bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.3390/genes11091066

Transcriptome Analysis Reveals a Gene Expression Pattern Associated with Fuzz Fiber Initiation Induced by High Temperature in Gossypium barbadense
Cited by: 6
Author(s): Gongmin Cheng, Longyan Zhang, Hengling Wei, Hantao Wang, Jianhua Lü, Shuxun Yu
Software Mentions: 4
Published: almost 6 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: over 5 years ago

10.3390/genes11091049

The Transcriptomic Landscape of Cupriavidus metallidurans CH34 Acutely Exposed to Copper
Cited by: 3
Author(s): Laurens Maertens, Natalie Leys, Jean-Yves Matroule, Rob Van Houdt
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0204038

Shifts in ovine cardiopulmonary microRNA expression in late gestation and the perinatal period
Cited by: 3
Author(s): Ramona Krauss, Belinda Phipson, Alicia Oshlack, Nikita Prasad-Gupta, Michael Cheung, Joseph J. Smolich, Salvatore Pepe
Software Mentions: 4
Published: almost 8 years ago

10.3390/genes11070794

Co-Expression Networks for Causal Gene Identification Based on RNA-Seq Data of Corynebacterium pseudotuberculosis
Cited by: 3
Author(s): Edian F. Franco, Pratip Rana, Ana Lídia Queiroz Cavalcante, Artur da Costa da Luiz Silva, Anne Cybelle Pinto Gomide, Adriana Ribeiro Carneiro Folador, Vasco Azevedo, Preetam Ghosh, Rommel Thiago Jucá Ramos
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0125224

An Iterative Leave-One-Out Approach to Outlier Detection in RNA-Seq Data
Cited by: 31
Author(s): Nysia I. George, John F. Bowyer, Nathaniel M. Crabtree, Ching‐Wei Chang
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pone.0255915

Reciprocal interplay between asporin and decorin: Implications in gastric cancer prognosis
Cited by: 6
Author(s): Dipjit Basak, Zarqua Jamal, Arnab Ghosh, Pronoy Kanti Mondal, Priyanka Dey Talukdar, Semanti Ghosh, Biswadeep Ghosh Roy, Ranajoy Ghosh, Ajay Halder, Abhijit Chowdhury, Gopal Krishna Dhali, Brajadulal Chattopadhyay, Makhan Saha, Abhimanyu Basu, Sukanta Roy, Chitranjan Mukherjee, Nidhan K. Biswas, Urmi Chatterji, Shalini Datta
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0131504

A Comparative Transcriptome Analysis between Wild and Albino Yellow Catfish (Pelteobagrus fulvidraco)
Cited by: 31
Author(s): Ming Zou, Xiaoting Zhang, Ze-Chao Shi, Li Lin, Gang Ouyang, Guirong Zhang, Huan Zheng, Kai-Jian Wei, Wei Ji
Software Mentions: 4
Published: about 11 years ago

10.1534/g3.120.401166

DAF-16 and SMK-1 Contribute to Innate Immunity During Adulthood in<i>Caenorhabditis elegans</i>
Cited by: 14
Author(s): Daniel R. McHugh, Elena Koumis, Paul Jacob, Jennifer Goldfarb, Michelle Schlaubitz-Garcia, Safae Bennani, Paul Regan, Prem Patel, Matthew J. Youngman
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-27476-0

Host-plant induced changes in microbial community structure and midgut gene expression in an invasive polyphage (Anoplophora glabripennis)
Cited by: 20
Author(s): Erin D. Scully, Scott M. Geib, Charles J. Mason, John E. Carlson, Ming Tien, Han Yi Chen, Chung‐Jui Tsai, Chung‐Jui Tsai, Kelli Hoover
Software Mentions: 4
Published: about 8 years ago

10.1186/s13568-021-01225-5

Manipulating the soil microbiomes during a community recovery process with plant beneficial species for the suppression of Fusarium wilt of watermelon
Cited by: 14
Author(s): Xu Zhang, Cong Xue, D. C. Fang, Xiangming He, Mengyu Wei, Chenjin Zhuo, Junyao Jin, Biao Shen, Rong Li, Ning Ling, Qirong Shen
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-018-27493-z

A gene co-expression network model identifies yield-related vicinity networks in Jatropha curcas shoot system
Cited by: 5
Author(s): Nisha Govender, Siju Senan, Zeti‐Azura Mohamed‐Hussein, R Wickneswari V Ratnam
Software Mentions: 4
Published: about 8 years ago

