pypi: TopHat | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0231898

Podocyte RNA sequencing reveals Wnt- and ECM-associated genes as central in FSGS
Cited by: 8
Author(s): Éva Nóra Bukosza, Klaus Kratochwill, Christoph Kornauth, Helga Schachner, Christoph Aufricht, Christoph A. Gebeshuber
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0137157

Transcriptome Characterization of Developing Bean (Phaseolus vulgaris L.) Pods from Two Genotypes with Contrasting Seed Zinc Concentrations
Cited by: 13
Author(s): Carolina Astudillo-Reyes, Andrea C. Fernandez, Karen A. Cichy
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0060837

Generation of Mast Cells from Mouse Fetus: Analysis of Differentiation and Functionality, and Transcriptome Profiling Using Next Generation Sequencer
Cited by: 8
Author(s): Nobuyuki Fukuishi, Yuusuke Igawa, Tomoyo Kunimi, Hirofumi Hamano, Masao Toyota, Hironobu Takahashi, Hiromichi Kenmoku, Yasuyuki Yagi, Nobuaki Matsui, Masaaki Akagi
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0121117

Dual RNA Sequencing Reveals the Expression of Unique Transcriptomic Signatures in Lipopolysaccharide-Induced BV-2 Microglial Cells
Cited by: 35
Author(s): Amitabh Das, Jin Choul Chai, Sun Hwa Kim, Kyoung Sun Park, Young Seek Lee, Kyoung Hwa Jung, Young Gyu Chai
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0206765

An integrated analysis of mRNA and sRNA transcriptional profiles in tomato root: Insights on tomato wilt disease
Cited by: 15
Author(s): Min Zhao, Huimin Ji, Ying Gao, Xin-Xin Cao, Hui‐Ying Mao, Shan Ouyang, Peng Liu
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0177066

Characterization of joining sites of a viral histone H4 on host insect chromosomes
Cited by: 4
Author(s): Sunil Kumar, Jin Kyo Jung, Yonggyun Kim
Software Mentions: 1
Published: over 9 years ago

10.18632/oncotarget.8433

REST reduction is essential for hypoxia-induced neuroendocrine differentiation of prostate cancer cells by activating autophagy signaling
Cited by: 48
Author(s): Tzu Ping Lin, Yi Ting Chang, Sung Yuan Lee, Mel Campbell, Tien Chiao Wang, Shu Shen, Hsiao Jen Chung, Yen Chang, Allen W. Chiu, Chin Chen Pan, Chi Lin, Cheng Ying Chu, Hsing Jien Kung, Chia Yang Cheng, Pei Ching Chang
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-020-6732-8

A chromosome-scale assembly of the smallest Dothideomycete genome reveals a unique genome compaction mechanism in filamentous fungi
Cited by: 6
Author(s): Bo Wang, Xiaofei Liang, Mark L. Gleason, Tom Hsiang, Rong Zhang
Software Mentions: 1
Published: over 6 years ago

10.1177/0963689718780942

Mesenchymal Stem Cell-Derived Extracellular Vesicles Improve the Renal Microvasculature in Metabolic Renovascular Disease in Swine
Cited by: 70
Author(s): Alfonso Eirin, Xiang Yang Zhu, Sreela Jonnada, Amir Lerman, André J. van Wijnen, Lilach O. Lerman
Software Mentions: 1
Published: over 8 years ago

10.18632/oncotarget.8556

Read-through transcripts in normal human lung parenchyma are down-regulated in lung adenocarcinoma
Cited by: 14
Author(s): Giulia Pintarelli, Alice Dassano, Chiara E. Cotroneo, Antonella Galvan, Sara Noci, Rocco Piazza, Alessandra Pirola, Roberta Spinelli, Matteo Incarbone, Alessandro Palleschi, Lorenzo Rosso, Luigi Santambrogio, Tommaso A. Dragani, Francesca Colombo
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0160751

