lennartsson, Shintaro Katayama, Francesco Marabita, Annick De Paepe, Mohsen Karimi, Kaarel Krjutškov, Elisabet Einarsdottir, Michael Grövdal, Monika Jansson, Asmaa Ben Azenkoud, Lina Corddedu, Sören Lehmann, Karl Ekwall, Juha Kere, Eva Hellström‐Lindberg, Johanna Ungerstedt
Software Mentions: 4
Published: almost 8 years ago

10.3389/fgene.2020.00650

Genome Regulation and Gene Interaction Networks Inferred From Muscle Transcriptome Underlying Feed Efficiency in Pigs
Cited by: 9
Author(s): Victor Adriano Okstoft Carmelo, Haja N. Kadarmideen
Software Mentions: 4
Published: over 4 years ago

10.1534/g3.114.013508

De Novo Assembly and Annotation of the Transcriptome of the Agricultural Weed Ipomoea purpurea Uncovers Gene Expression Changes Associated with Herbicide Resistance
Cited by: 41
Author(s): Trent A Leslie, Regina S. Baucom
Software Mentions: 4
Published: about 10 years ago

10.1186/s12918-016-0344-6

A method for automated pathogenic content estimation with application to rheumatoid arthritis
Cited by: 9
Author(s): Xiaoyuan Zhou, Christine Nardini
Software Mentions: 4
Published: about 8 years ago

10.1186/s12918-018-0582-x

A powerful nonparametric method for detecting differentially co-expressed genes: distance correlation screening and edge-count test
Cited by: 6
Author(s): Qingyang Zhang
Software Mentions: 4
Published: over 6 years ago

10.1038/s41419-018-1141-5

Plau and Tgfbr3 are YAP-regulated genes that promote keratinocyte proliferation
Cited by: 18
Author(s): Susan M. Corley, Veronica Mendoza-Reinoso, Nichole Giles, Emma Suwanun Singer, John E.A. Common, Marc R. Wilkins, Annemiek Beverdam
Software Mentions: 4
Published: about 6 years ago

10.1186/s12917-020-02373-9

Transcriptome profiling of porcine testis tissue reveals genes related to sperm hyperactive motility
Cited by: 5
Author(s): Maren van Son, Nina Hårdnes Tremoen, Ann Helen Gaustad, Dag Inge Våge, Teklu Tewoldebrhan Zeremichael, Frøydis Deinboll Myromslien, Eli Grindflek
Software Mentions: 4
Published: over 4 years ago

10.3389/fgene.2018.00321

DECtp: Calling Differential Gene Expression Between Cancer and Normal Samples by Integrating Tumor Purity Information
Cited by: 7
Author(s): Weiwei Zhang, Hang Long, Binsheng He, Jialiang Yang
Software Mentions: 4
Published: over 6 years ago

10.1007/s00395-021-00862-y

Fibroblast GATA-4 and GATA-6 promote myocardial adaptation to pressure overload by enhancing cardiac angiogenesis
Cited by: 29
Author(s): Gesine M. Dittrich, Natali Froese, Xue Wang, Hannah Kröger, Honghui Wang, Malgorzata Szaroszyk, Mona Malek Mohammadi, Julio Cordero, Merve Keles, Mortimer Korf‐Klingebiel, Kai C. Wollert, Robert Geffers, Manuel Mayr, Simon J. Conway, Gergana Dobreva, Johann Bauersachs, Joerg Heineke
Software Mentions: 4
Published: over 3 years ago

10.1016/j.bbr.2017.04.007

Recognition memory-induced gene expression in the perirhinal cortex: A transcriptomic analysis
Cited by: 6
Author(s): Hannah Scott, Mark F. Rogers, Helen L. Scott, Colin Campbell, E. Clea Warburton, James B. Uney
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-019-2623-x

MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations
Cited by: 2
Author(s): Aleksandra Perz, Cory B. Giles, Chase A. Brown, Hunter Porter, Xiavan Roopnarinesingh, Jonathan D. Wren
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-74128-3

