10.1186/s12864-019-5525-4

Polygenic and sex specific architecture for two maturation traits in farmed Atlantic salmon
Cited by: 22
Author(s): Amin R. Mohamed, Klara L. Verbyla, Hawlader Abdullah Al-Mamun, Sean McWilliam, Bradley S. Evans, Hilary King, Peter D. Kube, James W. Kijas
Software Mentions: 3
Published: over 7 years ago

10.1186/s12967-020-02550-2

Classification models using circulating neutrophil transcripts can detect unruptured intracranial aneurysm
Cited by: 13
Author(s): Kerry E. Poppenberg, Vincent M. Tutino, Li Lü, Muhammad Waqas, Armond June, Lee Chaves, Kaiyu Jiang, James N. Jarvis, Yijun Sun, Kenneth V. Snyder, Elad I. Levy, Adnan H. Siddiqui, John Kolega, Hui Meng
Software Mentions: 3
Published: almost 6 years ago

10.7150/thno.46642

Precise and efficient silencing of mutant Kras^G12D by CRISPR-CasRx controls pancreatic cancer progression
Cited by: 26
Author(s): Wang Jiang, Hao Li, Xiyu Liu, Jianping Zhang, Wuhu Zhang, Tianjiao Li, Liang Liu, Xianjun Yu
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-015-1461-0

GRACOMICS: software for graphical comparison of multiple results with omics data
Cited by: 7
Author(s): Minseok Seo, Joon Yoon, Taesung Park
Software Mentions: 3
Published: over 11 years ago

10.1186/s12864-016-2574-9

De novo transcriptomic assembly and profiling of Rigidoporus microporus during saprotrophic growth on rubber wood
Cited by: 12
Author(s): Abbot O. Oghenekaro, Tommaso Raffaello, Andriy Kovalchuk, Fred O. Asiegbu
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-015-2088-x

De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum
Cited by: 22
Author(s): Valeria Petrella, Serena Aceto, Francesco Musacchia, Vincenza Colonna, Mark D. Robinson, Vladimı́r Beneš, G. Cicotti, Gioia Bongiorno, Luigi Gradoni, Petr Volf, Marco Salvemini
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2164-14-171

Transcriptomics of morphological color change in polychromatic Midas cichlids
Cited by: 76
Author(s): Frederico Henning, Julia C. Jones, Paolo Franchini, Axel Meyer
Software Mentions: 3
Published: over 13 years ago

10.1186/s12864-016-2906-9

An integrative genomics approach for identifying novel functional consequences of PBRM1 truncated mutations in clear cell renal cell carcinoma (ccRCC)
Cited by: 18
Author(s): Yuanyuan Wang, Xingyi Guo, Michael J. Bray, Zhiyong Ding, Zhongming Zhao
Software Mentions: 3
Published: about 10 years ago

10.7150/thno.44456

Cartilage Oligomeric Matrix Protein promotes epithelial-mesenchymal transition by interacting with Transgelin in Colorectal Cancer
Cited by: 57
Author(s): Weilong Zhong, Huiqin Hou, Tianyu Li, Shuai Su, Xiaonan Xi, Yusheng Liao, Runxiang Xie, Ge Jin, Xiang Liu, Lanping Zhu, Hongxia Zhang, Xueli Song, Cheng Yang, Tao Sun, Hailong Cao, Bangmao Wang
Software Mentions: 3
Published: over 6 years ago

10.3390/antibiotics9100715

Aureolic Acid Group of Agents as Potential Antituberculosis Drugs
Cited by: 2
Author(s): Julia Bespyatykh, Dmitry Bespiatykh, Maja V. Malakhova, Ksenia M. Klimina, Andrey Bespyatykh, Anna M. Varizhuk, Anna N. Tevyashova, Tatiana A Nikolenko, Galina E. Pozmogova, Elena N. Ilina, Egor Shitikov
Software Mentions: 3
Published: almost 6 years ago

10.7150/thno.42986

The molecular landscape and microenvironment of salivary duct carcinoma reveal new therapeutic opportunities
Cited by: 25
Author(s): Mélissa Alame, Emmanuel Cornillot, Valère Cacheux, Guillaume Tosato, Marion Four, Laura de Oliveira, Stéphanie Gofflot, Philippe Delvenne, Evgenia Turtoi, Simon Cabello-Aguilar, Masahiko Nishiyama, Andrei Turtoï, Valérie Costes‐Martineau, Jacques Colinge
Software Mentions: 3
Published: over 6 years ago

10.18632/aging.203425

ADAM15 correlates with prognosis, immune infiltration and apoptosis in hepatocellular carcinoma
Cited by: 9
Author(s): Jun Xu, Yong Guan, Yi Chao Zhang, Zhendong Qiu, Yu Zhou, Chen Chen, Jie-Ping Yu, Weixing Wang
Software Mentions: 3
Published: about 5 years ago