Transcriptome Analysis Reveals Regulation of Gene Expression for Lipid Catabolism in Young Broilers by Butyrate Glycerides
Cited by: 30
Author(s): Fugui Yin, Hai Yu, Dion Lepp, Xuejiang Shi, Xiaojian Yang, Jielun Hu, S. Leeson, Chengbo Yang, Shaoping Nie, Yongqing Hou, Joshua Gong
Software Mentions: 1
Published: about 10 years ago

10.3390/cells9030732

Interferon-β Stimulation Elicited by the Influenza Virus Is Regulated by the Histone Methylase Dot1L through the RIG-I-TRIM25 Signaling Axis
Cited by: 4
Author(s): Laura Marcos-Villar, Estanislao Nistal-Villán, Noelia Zamarreño, Urtzi Garaigorta, Pablo Gastaminza, Amelia Nieto
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0161410

Elevating CLIC4 in Multiple Cell Types Reveals a TGF-β Dependent Induction of a Dominant Negative Smad7 Splice Variant
Cited by: 11
Author(s): Anjali Shukla, Yihan Yang, Sara Madanikia, Yan Ho, Mangmang Li, Vanesa C. Sanchez, Christophe Cataisson, Jing Huang, Stuart H. Yuspa
Software Mentions: 1
Published: about 10 years ago

10.1186/s12864-019-6244-6

Transcriptomic analysis of α-synuclein knockdown after T3 spinal cord injury in rats
Cited by: 5
Author(s): Hong Zeng, Bao‐Fu Yu, Nan Liu, Yanyan Yang, Huayi Xing, Xiao-xie Liu, Mouwang Zhou
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-33891-0

Identification of Differentially Expressed Non-coding RNA in Porcine Alveolar Macrophages from Tongcheng and Large White Pigs Responded to PRRSV
Cited by: 19
Author(s): Yueran Zhen, Fengqing Wang, Wan Liang, Jianjian Liu, Guangzhen Gao, Yan Wang, Xuewen Xu, Qiuju Su, Qingde Zhang, Bang Liu
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-020-71002-0

Global identification of a marine diatom long noncoding natural antisense transcripts (NATs) and their response to phosphate fluctuations
Cited by: 13
Author(s): Maria Helena Cruz de Carvalho, Chris Bowler
Software Mentions: 1
Published: about 6 years ago

10.3390/cells10040763

Mesenchymal Stem/Stromal Cell-Derived Extracellular Vesicles Elicit Better Preservation of the Intra-Renal Microvasculature Than Renal Revascularization in Pigs with Renovascular Disease
Cited by: 8
Author(s): Christopher M. Ferguson, Rahele A. Farahani, Xiang Yang Zhu, Hui Tang, Kyra L. Jordan, Ishran M. Saadiq, Amir Lerman, Lilach O. Lerman, Alfonso Eirin
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0142434

Digital Gene Expression Analysis Based on De Novo Transcriptome Assembly Reveals New Genes Associated with Floral Organ Differentiation of the Orchid Plant Cymbidium ensifolium
Cited by: 12
Author(s): Fengming Yang, Genfa Zhu
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0185455

Genome-wide expression analysis of salt-stressed diploid and autotetraploid Paulownia tomentosa
Cited by: 20
Author(s): Zhao Zhong, Yongsheng Li, Haifang Liu, Xiaoqiao Zhai, Mei Deng, Yanpeng Dong, Guoqiang Fan
Software Mentions: 1
Published: almost 9 years ago

10.3390/cells9051195

TNF-α Pretreatment Improves the Survival and Function of Transplanted Human Neural Progenitor Cells Following Hypoxic-Ischemic Brain Injury
Cited by: 10
Author(s): Miri Kim, Kwangsoo Jung, Yun Woong Ko, Il-Sun Kim, Kyujin Hwang, Jae‐Hyung Jang, Jeong Eun Shin, Kook In Park
Software Mentions: 1
Published: over 6 years ago