Magnetic separation of peripheral nerve-resident cells underscores key molecular features of human Schwann cells and fibroblasts: an immunochemical and transcriptomics approach
Cited by: 18
Author(s): Kangqiang Peng, David W. Sant, Natalia Denise Andersen, Risset Silvera, Vladimir Camarena, Gonzalo Piñero, Regina M. Graham, Aisha Khan, Xiao Ming Xu, Gaofeng Wang, Paula V. Monje
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-020-75060-2

Differential immune gene expression associated with contemporary range expansion in two invasive rodents in Senegal
Cited by: 1
Author(s): Nathalie Charbonnel, Maxime Galan, Caroline Tatard, Anne Loiseau, Christophe Diagne, Ambroise Dalecky, Hugues Parrinello, Stéphanie Rialle, Dany Séverac, Carine Brouat
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-016-3130-3

Differential gene expression in Varroa jacobsoni mites following a host shift to European honey bees (Apis mellifera)
Cited by: 15
Author(s): Gladys K. Andino, Michael Gribskov, Denis L. Anderson, Jay D. Evans, Greg J. Hunt
Software Mentions: 4
Published: about 8 years ago

10.1093/gbe/evy041

Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee
Cited by: 19
Author(s): Jason Pizzollo, William Nielsen, Yoichiro Shibata, Alexias Safi, Gregory E. Crawford, Gregory A. Wray, Courtney C. Babbitt
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12859-018-2261-8

Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods
Cited by: 43
Author(s): Thomas P. Quinn, Tamsyn M. Crowley, Mark F. Richardson
Software Mentions: 4
Published: over 6 years ago

10.1093/bioinformatics/bts394

An accurate paired sample test for count data
Cited by: 58
Author(s): Thang V. Pham, Connie R. Jiménez
Software Mentions: 4
Published: over 12 years ago

10.1186/1471-2105-12-323

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Cited by: 14,016
Author(s): Bo Li, Colin N. Dewey
Software Mentions: 4
Published: over 13 years ago

10.18632/oncotarget.11788

Identification of candidate anti-cancer molecular mechanisms of Compound Kushen Injection using functional genomics
Cited by: 64
Author(s): Zhibo Qu, Jingang Cui, Yuka Harata-Lee, Thazin Nwe Aung, Qi Feng, Joy M. Raison, R. Daniel Kortschak, David L. Adelson
Software Mentions: 4
Published: over 8 years ago

10.18632/aging.102190

Long non-coding RNA CASC19 is associated with the progression and prognosis of advanced gastric cancer
Cited by: 23
Author(s): Wenjie Wang, Changan Guo, Rui Li, Zipeng Xu, Jianping Yu, Ye Yan, Jun Zhao, Jing Wang, Wen-An Wang, An Zhang, Hongtao Li, Chen Wang, Hongbin Liu
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2018.01624

Integration of RNAi and RNA-seq Reveals the Immune Responses of Epinephelus coioides to sigX Gene of Pseudomonas plecoglossicida
Cited by: 54
Author(s): Yujia Sun, Gang Luo, Lingmin Zhao, Lixing Huang, Yingxue Qin, Yongquan Su, Qingpi Yan
Software Mentions: 4
Published: over 6 years ago

10.3390/jpm9020018

Aligning the Aligners: Comparison of RNA Sequencing Data Alignment and Gene Expression Quantification Tools for Clinical Breast Cancer Research
Cited by: 12
Author(s): Isaac Raplee, Alexei V. Evsikov, Caralina Marín de Evsikova
Software Mentions: 4
Published: over 5 years ago

10.1093/bioinformatics/btu274

Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation
Cited by: 64
Author(s): Tarmo Äijö, Vincent Butty, Zhi Chen, Verna Salo, Subhash Tripathi, Christopher B. Burge, Riitta Lahesmaa, Harri Lähdesmäki
Software Mentions: 4
Published: over 10 years ago