10.1186/s12967-018-1535-2

In silico identification of drug target pathways in breast cancer subtypes using pathway cross-talk inhibition
Cited by: 22
Author(s): Claudia Cava, Gloria Bertoli, Isabella Castiglioni
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-020-6721-y

On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments
Cited by: 50
Author(s): Alemu Takele Assefa, Jo Vandesompele, Olivier Thas
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-019-5460-4

RNA-sequencing analysis of shell gland shows differences in gene expression profile at two time-points of eggshell formation in laying chickens
Cited by: 22
Author(s): Samiullah Khan, Shu‐Biao Wu, Juliet R. Roberts
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0079874

Phenotypic and Transcriptional Fidelity of Patient-Derived Colon Cancer Xenografts in Immune-Deficient Mice
Cited by: 31
Author(s): Jeffrey Chou, Matthew Fitzgibbon, Christie-Lynn Mortales, Andrea M. H. Towlerton, Melissa P. Upton, Raymond S. Yeung, Martin W. McIntosh, Edus H. Warren
Software Mentions: 3
Published: almost 13 years ago

10.1111/acel.13357

Age‐related telomere attrition causes aberrant gene expression in sub‐telomeric regions
Cited by: 8
Author(s): Xiao Dong, Shixiang Sun, Lei Zhang, Seung-Soo Kim, Zhidong Tu, Cristina Montagna, Alexander Y. Maslov, Yousin Suh, Tao Wang, Judith Campisi, Jan Vijg
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-3433-4

Short bowel syndrome results in increased gene expression associated with proliferation, inflammation, bile acid synthesis and immune system activation: RNA sequencing a zebrafish SBS model
Cited by: 24
Author(s): Kathy Schall, Matthew E. Thornton, Mubina Isani, Kathleen A. Holoyda, Xiaogang Hou, Ching‐Ling Lien, Brendan H. Grubbs, Tracy C. Grikscheit
Software Mentions: 3
Published: over 9 years ago

10.1177/1533033819853237

Comprehensive Analysis of lncRNA–miRNA– mRNA Network Ascertains Prognostic Factors in Patients with Colon Cancer
Cited by: 20
Author(s): Zhenzhen Gao, Peng Fu, Zuwei Yu, Fuxi Zhen, Weimin Fan
Software Mentions: 3
Published: over 7 years ago

10.5966/sctm.2015-0401

Human Adipose-Derived Stem Cells Expanded Under Ambient Oxygen Concentration Accumulate Oxidative DNA Lesions and Experience Procarcinogenic DNA Replication Stress
Cited by: 12
Author(s): Rémy Bétous, Marie-Laure Renoud, Claire Hoede, Ignacio González, Natalie Jones, Michel Longy, Luc Sensebé, Christophe Cazaux, Jean-Sébastien Hoffmann
Software Mentions: 3
Published: about 10 years ago

10.1155/2018/5692840

Noncoding RNA Transcripts during Differentiation of Induced Pluripotent Stem Cells into Hepatocytes
Cited by: 5
Author(s): Aniela Skrzypczyk, Stephanie Kehr, Ilona Krystel, Stephan H. Bernhart, Shibashish Giri, Augustinus Bader, Peter F. Stadler
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-017-3973-2

Comparative transcriptome analysis reveals key cadmium transport-related genes in roots of two pak choi (Brassica rapa L. ssp. chinensis) cultivars
Cited by: 37
Author(s): Rugang Yu, Dan Li, Xiaodong Du, Shenglan Xia, Caifeng Liu, Gangrong Shi
Software Mentions: 3
Published: about 9 years ago

10.1186/1471-2164-15-954

Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples
Cited by: 33
Author(s): Igseo Choi, Hua Bao, Arun Kommadath, Afshin Hosseini, Xinwei Sun, Yan Meng, Paul Stothard, Graham Plastow, Christopher K. Tuggle, James M. Reecy, Eric R. Fritz-Waters, Samuel M. Abrams, Joan K. Lunney, Leluo Guan
Software Mentions: 3
Published: almost 12 years ago

10.3390/antiox9121190

Differential Sex-Dependent Regulation of the Alveolar Macrophage miRNome of SP-A2 and co-ex (SP-A1/SP-A2) and Sex Differences Attenuation after 18 h of Ozone Exposure
Cited by: 7
Author(s): Nithyananda Thorenoor, David S. Phelps, Joanna Floros
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-020-07099-4

Development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between Muscovy and common duck species and their reciprocal inter-specific mule and hinny hybrids fed ad libitum and overfed
Cited by: 3
Author(s): Xi Liu, Frédéric Herault, Christian Diot, Erwan Corre
Software Mentions: 3
Published: almost 6 years ago