10.3390/cells9030550

The Drosophila RNA Helicase Belle (DDX3) Non-Autonomously Suppresses Germline Tumorigenesis Via Regulation of a Specific mRNA Set
Cited by: 2
Author(s): А. А. Котов, Baira Godneeva, Oxana M. Olenkina, Vladimir E. Adashev, Mikhail V. Trostnikov, Ludmila V. Olenina
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0106818

Transcriptome Profiling of Spinal Muscular Atrophy Motor Neurons Derived from Mouse Embryonic Stem Cells
Cited by: 36
Author(s): Miho Matsushima, Ashlee W. Harris, Brewster F. Kingham, Casey J. Lumpkin, Lynn M. Opdenaker, Suzanne M. McCahan, Wenlan Wang, Matthew E.R. Butchbach
Software Mentions: 1
Published: about 12 years ago

10.3390/cells9081885

Ischemic Stroke Risk Associated with Mitochondrial Haplogroup F in the Asian Population
Cited by: 11
Author(s): Meng-Han Tsai, Chung-Wen Kuo, Tay-Jyi Lin, Chen-Jui Ho, Pei-Wen Wang, Jiin‐Haur Chuang, Chia‐Wei Liou
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0128951

RNA-Seq Analysis of Human Trigeminal and Dorsal Root Ganglia with a Focus on Chemoreceptors
Cited by: 146
Author(s): Caroline Flegel, Nicole Schöbel, Janine Altmüller, Christian Becker, Andrea Tannapfel, Hanns Hatt, Günter Gisselmann
Software Mentions: 1
Published: over 11 years ago

10.1186/s12864-019-6095-1

Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae
Cited by: 20
Author(s): Yang Yang, Xiaobao Liu, Jing Cai, Yipeng Chen, Boxun Li, Zhi‐Kai Guo, Huang Guixiu
Software Mentions: 1
Published: almost 7 years ago

10.3390/cells9061472

Blood Serum Stimulates p38-Mediated Proliferation and Changes in Global Gene Expression of Adult Human Cardiac Stem Cells
Cited by: 11
Author(s): Anna L. Höving, Kazuko E. Schmidt, Madlen Merten, Jassin Hamidi, Ann-Katrin Rott, Isabel Faust, Johannes F. W. Greiner, Jan Gummert, Barbara Kaltschmidt, Christian Kaltschmidt, Cornelius Knabbe
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-71968-x

Identification of effector candidate genes of Rhizoctonia solani AG-1 IA expressed during infection in Brachypodium distachyon
Cited by: 4
Author(s): Sobhy S. H. Abdelsalam, Yusuke Kouzai, Megumi Watanabe, Komaki Inoue, Hidenori Matsui, Mikihiro Yamamoto, Yuki Ichinose, Kazuhiro Toyoda, Seiji Tsuge, Keiichi Mochida, Yoshiteru Noutoshi
Software Mentions: 1
Published: about 6 years ago

10.1007/s00412-021-00762-z

The Trithorax group protein ASH1 requires a combination of BAH domain and AT hooks, but not the SET domain, for mitotic chromatin binding and survival
Cited by: 1
Author(s): Philipp A. Steffen, Christina Altmutter, Eva Dworschak, Sini Junttila, Attila Gyenesei, Xinzhou Zhu, Tobias Kockmann, Leonie Ringrose
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0213305

Transcriptome response of roots to salt stress in a salinity-tolerant bread wheat cultivar
Cited by: 61
Author(s): Nazanin Amirbakhtiar, Ahmad Ismaili, Mohammad Reza Ghaffari, Farhad Nazarian Firouzabadi, Zahra‐Sadat Shobbar
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0173824

Transcriptomic profile of leg muscle during early growth in chicken
Cited by: 52
Author(s): Qingwu Xue, Genxi Zhang, Tingting Li, Jiaojiao Ling, Xiangqian Zhang, Jinyu Wang
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-020-71701-8