10.3389/fimmu.2018.01626

Transcriptomic Profiles of Senegalese Sole Infected With Nervous Necrosis Virus Reassortants Presenting Different Degree of Virulence
Cited by: 23
Author(s): Alejandro M. Labella, Esther García-Rosado, Isabel Bandı́n, Carlos P. Dopazo, Dolores Castro, M. Carmen Alonso, Juan J. Borrego
Software Mentions: 4
Published: over 6 years ago

10.1186/s13071-019-3534-4

Eimeria maxima-induced transcriptional changes in the cecal mucosa of broiler chickens
Cited by: 15
Author(s): Charles Li, Xianghe Yan, Hyun S. Lillehoj, Seong-Hwan Oh, Liheng Liu, Zhifeng Sun, Changqin Gu, Youngsub Lee, Zhezi Xianyu, Hongyan Zhao
Software Mentions: 4
Published: over 5 years ago

10.1093/gbe/evv115

Complete Dosage Compensation inAnopheles stephensiand the Evolution of Sex-Biased Genes in Mosquitoes
Cited by: 40
Author(s): Xiaofang Jiang, James K. Biedler, Yumin Qi, Andrew Brantley Hall, Zhijian Tu
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-016-2694-2

RNA-Seq following PCR-based sorting reveals rare cell transcriptional signatures
Cited by: 21
Author(s): Maurizio Pellegrino, Adam Sciambi, Jamie Yates, Joshua D. Mast, Charles Silver, Dennis J. Eastburn
Software Mentions: 4
Published: over 8 years ago

10.1186/s13071-021-04597-6

Gene co-expression network analysis of Trypanosoma brucei in tsetse fly vector
Cited by: 5
Author(s): Kennedy W. Mwangi, Rosaline W. Macharia, Joel L. Bargul
Software Mentions: 4
Published: almost 4 years ago

10.3390/cancers13030559

Type 2 Innate Lymphoid Cells Protect against Colorectal Cancer Progression and Predict Improved Patient Survival
Cited by: 29
Author(s): Qiutong Huang, Nicolas Jacquelot, Adele Preaudet, Soroor Hediyeh-Zadeh, Fernando Souza-Fonseca-Guimarães, Andrew N. J. McKenzie, Philip M. Hansbro, Melissa J. Davis, Lisa A. Mielke, Tracy L. Putoczki, Gabrielle T. Belz
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmed.2021.675842

Exosomal Circular RNA RNA-seq Profiling and the Carcinogenic Role of Exosomal circ-CYP24A1 in Cutaneous Squamous Cell Carcinoma
Cited by: 9
Author(s): Zheng Zhang, Hao Guo, Wen‐Jia Yang, Jiu‐Hong Li
Software Mentions: 4
Published: over 3 years ago

10.3390/pathogens8040183

Whole Transcriptome Analyses Reveal Differential mRNA and microRNA Expression Profiles in Primary Human Dermal Fibroblasts Infected with Clinical or Vaccine Strains of Varicella Zoster Virus
Cited by: 12
Author(s): Soo Jin Oh, Soo Yeon Lim, Mee Hyun Song, Jinhee Ahn, Chan Hee Lee, Ok Sarah Shin
Software Mentions: 4
Published: about 5 years ago

10.1093/bioinformatics/btx094

Glimma: interactive graphics for gene expression analysis
Cited by: 120
Author(s): Shian Su, Charity W. Law, Casey Ah-Cann, Marie Liesse Asselin-Labat, Marnie E. Blewitt, Matthew E. Ritchie
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0207497

Response of Tribolium castaneum to dietary mannitol, with remarks on its possible nutritive effects
Cited by: 8
Author(s): Shingo Kikuta
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2164-12-11

The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis
Cited by: 142
Author(s): Xuefeng Fang, Jae-Geun Yoon, Lisha Li, Wei Yu, Jiaofang Shao, Dasong Hua, Suiping Zheng, Leroy Hood, David R. Goodlett, Gregory Foltz, Biaoyang Lin
Software Mentions: 3
Published: almost 14 years ago