10.3390/genes11060634

metaRE R Package for Meta-Analysis of Transcriptome Data to Identify the cis-Regulatory Code behind the Transcriptional Reprogramming
Cited by: 7
Author(s): Daria D. Novikova, Pavel Cherenkov, Yana Sizentsova, В. В. Миронова
Software Mentions: 4
Published: about 6 years ago

10.3389/fpls.2016.01431

Quantitative Resistance to Verticillium Wilt in Medicago truncatula Involves Eradication of the Fungus from Roots and Is Associated with Transcriptional Responses Related to Innate Immunity
Cited by: 13
Author(s): Maoulida Toueni, Cécile Ben, Aurélie Le Ru, Laurent Gentzbittel, Martina Rickauer
Software Mentions: 4
Published: almost 10 years ago

10.31557/APJCP.2020.21.6.1787

Risk Scoring System based on lncRNA Expression for Predicting Survival in Hepatocellular Carcinoma with Cirrhosis
Cited by: 13
Author(s): Jiaxiang Ye, Haixia Li, Jiazhang Wei, Yue Luo, Hongmei Li, Jinyan Zhang, Xi Luo
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0166862

Drosophila DDX3/Belle Exerts Its Function Outside of the Wnt/Wingless Signaling Pathway
Cited by: 1
Author(s): Fabian H. Jenny, Konrad Basler
Software Mentions: 4
Published: over 9 years ago

10.1099/mgen.0.000319

Landscape of gene expression variation of natural isolates of Cryptococcus neoformans in response to biologically relevant stresses
Cited by: 22
Author(s): Yu Chen, Chen Yuan, Christopher A. Desjardins, Jennifer L. Tenor, Dena L. Toffaletti, Charles Giamberardino, Anastasia P. Litvintseva, John R. Perfect, Christina A. Cuomo
Software Mentions: 4
Published: over 6 years ago

10.1186/s13148-020-00989-0

Identification and validation of methylated differentially expressed miRNAs and immune infiltrate profile in EBV-associated gastric cancer
Cited by: 4
Author(s): Man-Sheng Zhu, Qi Liang, Tao Chen, Qian Kong, Gengtai Ye, Shitong Yu, Xunjun Li, Qinglie He, Hao Líu, Yanfeng Hu, Jiang Yu, Guoxin Li
Software Mentions: 4
Published: over 5 years ago

10.3390/genes11050472

Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii
Cited by: 7
Author(s): Mushtaque Ali, Hongyan Cheng, Mahtab Soomro, Shuyan Li, Muhammad Tufail, Mian Faisal Nazir, Feng Xu, Youping Zhang, Dongyun Zuo, Limin Lv, Qiaolian Wang, Guoli Song
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0114461

Inference of the Oxidative Stress Network in Anopheles stephensi upon Plasmodium Infection
Cited by: 10
Author(s): Jatin Shrinet, Umesh K. Nandal, T. Adak, Raj K. Bhatnagar, Sujatha Sunil
Software Mentions: 4
Published: over 11 years ago

10.1007/s00401-019-02109-6

Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform-specific start-loss mutations of essential genes can cause genetic diseases
Cited by: 37
Author(s): Elena Perenthaler, Anita Nikoncuk, Soheil Yousefi, Woutje M. Berdowski, Maysoon Alsagob, Ivan Čapo, Herma C. van der Linde, Paul van den Berg, Edwin H. Jacobs, Darija Putar, Mehrnaz Ghazvini, Eleonora Aronica, Wilfred F. J. van IJcken, Walter G. de Valk, Evita Medici-van den Herik, Marjon van Slegtenhorst, Lauren Brick, Mariya Kozenko, Jennefer N. Kohler, Jonathan A. Bernstein, Kristin G. Monaghan, Amber Begtrup, Rebecca Torene, Amna Al Futaisi, Fathiya Al Murshedi, Renjith Mani, Faisal Al Azri, Erik‐Jan Kamsteeg, Majid Mojarrad, Atieh Eslahi, Zaynab Khazaei, Fateme Massinaei Darmiyan, Mohammad Doosti, Ehsan Ghayoor Karimiani, Jana Vandrovcová, Faisal Zafar, Nuzhat Rana, Krishna Kumar Kandaswamy, Jozef Hertecant, Péter Bauer, Mohammed A. AlMuhaizea, Mustafa A. Salih, Mazhor Aldosary, Rawan Almass, Laila AlQuait, Wafa Qubbaj, Serdar Coşkun, Khaled O. Alahmadi, Muddathir H. Hamad, Salem Alwadaee, Khalid Awartani, Anas Dababo, Futwan Al‐Mohanna, Dilek Çolak, Mohammadreza Dehghani, Mohammad Yahya Vahidi Mehrjardi, Murat Günel, A. Gülhan Ercan-Şençiçek, Gouri Rao Passi, Huma Arshad Cheema, Stéphanie Efthymiou, Henry Houlden, Aida M. Bertoli‐Avella, Alice S. Brooks, Kyle Retterer, Reza Maroofian, Namik Kaya, Tjakko J. van Ham, Tahsin Stefan Barakat
Software Mentions: 4
Published: over 6 years ago