Humic acid enhances heat stress tolerance via transcriptional activation of Heat-Shock Proteins in Arabidopsis
Cited by: 28
Author(s): Joon‐Yung Cha, Sang-Ho Kang, Imdad Ali, Sang Cheol Lee, Myung Geun Ji, Song Yi Jeong, Gyeong-Im Shin, Min Gab Kim, Jong-Rok Jeon, Woe‐Yeon Kim
Software Mentions: 1
Published: about 6 years ago

10.1186/s13148-018-0442-y

Aberrant expression and DNA methylation of lipid metabolism genes in PCOS: a new insight into its pathogenesis
Cited by: 64
Author(s): Jiexue Pan, Ya‐Jing Tan, Fangfang Wang, Ningning Hou, Xiangxian Ying, Junyu Zhang, Ye Liu, Fan Qu, Qingguo Meng, Jian Xu, Jian‐Zhong Sheng, He‐Feng Huang
Software Mentions: 1
Published: over 8 years ago

10.1186/s13148-021-01116-3

Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes
Cited by: 6
Author(s): Florence Naillat, Heba Saadeh, Joanna Nowacka‐Woszuk, Lenka Gahurová, Fátima Santos, Shin-ichi Tomizawa, Gavin Kelsey
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0194393

Application of ribonucleoside vanadyl complex (RVC) for developing a multifunctional tissue preservative solution
Cited by: 7
Author(s): Tzong‐Ming Shieh, Chi-Yuan Chen, Chuen Hsueh, Cheng–Chia Yu, Chi-Yuan Chen, Tong Hong Wang
Software Mentions: 1
Published: over 8 years ago

10.5713/ajas.18.0718

Selection of candidate genes affecting meat quality and preliminary exploration of related molecular mechanisms in the Mashen pig
Cited by: 14
Author(s): Pengfei Gao, Zhimin Cheng, Meng Li, Ningfang Zhang, Baoyu Le, Wanfeng Zhang, Pengkang Song, Xiaohong Guo, Guoqing Cao
Software Mentions: 1
Published: about 7 years ago

10.18632/oncotarget.9152

RNA-Seq analysis reveals new evidence for inflammation-related changes in aged kidney
Cited by: 14
Author(s): Daeui Park, Byoung-Chul Kim, Chulhong Kim, Yeon Ja Choi, Hyoung Oh Jeong, Mi Eun Kim, Jun Sik Lee, Min Hi Park, Ki Wung Chung, Dae Hyun Kim, Jaewon Lee, Dong‐Soon Im, Seokjoo Yoon, Sung-Hoon Lee, Byung Pal Yu, Jong Bhak, Hae Young Chung
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0199437

Comparative analysis of the male inflorescence transcriptome profiles of an ms22 mutant of maize
Cited by: 2
Author(s): Yanni Gao, Lijuan Zhang, ShengChao Zhao, Yongjun Yan
Software Mentions: 1
Published: about 8 years ago

10.1002/cre2.301

Mandibular undifferentiated pleomorphic sarcoma: Molecular analysis of a primary cell population
Cited by: 5
Author(s): Hope M. Amm, Patricia DeVilliers, Ambika R. Srivastava, Marina Gonçalves Diniz, Gene P. Siegal, Mary MacDougall
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-020-73713-w

Rosettes integrity protects Plasmodium vivax of being phagocytized
Cited by: 13
Author(s): Letusa Albrecht, Stefanie Costa Pinto Lopes, Ana Beatriz Iung Enembreck da Silva, Vanessa Carneiro Barbosa, Rodrigo Pm de Almeida, André Machado Siqueira, Juliana Almeida Leite, Najara Bittencourt, Hellen Geremias dos Santos, Catarina Bourgard, Luiz Fernando Cardoso Garcia, Ana Carolina Andrade Vitor Kayano, Irene S. Soares, Bruce Russell, Laurent Rénia, Marcus Lacerda, Fabio T. M. Costa
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0140756

Functional Analysis and RNA Sequencing Indicate the Regulatory Role of Argonaute1 in Tomato Compound Leaf Development
Cited by: 7
Author(s): Tian Wang, Rui Lin, Liwei Wen, Daqi Fu, Beiwei Zhu, Yunbo Luo, Hongliang Zhu
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2164-14-304