10.3390/antiox9090884

The Transcriptomic Response of the Murine Thyroid Gland to Iodide Overload and the Role of the Nrf2 Antioxidant System
Cited by: 7
Author(s): Dionysios V. Chartoumpekis, Panos G. Ziros, Ilias Georgakopoulos-Soares, Alexander Smith, Ana C. Marques, Mark Ibberson, Peter Kopp, Ioannis Habeos, Ioannis P. Trougakos, Nicholas K.H. Khoo, Gerasimos P. Sykiotis
Software Mentions: 3
Published: almost 6 years ago

10.18632/oncotarget.19557

cFLIP critically modulates apoptotic resistance in epithelial-to-mesenchymal transition
Cited by: 6
Author(s): Chandrasekhar Padmanabhan, Eric J. Rellinger, Jing Zhu, Hanbing An, Luke Woodbury, Dai H. Chung, Alex G. Waterson, Craig W. Lindsley, Anna L. Means, R. Daniel Beauchamp
Software Mentions: 3
Published: about 9 years ago

10.1186/s12864-020-6482-7

Dynamic accumulation of fatty acids in duck (Anas platyrhynchos) breast muscle and its correlations with gene expression
Cited by: 15
Author(s): Wenlei Fan, Wenjing Liu, Hehe Liu, Qingshi Meng, Yaxi Xu, Yuming Guo, Baowei Wang, Zhengkui Zhou, Shuisheng Hou
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-019-5984-7

An insight into the sialome, mialome and virome of the horn fly, Haematobia irritans
Cited by: 14
Author(s): José M. C. Ribeiro, Humberto Julio Debat, Mariana Boiani, X. Ures, Sérgio Paulo Dejato da Rocha, Martı́n Breijo
Software Mentions: 3
Published: about 7 years ago

10.18632/aging.104004

Integrated analysis of transcriptomic and metabolomic data demonstrates the significant role of pyruvate carboxylase in the progression of ovarian cancer
Cited by: 9
Author(s): Hongjing Shang, Jianfeng Zheng, Jinyi Tong
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2164-13-484

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing
Cited by: 180
Author(s): José A Robles, Sumaira Qureshi, Stuart Stephen, Susan R. Wilson, Conrad J. Burden, Jennifer Taylor
Software Mentions: 3
Published: almost 14 years ago

10.1002/stem.2558

New Monoclonal Antibodies to Defined Cell Surface Proteins on Human Pluripotent Stem Cells
Cited by: 17
Author(s): Carmel O'Brien, Hun S. Chy, Qi Zhou, Shiri Blumenfeld, Jack Lambshead, Xiaodong Liu, Joshua Kie, Bianca D. Capaldo, Tung Liang Chung, Timothy E. Adams, Tram Phan, John D. Bentley, William J. McKinstry, Karen Oliva, Paul McMurrick, Yu-Chieh Wang, Fernando Rossello, Geoffrey J. Lindeman, Di Chen, Thierry Jardé, Amander T. Clark, Helen E. Abud, Jane E. Visvader, Christian M. Nefzger, José M. Polo, Jeanne F. Loring, Andrew L. Laslett
Software Mentions: 3
Published: over 9 years ago

10.1186/s13287-021-02585-2

In vitro genome editing rescues parkinsonism phenotypes in induced pluripotent stem cells-derived dopaminergic neurons carrying LRRK2 p.G2019S mutation
Cited by: 14
Author(s): Kuo‐Hsuan Chang, Cheng‐Yen Huang, Chih-Hsin Ou-Yang, Chang-Han Ho, Hon‐Yi Lin, Chih‐Cheng Hsu, You-Tzung Chen, Yu‐Chi Chou, Yijing Chen, Ying Chen, Jiali Lin, Ji-Kuan Wang, Pei‐Wen Lin, Ying-Ru Lin, Miao-Hsia Lin, C. K. Tseng, Chin-Hsien Lin
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13287-021-02310-z

Hypoxic preconditioning induces epigenetic changes and modifies swine mesenchymal stem cell angiogenesis and senescence in experimental atherosclerotic renal artery stenosis
Cited by: 20
Author(s): Busra Isik, Roman Thaler, Busra B. Goksu, Sabena M. Conley, Hayder Al-Khafaji, Arjunmohan Mohan, Mohsen Afarideh, Abdelrhman Abumoawad, Xiang Yang Zhu, James D. Krier, Ishran M. Saadiq, Hui Tang, Alfonso Eirin, La Tonya J. Hickson, André J. van Wijnen, Stephen C. Textor, Lilach O. Lerman, Sandra M. Herrmann
Software Mentions: 3
Published: over 5 years ago

10.1186/s13287-019-1335-5

High temperature suppressed SSC self-renewal through S phase cell cycle arrest but not apoptosis
Cited by: 12
Author(s): Jia Wang, Wei-Jun Gao, Shoulong Deng, Lei Xiang, Jia Hua, Wenzhi Ma
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-016-2784-1