10.3390/antiox10091380

NRF2 Mediates Therapeutic Resistance to Chemoradiation in Colorectal Cancer through a Metabolic Switch
Cited by: 7
Author(s): Séan M. O’Cathail, Chieh‐Hsi Wu, Russell J. Thomas, M. Hawkins, Tim Maughan, Annabelle Lewis
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13148-020-00836-2

Alterations in the methylome of the stromal tumour microenvironment signal the presence and severity of prostate cancer
Cited by: 15
Author(s): Mitchell G. Lawrence, Ruth Pidsley, Birunthi Niranjan, Melissa Papargiris, Brooke A. Pereira, Michelle Richards, Linda Teng, Sam Norden, Andrew Ryan, Mark Frydenberg, Clare Stirzaker, Renea A. Taylor, Gail P. Risbridger, Susan J. Clark
Software Mentions: 4
Published: over 6 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 6 years ago

10.1186/s12915-019-0646-4

Enabling cell-type-specific behavioral epigenetics in Drosophila: a modified high-yield INTACT method reveals the impact of social environment on the epigenetic landscape in dopaminergic neurons
Cited by: 15
Author(s): Pavan Agrawal, Phuong Chung, Ulrike Heberlein, Clement F. Kent
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-019-5767-1

Transcriptomic responses to diet quality and viral infection in Apis mellifera
Cited by: 23
Author(s): Lindsay Rutter, Jimena Carrillo-Tripp, Bryony C. Bonning, Dianne Cook, Amy L. Toth, Adam Doležal
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-016-2973-y

Transcriptome analysis of seed dormancy after rinsing and chilling in ornamental peaches (Prunus persica (L.) Batsch)
Cited by: 15
Author(s): Kanjana Worarad, Tomohiro Suzuki, Kazuo Ishii, Toshinori Kozaki, Masayuki Iigo, Kenji Yamane
Software Mentions: 4
Published: about 10 years ago

10.1186/s13148-015-0086-0

Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis
Cited by: 26
Author(s): Warwick J. Locke, Elena Zotenko, Clare Stirzaker, Mark D. Robinson, Rebecca A. Hinshelwood, Andrew Stone, Roger R. Reddel, Lily I. Huschtscha, Susan J. Clark
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0145257

Comparative Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Characterized by Shell Colors: Identification of Genetic Bases Potentially Involved in Pigmentation
Cited by: 73
Author(s): Dandan Feng, Qi Li, Hong Yu, Xuelin Zhao, Lingfeng Kong
Software Mentions: 4
Published: over 10 years ago

10.1186/s12864-015-1660-8

Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus
Cited by: 59
Author(s): Michael H. Perlin, Joëlle Amselem, Eric Fontanillas, Su San Toh, Zehua Chen, Jonathan M. Goldberg, Sébastien Duplessis, Bernard Henrissat, Sarah Young, Qiandong Zeng, Gabriela Aguileta, Elsa Petit, Hélène Badouin, Jared Andrews, Dominique Razeeq, Toni Gabaldón, Hadi Quesneville, Tatiana Giraud, Michael E. Hood, David J. Schultz, Christina A. Cuomo
Software Mentions: 4
Published: about 11 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: about 7 years ago

10.3389/fimmu.2018.02533

Adenosinergic Signaling Alters Natural Killer Cell Functional Responses
Cited by: 72
Author(s): Andrea M. Chambers, Jiao Wang, Kyle B. Lupo, Hao Yu, Nadia A. Lanman, Sandro Matosevic
Software Mentions: 4
Published: almost 8 years ago

10.3389/fgene.2019.01018

Transcriptome Analysis Identifies Piwi-Interacting RNAs as Prognostic Markers for Recurrence of Prostate Cancer
Cited by: 12
Author(s): Yuanli Zuo, Liang Yu, Jiting Zhang, You-Zeng Hao, Menglong Li, Zhining Wen, Yun Zhao
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13148-021-01050-4