Functional transcriptomic analysis of the role of MAB-5/Hox in Q neuroblast migration in Caenorhabditis elegans
Cited by: 13
Author(s): Joel V. Tamayo, Mahekta R Gujar, Stuart J. Macdonald, Erik A. Lundquist
Software Mentions: 1
Published: over 13 years ago

10.1002/advs.202100250

Focal Adhesion Kinase (FAK) Inhibition Synergizes with KRAS G12C Inhibitors in Treating Cancer through the Regulation of the FAK–YAP Signaling
Cited by: 18
Author(s): Baoyuan Zhang, Yan Zhang, Jiangwei Zhang, Ping Liu, Bo Jiao, Zaiqi Wang, Ruibao Ren
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0158195

Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia
Cited by: 9
Author(s): Inken Körber, Shintaro Katayama, Elisabet Einarsdottir, Kaarel Krjutškov, Paula Hakala, Juha Kere, Anna‐Elina Lehesjoki, Tarja Joensuu
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0236823

Unraveling the mechanisms of resistance to Sclerotium rolfsii in peanut (Arachis hypogaea L.) using comparative RNA-Seq analysis of resistant and susceptible genotypes
Cited by: 25
Author(s): Tejas C. Bosamia, Sneha M. Dodia, Gyan P. Mishra, Suhail Ahmad, Binal Joshi, Polavakkalipalayam P. Thirumalaisamy, Narendra Kumar, A. L. Rathnakumar, Chandramohan Sangh, Abhay Kumar, Radhakrishnan Thankappan
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0157727

Differential Transcriptome Networks between IDO1-Knockout and Wild-Type Mice in Brain Microglia and Macrophages
Cited by: 12
Author(s): Dianelys González-Peña, Scott E. Nixon, Bruce R. Southey, Marcus A. Lawson, Robert H. McCusker, Álvaro González Hernández, Robert Dantzer, Keith W. Kelley, Sandra L. Rodriguez-Zas
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0158349

Supervillin Is a Component of the Hair Cell’s Cuticular Plate and the Head Plates of Organ of Corti Supporting Cells
Cited by: 6
Author(s): Lana M. Pollock, Nilay Gupta, Xi Chen, Elizabeth J. Luna, Brian M. McDermott
Software Mentions: 1
Published: about 10 years ago

10.1038/s42003-021-01879-8

β-catenin-promoted cholesterol metabolism protects against cellular senescence in naked mole-rat cells
Cited by: 11
Author(s): Woei Yaw Chee, Yuriko Kurahashi, Junhyeong Kim, Kyoko Miura, Daisuke Okuzaki, Tohru Ishitani, Kentaro Kajiwara, Shigeyuki Nada, Hideyuki Okano, Masato Okada
Software Mentions: 1
Published: over 5 years ago

10.1038/s42003-020-01120-y

Identification of long non-coding RNAs in advanced prostate cancer associated with androgen receptor splicing factors
Cited by: 29
Author(s): Ken‐ichi Takayama, Tetsuya Fujimura, Yutaka Suzuki, Satoshi Inoue
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2164-15-226

Transcriptional profiling of mammary gland in Holstein cows with extremely different milk protein and fat percentage using RNA sequencing
Cited by: 109
Author(s): Xiaogang Cui, Yali Hou, Shaohua Yang, Yan Xie, Shengli Zhang, Yuan Zhang, Qin Zhang, Xuemei Lu, George E. Liu, Dongxiao Sun
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0043713

Transcriptome Analysis of the Silkworm (Bombyx mori) by High-Throughput RNA Sequencing
Cited by: 43
Author(s): Yinü Li, Guozeng Wang, Jian Tian, Huifen Liu, Huipeng Yang, Yi Yao, Jinhui Wang, Xiaofeng Shi, Feng Jiang, Bin Yao, Zhifang Zhang
Software Mentions: 1
Published: about 14 years ago