Psychoactive pharmaceuticals at environmental concentrations induce in vitro gene expression associated with neurological disorders
Cited by: 15
Author(s): Gaurav Kaushik, Yu Xia, Luobin Yang, Michael A. Thomas
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2164-14-236

Transcriptional profiling of bud dormancy induction and release in oak by next-generation sequencing
Cited by: 73
Author(s): S. Ueno, Christophe Klopp, Jean‐Charles Leplé, Jérémy Derory, Céline Noirot, Valérie Leger, Elodie Prince, Antoine Kremer, Christophe Plomion, Grégoire Le Provost
Software Mentions: 3
Published: over 13 years ago

10.1186/s13287-019-1191-3

In vitro expansion affects the response of human bone marrow stromal cells to irradiation
Cited by: 8
Author(s): Yang Xiang, Chun Wu, Jiang Wu, Weili Quan, Chao Cheng, Jian Zhou, Li Chen, Lan Xiang, Fengjie Li, Kebin Zhang, Qian Ran, Yi Zhang, Zhongjun Li
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-015-2043-x

Whole transcriptome analysis of Penicillium digitatum strains treatmented with prochloraz reveals their drug-resistant mechanisms
Cited by: 41
Author(s): Jing Liu, Shengqiang Wang, Tingting Qin, Na Li, Yuhui Niu, Dandan Li, Yongze Yuan, Hui Geng, Xiong Li, De Li Liu
Software Mentions: 3
Published: almost 11 years ago

10.1186/s13287-018-1104-x

Comparative analysis of mesenchymal stem cells derived from amniotic membrane, umbilical cord, and chorionic plate under serum-free condition
Cited by: 62
Author(s): Jiao Ma, Jun Wu, Han Liu, Xiangxiang Jiang, Yan Long, Jie Hao, Hongmei Wang
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-018-5303-8

Higher plane of nutrition pre-weaning enhances Holstein calf mammary gland development through alterations in the parenchyma and fat pad transcriptome
Cited by: 13
Author(s): Mario Vailati-Riboni, Ryan Bucktrout, Siyuan Zhan, Ashley Geiger, Joshua C McCann, R.M. Akers, Juan J. Loor
Software Mentions: 3
Published: over 7 years ago

10.1111/acel.13420

Circulating microRNA profile in humans and mice with congenital GH deficiency
Cited by: 6
Author(s): Tatiana D. Saccon, Augusto Schneider, Cindi G. Marinho, Allancer D C Nunes, Sarah Noureddine, Joseph M. Dhahbi, Yury O. Nunez Lopez, Gage LeMunyan, Roberto Salvatori, Carla R. P. Oliveira, Alécia A Oliveira-Santos, Nicolas Musi, Andrzej Bartke, Manuel H. Aguiar‐Oliveira, Michał M. Masternak
Software Mentions: 3
Published: about 5 years ago

10.1186/s13287-016-0370-8

Identification and validation of multiple cell surface markers of clinical-grade adipose-derived mesenchymal stromal cells as novel release criteria for good manufacturing practice-compliant production
Cited by: 120
Author(s): Emily T. Camilleri, Michael P. Gustafson, Amel Dudakovic, Scott M. Riester, Catalina Galeano Garces, Christopher R. Paradise, Hideki Takai, Marcel Karperien, Simon M. Cool, Hee Jeong Im Sampen, A. Noelle Larson, Wenchun Qu, Jay Smith, Allan B. Dietz, André J. van Wijnen
Software Mentions: 3
Published: about 10 years ago

10.18632/oncotarget.20013

An integrated lncRNA, microRNA and mRNA signature to improve prognosis prediction of colorectal cancer
Cited by: 31
Author(s): Yong Xiong, Rong Wang, Linglong Peng, Wenxian You, Jinlai Wei, Shouru Zhang, Xingye Wu, Jun Guo, Jiaman Xu, Zhenbing Lv, Zhongxue Fu
Software Mentions: 3
Published: about 9 years ago

10.1186/s12864-019-5953-1

Systematic evaluation of RNA-Seq preparation protocol performance
Cited by: 26
Author(s): Hsueh-Ping Chao, Yueping Chen, Yoko Takata, Mary W. Tomida, Kevin Lin, Jason Kirk, Melissa S. Simper, Carol Mikulec, Joyce E. Rundhaug, Susan M. Fischer, Taiping Chen, Dean G. Tang, Yue Lu, Jianjun Shen
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-021-07516-2

Mitochondrial genotype alters the impact of rapamycin on the transcriptional response to nutrients in Drosophila
Cited by: 7
Author(s): John Santiago, Joan M. Boylan, Faye A Lemieux, Philip A. Gruppuso, Jennifer Sanders, David M. Rand
Software Mentions: 3
Published: over 5 years ago

10.1111/1462-2920.14788

Metatranscriptomic and metabolite profiling reveals vertical heterogeneity within a <i>Zygnema</i> green algal mat from Svalbard (High Arctic)
Cited by: 25
Author(s): Martin Rippin, Martina Pichrtová, Erwann Arc, Ilse Kranner, Burkhard Becker, Andreas Holzinger
Software Mentions: 3
Published: almost 7 years ago