Epigenetic evidence of an Ac/Dc axis by VPA and SAHA
Cited by: 10
Author(s): Sebastian Lunke, Scott Maxwell, Ishant Khurana, K N Harikrishnan, Jun Okabe, Keith Al-Hasani, Assam El‐Osta
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0123569

XomAnnotate: Analysis of Heterogeneous and Complex Exome- A Step towards Translational Medicine
Cited by: 5
Author(s): Asoke K. Talukder, Shashidhar Ravishankar, Krittika Sasmal, Santhosh Gandham, Jyothsna Prabhukumar, Prahalad Achutharao, Debmalya Barh, Francesco Blasi
Software Mentions: 4
Published: over 11 years ago

10.3390/ijms22073674

Can miRNA Indicate Risk of Illness after Continuous Exposure to M. tuberculosis?
Cited by: 3
Author(s): Cleonardo Augusto Silva, André M. Ribeiro-dos-Santos, Wanderson Gonçalves e Gonçalves, Pablo Diego do Carmo Pinto, Rafael Pompeu Pantoja, Tatiana Vinasco-Sandoval, André M. Ribeiro-dos-Santos, Mara H. Hutz, Amanda Ferreira Vidal, Gilderlanio Santana de Araújo, Sidney Emanuel Batista dos Santos
Software Mentions: 4
Published: over 5 years ago

10.3390/genes10100745

Differential Gene Expression in Articular Cartilage and Subchondral Bone of Neonatal and Adult Horses
Cited by: 4
Author(s): Ann M. Kemper, Jenny Drnevich, Molly E. McCue, Annette M. McCoy
Software Mentions: 4
Published: almost 7 years ago

10.3390/genes10090719

WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice
Cited by: 50
Author(s): Mei-Ling Zhu, Hongjun Xie, Xiangjin Wei, Komivi Dossa, Yaying Yu, Suozhen Hui, Guohua Tang, Xiaoshan Zeng, Ye Yu, Jianlong Wang
Software Mentions: 4
Published: almost 7 years ago

10.3389/fpls.2018.00204

Transcriptome and Cell Physiological Analyses in Different Rice Cultivars Provide New Insights Into Adaptive and Salinity Stress Responses
Cited by: 55
Author(s): Elide Formentin, Cristina Sudiro, Giorgio Perin, Samantha Riccadonna, Elisabetta Barizza, Elena Baldoni, Enrico Lavezzo, Piergiorgio Stevanato, Gian Attilio Sacchi, Paolo Fontana, Stefano Toppo, Tomas Morosinotto, Michela Zottini, Fiorella Lo Schiavo
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-018-4457-8

Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon
Cited by: 10
Author(s): Li Liu, Shuchao Ren, Junqiang Guo, Qingyi Wang, Xiaotuo Zhang, Peiran Liao, Shipeng Li, Ramanjulu Sunkar, Yun Zheng
Software Mentions: 4
Published: over 8 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: over 7 years ago

10.31557/APJCP.2020.21.9.2593

Transcriptome Related to Avoiding Immune Destruction in Nasopharyngeal Cancer in Indonesian Patients Using Next-Generation Sequencing
Cited by: 2
Author(s): Risky Hiskia Poluan, Digdo Sudigyo, Gisti Rahmawati, Dicka Wahyu Setiasari, Salsabila Luthfi Sesotyosari, Tirta Wardana, Indwiani Astuti, Didik Setyo Heriyanto, Sagung Rai Indrasari, Cita Herawati, FNU Afiahayati, Sofia Mubarika Haryana
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0071462

Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data
Cited by: 163
Author(s): Yan Guo, Quanhu Sheng, Li Jiang, Fei Ye, David C. Samuels, Yu Shyr
Software Mentions: 4
Published: about 13 years ago

10.1038/s41598-019-42485-3

Comparison of multi-tissue aging between human and mouse
Cited by: 13
Author(s): Jujuan Zhuang, Lijun Zhang, Shuang Dai, Lingyu Cui, Cheng Guo, Laura Sloofman, Jialiang Yang
Software Mentions: 4
Published: over 7 years ago

10.18632/aging.203322

Identification of prognostic long non-coding RNA signature with potential drugs in hepatocellular carcinoma
Cited by: 0
Author(s): Fang Hao, Nan Wang, Xiang Wang, Yongjun Chen, Junqing Wang
Software Mentions: 4
Published: about 5 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: almost 10 years ago