10.1038/s42003-021-02310-y

SCD2-mediated monounsaturated fatty acid metabolism regulates cGAS-STING-dependent type I IFN responses in CD4+ T cells
Cited by: 19
Author(s): Toshio Kanno, Takahiro Nakajima, Satoru Yokoyama, Hikari K. Asou, Shigemi Sasamoto, Yasuhiro Kamii, Koji Hayashizaki, Yasuo Ouchi, Taishi Onodera, Yoshimasa Takahashi, Kazutaka Ikeda, Yoshinori Hasegawa, Yuki Kinjo, Osamu Ohara, Toshinori Nakayama, Yusuke Endo
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-018-5316-3

Integrated microRNA and mRNA analysis in the pathogenic filamentous fungus Trichophyton rubrum
Cited by: 23
Author(s): Lingling Wang, Xingye Xu, Jian Yang, Lihong Chen, Bo Liu, Tao Liu, Qi Jin
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-020-07014-x

Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett)
Cited by: 16
Author(s): Weijun Li, Yujia Song, Hong-Liang Han, Hui-Qian Xu, Dong Wei, Guy Smagghe, Jinjun Wang
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0118295

RNA-Seq Analysis Identifies New Genes Regulated by the Histone-Like Nucleoid Structuring Protein (H-NS) Affecting Vibrio cholerae Virulence, Stress Response and Chemotaxis
Cited by: 53
Author(s): Hongxia Wang, Julio C. Ayala, Jorge A. Benítez, Alcino J. Silva
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0170441

Testicular Dysgenesis Syndrome and Long-Lasting Epigenetic Silencing of Mouse Sperm Genes Involved in the Reproductive System after Prenatal Exposure to DEHP
Cited by: 50
Author(s): Ludwig Stenz, Jessica Escoffier, Rita Rahban, Serge Nef, Ariane Paoloni-Giacobino
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0135337

Rapid Characterization of Microalgae and Microalgae Mixtures Using Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS)
Cited by: 26
Author(s): Duane Barbano, Regina Diaz, Lin Zhang, Todd R. Sandrin, Henri Gerken, Thomas A. Dempster
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0147053

Dynamic Effects of Topoisomerase I Inhibition on R-Loops and Short Transcripts at Active Promoters
Cited by: 39
Author(s): Jessica Marinello, Stefania Bertoncini, Iris Aloisi, Agnese Cristini, Guidantonio Malagoli Tagliazucchi, Mattia Forcato, Olivier Sordet, Giovanni Capranico
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0144118

Comparative Transcriptome Analysis of Recessive Male Sterility (RGMS) in Sterile and Fertile Brassica napus Lines
Cited by: 36
Author(s): Cunmin Qu, Fuyou Fu, Miao Liu, Hongwei Zhao, Chuan-Chuan Liu, Jiana Li, Zhongjie Tang, Xinhua Xu, Xiao‐Yang Qiu, Rui Wang, Kun Lu
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0173438

RNA-sequence analysis of gene expression from honeybees (Apis mellifera) infected with Nosema ceranae
Cited by: 43
Author(s): Bouabid Badaoui, A. Fougeroux, Fabien Petit, Anna Anselmo, C. Gorni, Marco Cucurachi, Antonella Cersini, Anna Granato, G. Cardeti, Giovanni Formato, Franco Mutinelli, Elisabetta Giuffra, J. L. Williams, Sara Botti
Software Mentions: 1
Published: over 9 years ago

10.5713/ajas.18.0302

Muscle differentiation induced up-regulation of calcium-related gene expression in quail myoblasts
Cited by: 16
Author(s): Jeong-Woong Park, Jeong Hyo Lee, Seo Woo Kim, Ji Seon Han, Ki Ser Kang, Sung-Jo Kim, Tae Sub Park
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0066740

YjcC, a c-di-GMP Phosphodiesterase Protein, Regulates the Oxidative Stress Response and Virulence of Klebsiella pneumoniae CG43
Cited by: 41
Author(s): Ching Jou Huang, Zhe Chong Wang, Hsi Yuan Huang, Hsien Da Huang, Hwei-Ling Peng
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0131559