10.3389/fpls.2018.01345

Co-expression and Transcriptome Analysis of Marchantia polymorpha Transcription Factors Supports Class C ARFs as Independent Actors of an Ancient Auxin Regulatory Module
Cited by: 37
Author(s): Eduardo Flores-Sandoval, Facundo Romani, John L. Bowman
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-018-5236-2

Power in pairs: assessing the statistical value of paired samples in tests for differential expression
Cited by: 24
Author(s): John R. Stevens, Jennifer S. Herrick, Roger K. Wolff, Martha L. Slattery
Software Mentions: 3
Published: over 7 years ago

10.18632/oncotarget.19483

Identification of hub genes involved in the development of hepatocellular carcinoma by transcriptome sequencing
Cited by: 8
Author(s): Yongchang Zheng, Junyu Long, Liangcai Wu, Haohai Zhang, Lin Li, Ying Zheng, Anqiang Wang, Jianzhen Lin, Xiaobo Yang, Xinting Sang, Ke Hu, Jie Pan, Haitao Zhao
Software Mentions: 3
Published: about 9 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: almost 5 years ago

10.7554/eLife.32323

An incoherent feedforward loop facilitates adaptive tuning of gene expression
Cited by: 19
Author(s): Jae‐Hee Hong, Nathan Brandt, Farah Abdul-Rahman, Ally Yang, Terence J. Hughes, David Gresham
Software Mentions: 3
Published: over 8 years ago

10.18632/aging.102652

Integrated transcriptome expression profiling reveals a novel lncRNA associated with L-DOPA-induced dyskinesia in a rat model of Parkinson’s disease
Cited by: 8
Author(s): Chunlei Han, Yunpeng Liu, Yun‐Peng Sui, Ning Chen, Tingting Du, Ying Jiang, Chenjia Guo, Kailiang Wang, Qiao Wang, Shiying Fan, Michio Shimabukuro, Fangang Meng, Yuan Fang, Jianguo Zhang
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-021-98420-y

Short-term transcriptomic response to plasma membrane injury
Cited by: 3
Author(s): Swantje Christin Häger, Catarina Dias, Stine Lauritzen Sønder, André Vidas Olsen, Isabelle da Piedade, Anne Sofie Busk Heitmann, Elena Papaleo, Jesper Nylandsted
Software Mentions: 3
Published: almost 5 years ago

10.18632/oncotarget.18162

Upregulation of long noncoding RNA HOXA-AS3 promotes tumor progression and predicts poor prognosis in glioma
Cited by: 53
Author(s): Fan Wu, Chuanbao Zhang, Jinquan Cai, Fan Yang, Tingyu Liang, Xiaoyan Yan, Haoyuan Wang, Wen Wang, Jing Chen, Tao Jiang
Software Mentions: 3
Published: over 9 years ago

10.3389/fpls.2019.01301

Differential Expression of Candidate Salivary Effector Genes in Pea Aphid Biotypes With Distinct Host Plant Specificity
Cited by: 25
Author(s): Hélène Boulain, Fabrice Legeai, Julie Jaquiéry, Endrick Guy, Stéphanie Morlière, Jean‐Christophe Simon, Akiko Sugio
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-015-1741-8

Whole blood microarray analysis of pigs showing extreme phenotypes after a porcine reproductive and respiratory syndrome virus infection
Cited by: 13
Author(s): Martine Schroyen, Juan P. Steibel, James E. Koltes, Igseo Choi, Nancy E. Raney, Christopher J. Eisley, Eric R. Fritz-Waters, James M. Reecy, Jack C. M. Dekkers, R. Rowland, Joan K. Lunney, Catherine W. Ernst, Christopher K. Tuggle
Software Mentions: 3
Published: about 11 years ago

10.1038/s41598-021-95698-w

PCA-based unsupervised feature extraction for gene expression analysis of COVID-19 patients
Cited by: 9
Author(s): Kota Fujisawa, Mamoru Shimo, Y-h. Taguchi, Shinya Ikematsu, Ryota Miyata
Software Mentions: 3
Published: almost 5 years ago

10.1186/1471-2164-15-18

Molecular response to the pathogen Phytophthora sojae among ten soybean near isogenic lines revealed by comparative transcriptomics
Cited by: 62
Author(s): Feng Lin, Meixia Zhao, Douglas Baumann, Jieqing Ping, Lianjun Sun, Yunfeng Liu, Biao Zhang, Ziyang Tang, Elisa Hughes, R. W. Doerge, Teresa J. Hughes, Jianxin Ma
Software Mentions: 3
Published: over 12 years ago