10.1038/s41598-019-41843-5

Different bacterial and viral pathogens trigger distinct immune responses in a globally invasive ant
Cited by: 20
Author(s): Philip J. Lester, Kaitlin H. Buick, James W. Baty, Antoine Felden, John Haywood
Software Mentions: 4
Published: over 7 years ago

10.3389/fimmu.2021.667177

CXCL8 Associated Dendritic Cell Activation Marker Expression and Recruitment as Indicators of Favorable Outcomes in Colorectal Cancer
Cited by: 20
Author(s): Enhao Li, Xiaobao Yang, Yuzhang Du, Guanzheng Wang, David Chan, Di Wu, Peiqing Xu, Peihong Ni, Dakang Xu, Yiqun Hu
Software Mentions: 4
Published: over 5 years ago

10.1186/s40168-015-0136-z

Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries
Cited by: 43
Author(s): Joel D. Rudney, Pratik Jagtap, Cavan Reilly, Ruoqiong Chen, Todd W. Markowski, LeeAnn Higgins, James E. Johnson, Timothy J. Griffin
Software Mentions: 4
Published: over 10 years ago

10.3389/fpls.2019.01605

De Novo Transcriptome Analysis of Durum Wheat Flag Leaves Provides New Insights Into the Regulatory Response to Elevated CO2 and High Temperature
Cited by: 26
Author(s): Rubén Vicente, Anthony Bolger, Rafael Martínez‐Carrasco, Pilar Pérez Pérez, Elena Gutiérrez, Björn Usadel, Rosa Morcuende
Software Mentions: 4
Published: over 6 years ago

10.3390/genes9090431

Comparative Transcriptomics of Root Development in Wild and Cultivated Carrots
Cited by: 16
Author(s): Gabriela Machaj, Hamed Bostan, Alicja Macko-Podgórni, Massimo Iorizzo, Dariusz Grzebelus
Software Mentions: 4
Published: almost 8 years ago

10.1111/eva.12463

Plasticity in gene transcription explains the differential performance of two invasive fish species
Cited by: 47
Author(s): Kyle Wellband, Daniel D. Heath
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-016-2801-4

RNA-Seq analysis of Gtf2ird1 knockout epidermal tissue provides potential insights into molecular mechanisms underpinning Williams-Beuren syndrome
Cited by: 8
Author(s): Susan M. Corley, Cesar P Canales, Paulina Carmona-Mora, Veronica Mendoza-Reinosa, Annemiek Beverdam, Edna C. Hardeman, Marc R. Wilkins, Steve Palmer
Software Mentions: 4
Published: about 10 years ago

10.1186/s12864-019-6384-8

Chicken adaptive response to low energy diet: main role of the hypothalamic lipid metabolism revealed by a phenotypic and multi-tissue transcriptomic approach
Cited by: 6
Author(s): Frédéric Jehl, Colette Désert, Christophe Klopp, M. Brenet, Andrea Rau, Sophie Leroux, Morgane Boutin, Laëtitia Lagoutte, Kévin Muret, Yuna Blum, Diane Esquerré, David Gourichon, Thierry Burlot, Anne Collin, Frédérique Pitel, Alexandre Bénani, Tatiana Zerjal, Sandrine Lagarrigue
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms22063125

A Transcriptomic Approach to Understanding the Combined Impacts of Supra-Optimal Temperatures and CO2 Revealed Different Responses in the Polyploid Coffea arabica and Its Diploid Progenitor C. canephora
Cited by: 12
Author(s): Isabel Marques, Isabel Fernandes, Octávio S. Paulo, Fernando C. Lidon, Fábio M. DaMatta, José C. Ramalho, Ana I. Ribeiro‐Barros
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-018-5146-3

Cell-type specific RNA-Seq reveals novel roles and regulatory programs for terminally differentiated Dictyostelium cells
Cited by: 18
Author(s): Koryu Kin, Gillian Forbes, Andrew Cassidy, Pauline Schaap
Software Mentions: 4
Published: almost 8 years ago

10.3390/ijerph18157975

Comprehensive Evaluation of Differential Methylation Analysis Methods for Bisulfite Sequencing Data
Cited by: 6
Author(s): Yongjun Piao, Wanxue Xu, Kwang Ho Park, Keun Ho Ryu, Rong Xiang
Software Mentions: 4
Published: about 5 years ago