10.18632/aging.202989

Integrated analysis of long noncoding RNAs and mRNA expression profiles reveals the potential role of lncRNAs in early stage of post-peripheral nerve injury in Sprague-Dawley rats
Cited by: 3
Author(s): Yujing Zhang, Zhaowei Zhu, Xiangxia Liu, Shuqia Xu, Yi Zhang, Yangbin Xu, Bo He
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0130891

Integrative Transcriptome Profiling of Cognitive Aging and Its Preservation through Ser/Thr Protein Phosphatase Regulation
Cited by: 4
Author(s): C. Sehwan Park, Amandine Valomon, Hans Welzl
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-016-3396-5

DEIVA: a web application for interactive visual analysis of differential gene expression profiles
Cited by: 37
Author(s): Jayson Harshbarger, Anton Kratz, Piero Carninci
Software Mentions: 3
Published: almost 8 years ago

10.3390/cancers13081903

Circular RNA in Chemonaive Lymph Node Negative Colon Cancer Patients
Cited by: 0
Author(s): I. van den Berg, Marcel Smid, Robert R.J. Coebergh van den Braak, Carolien H.M. van Deurzen, Vanja de Weerd, John A. Foekens, Jan N.M. IJzermans, John W.M. Martens, Saskia M. Wilting
Software Mentions: 3
Published: over 3 years ago

10.1093/gigascience/giy027

Whole-genome resequencing reveals signatures of selection and timing of duck domestication
Cited by: 70
Author(s): Zebin Zhang, Yaxiong Jia, Pedro Almeida, Judith E. Mank, Marcel van Tuinen, Qiong Wang, Zhihua Jiang, Yu Chen, Kai Zhan, Shuisheng Hou, Zhengkui Zhou, Huifang Li, Fan Yang, Yong He, Zhonghua Ning, Ning Yang, Lujiang Qu
Software Mentions: 3
Published: over 6 years ago

10.3390/cancers13163978

Drug Repurposing to Identify a Synergistic High-Order Drug Combination to Treat Sunitinib-Resistant Renal Cell Carcinoma
Cited by: 12
Author(s): Magdalena Rausch, Adriano Rutz, Pierre‐Marie Allard, Céline Delucinge-Vivier, Mylène Docquier, Olivier Dormond, Paul J. Dyson, Jean‐Luc Wolfender, Patrycja Nowak-Śliwińska
Software Mentions: 3
Published: over 3 years ago

10.1186/s13742-015-0091-4

Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells
Cited by: 52
Author(s): Liang Wu, Xiaolong Zhang, Zhikun Zhao, Ling Wang, Bo Li, Guibo Li, Michael Dean, Qichao Yu, Yanhui Wang, Xinxin Lin, Weijian Rao, Zhanlong Mei, Yang Li, Runze Jiang, Huan Yang, Fuqiang Li, Guoyun Xie, Liqin Xu, Kui Wu, Jie Zhang, Jianghao Chen, Ting Wang, Karsten Kristiansen, Xiuqing Zhang, Yingrui Li, Huanming Yang, Jian Wang, Yong Hou, Xun Xu
Software Mentions: 3
Published: about 9 years ago

10.1016/j.gpb.2020.12.001

Tissue-specific Gene Expression Changes Are Associated with Aging in Mice
Cited by: 19
Author(s): Akash Srivastava, Emanuel Barth, Maria A. Ermolaeva, Madlen Guenther, Christiane Frahm, Manja Marz, Otto W. Witte
Software Mentions: 3
Published: over 4 years ago