10.18632/oncotarget.16451

RNA sequencing analyses reveal novel differentially expressed genes and pathways in pancreatic cancer
Cited by: 43
Author(s): Yiming Mao, Jianjun Shen, Yue Lu, Kevin Lin, Huamin Wang, Yanan Li, Ping Chang, Mary G. Walker, Donghui Li
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-021-96150-9

Transcriptomic analysis of the mouse retina after acute and chronic normobaric and hypobaric hypoxia
Cited by: 10
Author(s): Lynn J. A. Ebner, Marijana Samardzija, Federica Storti, Vyara Todorova, Duygu Karademir, Julian Behr, Fraser Simpson, Markus Thiersch, Christian Grimm
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-021-95423-7

Evolutionary transition of doublesex regulation from sex-specific splicing to male-specific transcription in termites
Cited by: 14
Author(s): Shôzô Miyazaki, Kokuto Fujiwara, Keima Kai, Yudai Masuoka, Hiroki Gotoh, Teruyuki Niimi, Yoshinobu Hayashi, Shuji Shigenobu, Kazuyuki Maekawa
Software Mentions: 3
Published: about 5 years ago

10.18632/oncotarget.16051

Identification of molecular targets for esophageal carcinoma diagnosis using miRNA-seq and RNA-seq data from The Cancer Genome Atlas: a study of 187 cases
Cited by: 29
Author(s): Jiang‐Hui Zeng, Dandan Xiong, Yu‐Yan Pang, Yu Zhang, Rongjiang Tang, Dan Luo, Gang Chen
Software Mentions: 3
Published: over 9 years ago

10.18632/oncotarget.16518

Novel RNA biomarkers of prostate cancer revealed by RNA-seq analysis of formalin-fixed samples obtained from Russian patients
Cited by: 29
Author(s): Anastasia S. Nikitina, Е. И. Шарова, S. A. Danilenko, Т. Б. Бутусова, A.O. Vasiliev, А. В. Говоров, Elena A. Prilepskaya, Dmitry Pushkar, Elena S. Kostryukova
Software Mentions: 3
Published: over 9 years ago

10.3389/fpls.2016.01920

Glutathione S-transferases and UDP-glycosyltransferases Are Involved in Response to Aluminum Stress in Flax
Cited by: 45
Author(s): Alexey A. Dmitriev, George S. Krasnov, Tatiana A. Rozhmina, Natalya V. Kishlyan, Alexander V. Zyablitsin, А. Ф. Садритдинова, Anastasiya V. Snezhkina, Maria Fedorova, Olga Yu. Yurkevich, Olga V. Muravenko, Nadezhda L. Bolsheva, Anna V. Kudryavtseva, Nataliya V. Melnikova
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-019-5429-3

Re-analysis of the coral Acropora digitifera transcriptome reveals a complex lncRNAs-mRNAs interaction network implicated in Symbiodinium infection
Cited by: 11
Author(s): Chen Huang, Dongliang Leng, Shixue Sun, Xiaohua Douglas Zhang
Software Mentions: 3
Published: over 7 years ago

10.18632/aging.202410

Systems pharmacology dissection of Epimedium targeting tumor microenvironment to enhance cytotoxic T lymphocyte responses in lung cancer
Cited by: 11
Author(s): Chao Huang, Zhihua Li, Jinglin Zhu, Xuetong Chen, Yuanyuan Hao, Ruijie Yang, Ruifei Huang, Jun Zhou, Zhenzhong Wang, Wei Xiao, Chunli Zheng, Yonghua Wang
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-94386-z

An epigenetic GPI anchor defect impairs TLR4 signaling in the B cell transdifferentiation model for primary human monocytes BLaER1
Cited by: 3
Author(s): Julia Wegner, Thomas Zillinger, Thais Marina Schlee-Guimarães, Eva Bartok, Martin Schlee
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2164-15-808

De novo transcriptome of Ischnura elegans provides insights into sensory biology, colour and vision genes
Cited by: 47
Author(s): Pallavi Chauhan, Bengt Hansson, Ken Kraaijeveld, Peter de Knijff, Erik I. Svensson, Maren Wellenreuther
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0250758

Comprehensive at-arrival transcriptomic analysis of post-weaned beef cattle uncovers type I interferon and antiviral mechanisms associated with bovine respiratory disease mortality
Cited by: 9
Author(s): Matthew A. Scott, Amelia R. Woolums, Cyprianna E. Swiderski, Andy D. Perkins, Bindu Nanduri, David R. Smith, Brandi B. Karisch, William B. Epperson, J. R. Blanton
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-020-07272-9

Genome-wide identification and characterization of long non-coding RNAs related to grain yield in foxtail millet [Setaria italica (L.) P. Beauv.]
Cited by: 5
Author(s): Zilong Zhao, Dan Liu, Yanjiao Cui, Suying Li, Dan Liang, Daizhen Sun, Jianhe Wang, Zhengli Liu
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.16252