10.3390/genes9120579

Integrated Proteomic and Transcriptomic Analysis of Differential Expression of Chicken Lung Tissue in Response to NDV Infection during Heat Stress
Cited by: 19
Author(s): Perot Saelao, Ying Wang, Ganrea Chanthavixay, Vivian M. Yu, Rodrigo A. Gallardo, Jack C. M. Dekkers, Susan J. Lamont, T. Ross Kelly, Huaijun Zhou
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-019-40883-1

Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315
Cited by: 13
Author(s): Jonna Teikari, Rafael Vicentini Popin, Songjun Hou, Matti Wahlsten, Wolfgang R. Hess, Kaarina Sivonen
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-016-2397-8

Transcriptome analysis reveals differentially expressed genes associated with germ cell and gonad development in the Southern bluefin tuna (Thunnus maccoyii)
Cited by: 38
Author(s): Ido Bar, Scott F. Cummins, Abigail Elizur
Software Mentions: 4
Published: over 10 years ago

10.1038/s41598-018-26854-y

Transcriptome analysis in Hevea brasiliensis latex revealed changes in hormone signalling pathways during ethephon stimulation and consequent Tapping Panel Dryness
Cited by: 23
Author(s): Pascal Montoro, Shizhou Wu, Bénédicte Favreau, Eva Herlinawati, Cécile Labrune, Marie‐Laure Martin‐Magniette, Stéphanie Pointet, Maryannick Rio, Julie Leclercq, Sigit Ismawanto, Kuswanhadi
Software Mentions: 4
Published: about 8 years ago

10.7554/eLife.53237

Rapid sex-specific adaptation to high temperature in Drosophila
Cited by: 20
Author(s): Sheng‐Kai Hsu, Ana Marija Jakšić, Viola Nolte, Manolis Lirakis, Robert Kofler, Neda Barghi, Elisabetta Versace, Christian Schlötterer
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2164-14-266

Characterization of differential transcript abundance through time during Nematostella vectensis development
Cited by: 73
Author(s): Rebecca R. Helm, Stefan Siebert, Sarah Tulin, Joel Smith, Casey W. Dunn
Software Mentions: 4
Published: over 13 years ago

10.1186/s40168-017-0356-5

Indoor microbiota in severely moisture damaged homes and the impact of interventions
Cited by: 38
Author(s): Balamuralikrishna Jayaprakash, Rachel I. Adams, Pirkka V. Kirjavainen, Anne M. Karvonen, Asko Vepsäläinen, Maria Valkonen, Kati Järvi, Michael Sulyok, Juha Pekkanen, Anne Hyvärinen, Martin Täubel
Software Mentions: 4
Published: almost 9 years ago

10.3390/ijerph17207386

Environmental Epigenetics of Diesel Particulate Matter Toxicogenomics
Cited by: 0
Author(s): Stephanie M. Bilinovich, Kristy Lewis, Barbara L. Thompson, Jeremy W. Prokop, Daniel B. Campbell
Software Mentions: 4
Published: almost 6 years ago

10.1186/1748-7188-7-5

A normalization strategy for comparing tag count data
Cited by: 72
Author(s): Koji Kadota, Tomoaki Nishiyama, Kentaro Shimizu
Software Mentions: 4
Published: over 14 years ago

10.3389/fimmu.2021.663736

MicroRNA Expression Differences in Blood-Derived CD19+ B Cells of Methotrexate Treated Rheumatoid Arthritis Patients
Cited by: 8
Author(s): Fatima Heinicke, Xiao Zhong, Siri Tennebø Flåm, Johannes Breidenbach, Magnus Leithaug, Marthe Thoresen Mæhlen, Siri Lillegraven, Anna‐Birgitte Aga, Ellen Sauar Norli, Maria D Mjaavatten, Espen A. Haavardsholm, Manuela Zucknick, Simon Rayner, Benedicte A. Lie
Software Mentions: 4
Published: over 5 years ago

10.1534/g3.119.400413

The Genome Sequence of the Eastern Woodchuck (<i>Marmota monax</i>) – A Preclinical Animal Model for Chronic Hepatitis B
Cited by: 13
Author(s): Tyler Alioto, Fernando Cruz, Jèssica Gómez-Garrido, Miriam Triyatni, Marta Gut, Leonor Frías, Anna Esteve‐Codina, Stephan Menne, Anna Kiialainen, Nadine Kumpesa, Fabian Birzele, Roland Schmucki, Ivo Gut, Olivia Spleiss
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2164-14-S8-S2