10.3390/cancers11020155

An Integrative Data Mining and Omics-Based Translational Model for the Identification and Validation of Oncogenic Biomarkers of Pancreatic Cancer
Cited by: 32
Author(s): Nguyen Phuoc Long, Kyung Hee Jung, Nguyễn Hoàng Anh, Pengcheng Zhang, Tran Diem Nghi, Seongoh Park, Sang Jun Yoon, Jung Eun Min, Hyung Min Kim, Joo Han Lim, Joon Mee Kim, Jong-Tae Lim, Sanghyuk Lee, Soon‐Sun Hong, Sung Won Kwon
Software Mentions: 3
Published: almost 6 years ago

10.3390/cancers11040479

Combined Targeting of Estrogen Receptor Alpha and XPO1 Prevent Akt Activation, Remodel Metabolic Pathways and Induce Autophagy to Overcome Tamoxifen Resistance
Cited by: 13
Author(s): Eylem Kulkoyluoglu-Cotul, Brandi Patrice Smith, Kinga Wrobel, Yijia Zhao, Karen Lee Ann Chen, Kadriye Hieronymi, Ozan Berk Imir, Kevin Duong, Caitlin O’Callaghan, Aditi Mehta, Sunati Sahoo, Barbara Haley, Hua Chang, Yosef Landesman, Zeynep Madak-Erdoğan
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.26575

Human embryonic lung epithelial tips are multipotent progenitors that can be expanded in vitro as long-term self-renewing organoids
Cited by: 206
Author(s): Marko Nikolić, Oriol Caritg, Quitz Jeng, Jo-Anne Johnson, Dawei Sun, Kate J. Howell, Jane Brady, Usua Laresgoiti, George E. Allen, Richard J. Butler, Matthias Zilbauer, Adam Giangreco, Emma L. Rawlins
Software Mentions: 3
Published: over 7 years ago

10.1128/JVI.01010-21

Kinetic Multi-omic Analysis of Responses to SARS-CoV-2 Infection in a Model of Severe COVID-19
Cited by: 19
Author(s): Angelene M. Cantwell, Harinder Singh, Maryann P. Platt, Yonghao Yu, Yi‐Han Lin, Yuji Ikeno, Gene B. Hubbard, Yan Xiang, Norberto González-Juarbe, Peter H. Dube
Software Mentions: 3
Published: about 3 years ago

10.3390/cancers13092161

Low Plasma Citrate Levels and Specific Transcriptional Signatures Associated with Quiescence of CD34+ Progenitors Predict Azacitidine Therapy Failure in MDS/AML Patients
Cited by: 1
Author(s): Pavla Kořalková, Monika Beličková, David Kundrát, Michaela Dostálová Merkerová, Zdeněk Krejčík, Katarína Szikszai, Monika Kaisrlikova, Jitka Veselá, Pavla Vyhlidalova, Jan Stetka, Alžběta Hlaváčková, Jiřı́ Suttnar, Patrik Flodr, J Stříteský, Anna Jonášová, Jaroslav Čermák, Vladimír Divoký
Software Mentions: 3
Published: over 3 years ago

10.3390/cancers13040681

Subcellular Localization of uc.8+ as a Prognostic Biomarker in Bladder Cancer Tissue
Cited by: 12
Author(s): Sara Terreri, Sara Mancinelli, Matteo Ferro, Maria Concetta Vitale, Sisto Perdoná, Luigi Castaldo, Vincenzo Gigantino, Vincenzo Mercadante, Rossella De Cecio, Gabriella Aquino, Marco Montella, Claudia Angelini, Eugenio Del Prete, Marianna Aprile, Angelo Ciaramella, Giovanna L. Liguori, Valerio Costa, George A. Calin, Evelina La Civita, Daniela Terracciano, Ferdinando Febbraio, Amelia Cimmino
Software Mentions: 3
Published: almost 4 years ago

10.3390/cancers12061642

The Liver Microbiome Is Implicated in Cancer Prognosis and Modulated by Alcohol and Hepatitis B
Cited by: 13
Author(s): Jaideep Chakladar, Lauren Wong, Selena Z. Kuo, Wei Tse Li, Michael Yu, Eric Y. Chang, Xiao Qi Wang, Weg M. Ongkeko
Software Mentions: 3
Published: over 4 years ago