Niclosamide is a potential therapeutic for familial adenomatosis polyposis by disrupting Axin-GSK3 interaction
Cited by: 26
Author(s): Ahn Sk, Nam Hee Kim, Kyungro Lee, Yong Hoon, Ji Hye Yang, So Young, Eunae Sandra Cho, Yoonmi Lee, Jeong Ho Seok, Hyun Soo Cho, Yongseok Jeon, Young Su Yuk, Suebean Cho, Kyoung Tai No, Hyun Sil Kim, Ho Lee, Jiwon Choi, Jong In Yook
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-018-4596-y

Divergent transcriptomic responses underlying the ranaviruses-amphibian interaction processes on interspecies infection of Chinese giant salamander
Cited by: 14
Author(s): Ke Fei, Jian‐Fang Gui, Zhongyuan Chen, Tao Li, Cun-Ke Lei, Zi-Hao Wang, Qi-Ya Zhang
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0210358

Ocean acidification at a coastal CO2 vent induces expression of stress-related transcripts and transposable elements in the sea anemone Anemonia viridis
Cited by: 11
Author(s): Ilona Urbárová, Sylvain Forêt, Mikael Dahl, Åse Emblem, Marco Milazzo, Jason M. Hall‐Spencer, Steinar Johansen
Software Mentions: 3
Published: over 7 years ago

10.18632/aging.103698

A two-gene-based prognostic signature for pancreatic cancer
Cited by: 8
Author(s): Shengqian Zhou, Yuanliang Yan, Xi Chen, Shuangshuang Zeng, Jie Wei, Xiang Wang, Zhicheng Gong, Zhijie Xu
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-021-93142-7

Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing
Cited by: 3
Author(s): Zoltán Maróti, Dóra Tombácz, Norbert Moldován, Gábor Torma, Victoria A Jefferson, Zsolt Csabai, Gábor Gulyás, Ákos Dörmő, Miklós Boldogkői, Tibor Kalmár, Florencia Meyer, Zsolt Boldogköi
Software Mentions: 3
Published: about 5 years ago

10.1002/ece3.5956

Transcriptomic regulation of seasonal coat color change in hares
Cited by: 13
Author(s): Mafalda S. Ferreira, Paulo C. Alves, Colin M. Callahan, Iwona Giska, Liliana Farelo, Hannes Jenny, L. Scott Mills, Klaus Hackländer, Jeffrey M. Good, José Melo‐Ferreira
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-14-688

Guide: a desktop application for analysing gene expression data
Cited by: 5
Author(s): Jarny Choi
Software Mentions: 3
Published: over 13 years ago

10.1002/ece3.5181

Differential gene expression in relation to mating system in Peromyscine rodents
Cited by: 2
Author(s): Jesyka Meléndez‐Rosa, Ke Bi, Eileen A. Lacey
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-015-1223-z

Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome
Cited by: 14
Author(s): Benjamin B. Green, Stephanie McKay, David E. Kerr
Software Mentions: 3
Published: over 11 years ago

10.1002/ece3.6688

Examining the molecular mechanisms contributing to the success of an invasive species across different ecosystems
Cited by: 0
Author(s): Sarah K. Lamar, Ian Beddows, Charlyn Partridge
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-019-5452-4

Usability of reference-free transcriptome assemblies for detection of differential expression: a case study on Aethionema arabicum dimorphic seeds
Cited by: 16
Author(s): Per K.I. Wilhelmsson, Jake O. Chandler, Noé Fernandez-Pozo, Kai Graeber, Kristian K. Ullrich, Waheed Arshad, Safina Khan, Johannes A. Hofberger, Karl Buchta, Patrick P. Edger, J. Chris Pires, M. Eric Schranz, Gerhard Leubner‐Metzger, Stefan A. Rensing
Software Mentions: 3
Published: over 7 years ago

10.1002/ece3.6377

Comparison of spleen transcriptomes of two wild rodent species reveals differences in the immune response against <i>Borrelia afzelii</i>
Cited by: 4
Author(s): Xianqiong Zhong, Max Lundberg, Lars Råberg
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-021-90412-2

Axonopathy precedes cell death in ocular damage mediated by blast exposure
Cited by: 9
Author(s): Nickolas Boehme, Adam Hedberg-Buenz, Nicole Tatro, Michael Bielecki, William C Castonguay, Todd E. Scheetz, Michael G. Anderson, Laura M. Dutca
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0173094

Transgenic expression of fungal accessory hemicellulases in Arabidopsis thaliana triggers transcriptional patterns related to biotic stress and defense response
Cited by: 6
Author(s): Alex Yi‐Lin Tsai, Kin Chan, Chi-Yip Ho, Thomas Canam, Resmi Capron, Emma R. Master, Katharina Bräutigam
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-019-5894-8

Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp
Cited by: 35
Author(s): Ming Luo, Lanmei Wang, Hao Yin, Wenbin Zhu, Jianjun Fu, Zaijie Dong
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-017-4107-6