Evaluation of read count based RNAseq analysis methods
Cited by: 50
Author(s): Yan Guo, Chung I. Li, Fei Ye, Yu Shyr
Software Mentions: 4
Published: over 13 years ago

10.18632/aging.102820

Development and validation of a prognostic classifier based on HIF-1 signaling for hepatocellular carcinoma
Cited by: 22
Author(s): Feiwen Deng, Chen Dong, Xiaoli Wei, Shilin Lu, Xuan Luo, Jincan He, Junting Liu, Tiebao Meng, Anli Yang, Huanwei Chen
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-40897-9

Extensive epigenetic and transcriptomic variability between genetically identical human B-lymphoblastoid cells with implications in pharmacogenomics research
Cited by: 17
Author(s): Lilla Ozgyin, Attila Horváth, Zsuzsanna Hevessy, Bálint László Bálint
Software Mentions: 4
Published: over 7 years ago

10.1186/s13227-019-0135-4

Comparative transcriptomic analysis of a wing-dimorphic stonefly reveals candidate wing loss genes
Cited by: 16
Author(s): Graham A. McCulloch, Andrew Oliphant, Peter K. Dearden, Andrew J. Veale, Charles W. Ellen, Jonathan M. Waters
Software Mentions: 4
Published: almost 7 years ago

10.1002/2211-5463.12983

Identification of modules and novel prognostic biomarkers in liver cancer through integrated bioinformatics analysis
Cited by: 5
Author(s): Bo Shen, Kun Li, Yuting Zhang
Software Mentions: 4
Published: almost 6 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: over 5 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 7 years ago

10.1371/journal.pone.0166944

Transcriptomic Analysis Shows Decreased Cortical Expression of NR4A1, NR4A2 and RXRB in Schizophrenia and Provides Evidence for Nuclear Receptor Dysregulation
Cited by: 23
Author(s): Susan M. Corley, Shan-Yuan Tsai, Marc R. Wilkins, Cynthia Shannon Weickert
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-019-5428-4

New insights in the control of antioxidants accumulation in tomato by transcriptomic analyses of genotypes exhibiting contrasting levels of fruit metabolites
Cited by: 20
Author(s): Adriana Sacco, Assunta Raiola, Roberta Calafiore, Amalia Barone, Maria Manuela Rigano
Software Mentions: 4
Published: over 7 years ago

10.3389/fimmu.2021.709466

Human Placental Trophoblasts Infected by Listeria monocytogenes Undergo a Pro-Inflammatory Switch Associated With Poor Pregnancy Outcomes
Cited by: 15
Author(s): Lauren J. Johnson, Siavash Azari, Amy Webb, Xiaoli Zhang, Mikhail A. Gavrilin, James L. Marshall, Kara M. Rood, Stéphanie Seveau
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2164-12-364

Somatic sex-specific transcriptome differences in Drosophila revealed by whole transcriptome sequencing
Cited by: 82
Author(s): Peter L. Chang, Joseph P. Dunham, Sergey V. Nuzhdin, Michelle N. Arbeitman
Software Mentions: 4
Published: about 15 years ago

10.1038/s41396-017-0043-3

Energy limitation of cyanophage development: implications for marine carbon cycling
Cited by: 54
Author(s): Richard John Puxty, David J. Evans, Andrew Millard, David J. Scanlan
Software Mentions: 4
Published: over 8 years ago

10.1016/j.isci.2021.102751

The effects of aging on molecular modulators of human embryo implantation
Cited by: 6
Author(s): Panagiotis Ntostis, Grace Swanson, Georgia Kokkali, David Iles, John Huntriss, Agni Pantou, Maria Tzetis, Konstantinos Pantos, Helen M. Picton, Stephen A. Krawetz, D. H. Miller
Software Mentions: 4
Published: about 5 years ago

10.7150/ijms.51297

Heat shock factor 5 correlated with immune infiltration serves as a prognostic biomarker in lung adenocarcinoma
Cited by: 5
Author(s): Aizemaiti Rusidanmu, Zhigang Wu, Jie Tang, Haimeng Yan, Xiaoshu Lv
Software Mentions: 4
Published: over 5 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: almost 8 years ago

10.3390/genes9120574

A Two-Cohort RNA-seq Study Reveals Changes in Endometrial and Blood miRNome in Fertile and Infertile Women
Cited by: 25
Author(s): Kadri Rekker, Signe Altmäe, Marina Suhorutshenko, Maire Peters, Juan F. Martínez-Blanch, Francisco M. Codoñer, Felipe Vilella, Carlos Simón, Andres Salumets, Agne Velthut-Meikas
Software Mentions: 4
Published: over 7 years ago