10.3390/cancers11060887

Utility of Circulating Cell-Free RNA Analysis for the Characterization of Global Transcriptome Profiles of Multiple Myeloma Patients
Cited by: 20
Author(s): Maoshan Chen, Sridurga Mithraprabhu, Malarmathy Ramachandran, Kawa Choi, Tiffany Khong, Andrew Spencer
Software Mentions: 3
Published: over 5 years ago

10.3390/cancers13071585

Aberrations of Chromosomes 1 and 16 in Breast Cancer: A Framework for Cooperation of Transcriptionally Dysregulated Genes
Cited by: 8
Author(s): Anna Privitera, Vincenza Barresi, D. F. Condorelli
Software Mentions: 3
Published: over 3 years ago

10.3390/cancers11111668

Transcription Factor and miRNA Interplays Can Manifest the Survival of ccRCC Patients
Cited by: 41
Author(s): Si Qin, Xuejia Shi, Canbiao Wang, Jin Park, Fei Ma
Software Mentions: 3
Published: about 5 years ago

10.3390/cancers12061635

Circulating miRNAs in Small Extracellular Vesicles Secreted by a Human Melanoma Xenograft in Mouse Brains
Cited by: 9
Author(s): Loredana Guglielmi, Marta Nardella, Carla Musa, Ingrid Cifola, Manuela Porru, Beatrice Cardinali, Ilaria Iannetti, Chiara Di Pietro, Giulia Bolasco, Valentina Palmieri, Laura Vilardo, Nicolò Panini, Fabrizio Bonaventura, Massimiliano Papi, Ferdinando Scavizzi, Marcello Raspa, Carlo Leonetti, Germana Falcone, Armando Felsani, Igea D’Agnano
Software Mentions: 3
Published: over 4 years ago

10.3390/cancers13040632

MicroRNA Profile for Diagnostic and Prognostic Biomarkers in Thyroid Cancer
Cited by: 9
Author(s): Jong‐Lyul Park, Seon‐Kyu Kim, Sora Jeon, Chan Kwon Jung, Yong‐Sung Kim
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13073-020-00796-5

Integrated analysis of microbiome and host transcriptome reveals correlations between gut microbiota and clinical outcomes in HBV-related hepatocellular carcinoma
Cited by: 73
Author(s): Hechen Huang, Zhigang Ren, Xingxing Gao, Xiaoyi Hu, Yuan Zhou, Jianwen Jiang, Haifeng Lü, Shengyong Yin, Junfang Ji, Lin Zhou, Shusen Zheng
Software Mentions: 3
Published: about 4 years ago

10.1186/s12864-018-4651-8

Transcriptional development of phospholipid and lipoprotein metabolism in different intestinal regions of Atlantic salmon (Salmo salar) fry
Cited by: 11
Author(s): Yang Jin, Rolf Erik Olsen, Mari‐Ann Östensen, Gareth Benjamin Gillard, Sven Arild Korsvoll, Nina Santi, Arne B. Gjuvsland, Jon Olav Vik, Jacob Torgersen, Simen Rød Sandve, Yngvar Ôlsen
Software Mentions: 3
Published: over 6 years ago

10.1186/s13578-019-0356-1

Transcriptome analysis reveals an important candidate gene involved in both nodal metastasis and prognosis in lung adenocarcinoma
Cited by: 42
Author(s): Xiao Zhu, Hui Luo, Ying Xu
Software Mentions: 3
Published: about 5 years ago

10.1186/s12964-019-0332-8

Low levels of pyruvate induced by a positive feedback loop protects cholangiocarcinoma cells from apoptosis
Cited by: 12
Author(s): Mingming Zhang, Yida Pan, Dehua Tang, Robert Dorfman, Lei Xu, Qian Zhou, Lixing Zhou, Yuming Wang, Li Yang, Yuyao Yin, Bo Kong, Helmut Frieß, Shimin Zhao, Jian‐Lin Wu, Lei Wang, Xiaoping Zou
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12964-016-0142-1