Impaired response of the bronchial epithelium to inflammation characterizes severe equine asthma
Cited by: 30
Author(s): Laurence Tessier, Olivier Côté, Mary E. Clark, Laurent Viel, Andrés Diaz-Méndez, Simon Anders, Dorothee Bienzle
Software Mentions: 3
Published: almost 9 years ago

10.18632/aging.202493

Identification of hub genes associated with adult acute myeloid leukemia progression through weighted gene co-expression network analysis
Cited by: 4
Author(s): Ruiqi Zhu, Wenyi Lin, Liang Tang, Yu Hu
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-018-4781-z

Impact of growth pH and glucose concentrations on the CodY regulatory network in Streptococcus salivarius
Cited by: 3
Author(s): Jianing Geng, Szu-Chuan Huang, Yueh-Ying Chen, Cheng-Hsun Chiu, Songnian Hu, Yi-Ywan M. Chen
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-015-1626-x

Characterizing the neurotranscriptomic states in alternative stress coping styles
Cited by: 37
Author(s): Ryan Y. Wong, Melissa S. Lamm, John Godwin
Software Mentions: 3
Published: about 11 years ago

10.1186/s12859-015-0873-9

TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation
Cited by: 34
Author(s): Markus Wolfien, Christian Rimmbach, Ulf Schmitz, Julia Jeannine Jung, Stefan Krebs, Gustav Steinhoff, Róbert Dávid, Olaf Wolkenhauer
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2164-15-754

Transcriptome profiling of natural dichromatism in the annual fishes Nothobranchius furzeri and Nothobranchius kadleci
Cited by: 21
Author(s): Enoch Ng’oma, Marco Groth, Roberto Ripa, Matthias Platzer, Alessandro Cellerino
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12864-017-3592-y

A reference gene set for sex pheromone biosynthesis and degradation genes from the diamondback moth, Plutella xylostella, based on genome and transcriptome digital gene expression analyses
Cited by: 46
Author(s): Peng He, Yun‐Fei Zhang, Duan‐Yang Hong, Jun Wang, Xingliang Wang, Ling-Hua Zuo, Xianfu Tang, Weiming Xu, Ming He
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-021-89207-2

Cold-induction of afadin in brown fat supports its thermogenic capacity
Cited by: 2
Author(s): Morten Lundh, Ali Altıntaş, Marco Tozzi, Odile Fabre, Tao Ma, Farnaz Shamsi, Zachary Gerhart-Hines, Romain Barrès, Yu–Hua Tseng, Brice Emanuelli
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-16-S6-S2

FunPat: function-based pattern analysis on RNA-seq time series data
Cited by: 56
Author(s): Tiziana Sanavia, Francesca Finotello, Barbara Di Camillo
Software Mentions: 3
Published: about 11 years ago

10.1186/s12864-021-07655-6

Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines
Cited by: 9
Author(s): Virginia Mwape, Fredrick M. Mobegi, Roshan Regmi, Toby E. Newman, Lars G. Kamphuis, Mark Derbyshire
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0031526

The Transcriptome of Compatible and Incompatible Interactions of Potato (Solanum tuberosum) with Phytophthora infestans Revealed by DeepSAGE Analysis
Cited by: 55
Author(s): Gabor Gyetvai, Mads Sønderkær, Ulrike Göbel, Rico Basekow, Agim Ballvora, Maren Imhoff, Birgit Kersten, Kåre Lehmann Nielsen, Christiane Gebhardt
Software Mentions: 3
Published: over 14 years ago

10.1038/s41598-021-88029-6

Transcriptomic analysis to infer key molecular players involved during host response to NDV challenge in Gallus gallus (Leghorn &amp; Fayoumi)
Cited by: 4
Author(s): Venkata Krishna Vanamamalai, Priyanka Garg, Gautham Kolluri, Ravi Kumar Gandham, Itishree Jali, Shailesh Sharma
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-2995-5

RNA-seq-based evaluation of bicolor tepal pigmentation in Asiatic hybrid lilies (Lilium spp.)
Cited by: 57
Author(s): Kazuma Suzuki, Tomohiro Suzuki, Takashi Nakatsuka, Hideo Dohra, Masumi Yamagishi, Kohei Matsuyama, Hideyuki Matsuura
Software Mentions: 3
Published: about 10 years ago

10.1186/s12864-016-3356-0

The influence of pro-longevity gene Gclc overexpression on the age-dependent changes in Drosophila transcriptome and biological functions
Cited by: 17
Author(s): Alexey Moskalev, Mikhail Shaposhnikov, Ekaterina Proshkina, А. С. Белый, Alexander Fedintsev, Svetlana Zhikrivetskaya, Zulfiya G. Guvatova, А. Ф. Садритдинова, А. В. Снежкина, George S. Krasnov, Anna V. Kudryavtseva
Software Mentions: 3
Published: over 9 years ago