10.3390/cells7110205

The Heterochromatin Landscape in Migrating Cells and the Importance of H3K27me3 for Associated Transcriptome Alterations
Cited by: 25
Author(s): Tamar Segal, Mali Salmon‐Divon, Gabi Gerlitz
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-019-5572-x

Differential isoform expression and alternative splicing in sex determination in mice
Cited by: 21
Author(s): Benjamín Planells, Isabel Gómez-Redondo, Eva Pericuesta, Patrick Lonergan, Alfonso Gutiérrez‐Adán
Software Mentions: 4
Published: over 7 years ago

10.1186/s12872-020-01838-x

Bioinformatics analysis of common key genes and pathways of intracranial, abdominal, and thoracic aneurysms
Cited by: 4
Author(s): Siwei Bi, Ruiqi Liu, Linfeng He, Jingyi Li, Jun Gu
Software Mentions: 4
Published: over 5 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 10 years ago

10.1534/g3.119.400757

Machine Learning Enables High-Throughput Phenotyping for Analyses of the Genetic Architecture of Bulliform Cell Patterning in Maize
Cited by: 9
Author(s): Pengfei Qiao, Lin Meng, Miguel Vasquez, Susanne Matschi, James Chamness, Matheus Baseggio, Laurie G. Smith, Mert R. Sabuncu, Michael A. Gore, Michael J. Scanlon
Software Mentions: 4
Published: over 6 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: almost 10 years ago

10.3390/cells9122593

Induced Pluripotent Stem Cells to Understand Mucopolysaccharidosis. I: Demonstration of a Migration Defect in Neural Precursors
Cited by: 3
Author(s): Silvin Lito, Adama Sidibé, Sten Ilmjärv, Patricie Burda, Matthias R. Baumgartner, Bernhard Wehrle-Haller, Karl‐Heinz Krause, Antoine Marteyn
Software Mentions: 4
Published: over 5 years ago

10.1002/2211-5463.13062

Chondroitin polymerizing factor promotes breast carcinoma cell proliferation, invasion and migration and affects expression of epithelial‐mesenchymal transition‐related markers
Cited by: 6
Author(s): Li Yang, Hui Gong, Lei Feng, Dan Mao, Yujie Xiao, Yunqi Wang, Huang Li-zhong
Software Mentions: 4
Published: over 5 years ago

10.1523/JNEUROSCI.0860-21.2021

Spinal Cord Injury Induces Permanent Reprogramming of Microglia into a Disease-Associated State Which Contributes to Functional Recovery
Cited by: 21
Author(s): Ramil Hakim, Vasilios Zachariadis, Sreenivasa Raghavan Sankavaram, Jinming Han, Robert A. Harris, Lou Brundin, Martin Enge, Mikael Svensson
Software Mentions: 4
Published: about 5 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: about 7 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 8 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: over 5 years ago

10.1186/s12859-019-3072-2

HTRgene: a computational method to perform the integrated analysis of multiple heterogeneous time-series data: case analysis of cold and heat stress response signaling genes in Arabidopsis
Cited by: 3
Author(s): Hongryul Ahn, Il Bong Jung, Han–Jung Chae, Dong‐Won Kang, Wi Hoon Jung, Sun Kim
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0091918

RNA-Sequence Analysis of Primary Alveolar Macrophages after In Vitro Infection with Porcine Reproductive and Respiratory Syndrome Virus Strains of Differing Virulence
Cited by: 34
Author(s): Bouabid Badaoui, Teresa Rutigliano, Anna Anselmo, Merijn Vanhee, Hans Nauwynck, Elisabetta Giuffra, Sara Botti
Software Mentions: 4
Published: over 12 years ago

10.1186/s12864-020-6564-6

Transcriptome analysis of fungicide-responsive gene expression profiles in two Penicillium italicum strains with different response to the sterol demethylation inhibitor (DMI) fungicide prochloraz
Cited by: 15
Author(s): Tingfu Zhang, Qing Cao, Na Li, De Li Liu, Yongze Yuan
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-24830-0

Novel analysis of the Harderian gland transcriptome response to Newcastle disease virus in two inbred chicken lines
Cited by: 21
Author(s): Melissa S. Deist, Rodrigo A. Gallardo, David Bunn, T. Ross Kelly, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont
Software Mentions: 4
Published: over 8 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568