Normalization of TAM post-receptor signaling reveals a cell invasive signature for Axl tyrosine kinase
Cited by: 26
Author(s): Stanley Kimani, Sushil Kumar, Viralkumar Davra, Yun‐Juan Chang, Canan Kasikara, Ke Geng, Wen-I Tsou, Shenyan Wang, Mainul Hoque, Andrej Boháč, Anita Lewis-Antes, Mariana S. De Lorenzo, Sergei V. Kotenko, Raymond B. Birge
Software Mentions: 3
Published: over 8 years ago

10.1128/JVI.02394-20

CAGE-Seq Reveals that HIV-1 Latent Infection Does Not Trigger Unique Cellular Responses in a Jurkat T Cell Model
Cited by: 1
Author(s): Hiroyuki Matsui, Kotaro Shirakawa, Yoshinobu Konishi, Shigeki Hirabayashi, Anamaria Daniela Sarca, Hirofumi Fukuda, Ryosuke Nomura, Emani Stanford, Yoshihito Horisawa, Yasuhiro Kazuma, Tadahiko Matsumoto, Hiroyuki Yamazaki, Yuji Murakawa, Emilie Battivelli, Eric Verdin, Yoshio Koyanagi, Akifumi Takaori‐Kondo
Software Mentions: 3
Published: over 3 years ago

10.1186/s13073-020-0715-x

A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons
Cited by: 29
Author(s): Sergio Espeso-Gil, Tobias B. Halene, Jaroslav Bendl, Bibi Kassim, Gabriella Ben Hutta, Marina Iskhakova, Neda Shokrian, Pavan K. Auluck, Behnam Javidfar, Prashanth Rajarajan, Sandhya Chandrasekaran, Cyril J. Peter, Alanna Cote, Rebecca Birnbaum, Will Liao, Tyler Borrman, Jennifer Wiseman, Aaron Bell, Michael J. Bannon, Panagiotis Roussos, John F. Crary, Zhiping Weng, Stefano Marenco, Barbara K. Lipska, Nadejda M. Tsankova, Laura Huckins, Yan Jiang, Schahram Akbarian
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13073-019-0697-8

Neoantigen-specific immunity in low mutation burden colorectal cancers of the consensus molecular subtype 4
Cited by: 37
Author(s): Jitske van den Bulk, Els M.E. Verdegaal, Dina Ruano, Marieke E. Ijsselsteijn, Marten Visser, Ruud van der Breggen, Thomas Duhen, Manon van der Ploeg, Natasja L. de Vries, Jan Oosting, Koen Peeters, Andrew D. Weinberg, Arantza Farina Sarasqueta, Sjoerd H. van der Burg, Noel F.C.C. de Miranda
Software Mentions: 3
Published: about 5 years ago

10.1186/s13073-019-0665-3

Identifying chemogenetic interactions from CRISPR screens with drugZ
Cited by: 106
Author(s): Medina Colic, Gang Wang, Michal Zimmermann, Keith Mascall, Megan McLaughlin, Lori Bertolet, Walter F. Lenoir, Jason Moffat, Stéphane Angers, Daniel Durocher, Traver Hart
Software Mentions: 3
Published: over 5 years ago

10.1038/s41419-020-2381-8

MOB2 suppresses GBM cell migration and invasion via regulation of FAK/Akt and cAMP/PKA signaling
Cited by: 41
Author(s): Ke Jiang, Gang Yao, Lulu Hu, Yumei Yan, Jia Liu, Jingwei Shi, Youwei Chang, Ye Zhang, Dapeng Liang, Dachuan Shen, Guirong Zhang, Meng Shao, Haozhe Piao
Software Mentions: 3
Published: over 4 years ago

Projects: bioconductor: edgeR

Papers Mentioning edgeR 6,568