Genome-, Transcriptome- and Proteome-Wide Analyses of the Gliadin Gene Families in Triticum urartu
Cited by: 23
Author(s): Yanlin Zhang, Guangbin Luo, Dongcheng Liu, Dongzhi Wang, Wenlong Yang, Jiazhu Sun, Aimin Zhang, Kai Zhan
Software Mentions: 1
Published: over 11 years ago

10.1038/s41598-020-76076-4

Vimentin protects differentiating stem cells from stress
Cited by: 31
Author(s): Sundararaghavan Pattabiraman, Gajendra Kumar Azad, Triana Amen, Shlomi Brielle, Jung Eun Park, Siu Kwan Sze, Eran Meshorer, Daniel Kaganovich
Software Mentions: 1
Published: almost 6 years ago

10.1111/1462-2920.14454

Formate cross‐feeding and cooperative metabolic interactions revealed by transcriptomics in co‐cultures of acetogenic and amylolytic human colonic bacteria
Cited by: 46
Author(s): Jenny A. Laverde Gomez, Indrani Mukhopadhya, Sylvia H. Duncan, Petra Louis, Sophie Shaw, Elaina Susan Renata Collie-Duguid, Emmanuelle H. Crost, Nathalie Juge, Harry J. Flint
Software Mentions: 1
Published: almost 8 years ago

10.1007/s11356-020-08899-7

Exposure to the environmental pollutant bisphenol A diglycidyl ether (BADGE) causes cell over-proliferation in Drosophila
Cited by: 12
Author(s): Michael J. Williams, Hao Cao, Therese Lindkvist, Tobias J. Mothes, Helgi B. Schiöth
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-74852-w

Identification and dereplication of endophytic Colletotrichum strains by MALDI TOF mass spectrometry and molecular networking
Cited by: 9
Author(s): Morgane Barthélémy, Vincent Guérineau, Grégory Genta‐Jouve, Mélanie Roy, Jérôme Chave, Régis Guillot, Léonie Pellissier, Jean‐Luc Wolfender, Didier Stien, Véronique Éparvier, David Touboul
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0148558

GAD2 Alternative Transcripts in the Human Prefrontal Cortex, and in Schizophrenia and Affective Disorders
Cited by: 23
Author(s): Kasey Davis, Ran Tao, Chao Li, Yuan Gao, Marjorie C. Gondré‐Lewis, Barbara K. Lipska, Joo Heon Shin, Bin Xie, Tianzhang Ye, Daniel R. Weinberger, Joel E. Kleinman, Thomas M. Hyde
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-020-76519-y

Gene duplication, rather than epigenetic changes, drives FGF4 overexpression in KIT/PDGFRA/SDH/RAS-P WT GIST
Cited by: 8
Author(s): Milena Urbini, Annalisa Astolfi, Valentina Indio, Margherita Nannini, Angela Schipani, Maria Giulia Bacalini, Sabrina Angelini, Gloria Ravegnini, Giovanni Calice, Massimo Del Gaudio, Paola Secchiero, Paola Ulivi, Elisa Gruppioni, Maria Abbondanza Pantaleo
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0184451

"Stealth dissemination" of macrophage-tumor cell fusions cultured from blood of patients with pancreatic ductal adenocarcinoma
Cited by: 50
Author(s): Gary A. Clawson, Gail L. Matters, Ping Xin, Christopher O. McGovern, Eric Wafula, Claude W. dePamphilis, Morgan Meckley, Joyce Y. Wong, Luke A. Stewart, Christopher D’Jamoos, Н. Д. Альтман, Yuka Imamura Kawasawa, Zhaohui Du, Loren Honaas, Thomas Abraham
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0182032

Identification of RNA biomarkers for chemical safety screening in mouse embryonic stem cells using RNA deep sequencing analysis
Cited by: 6
Author(s): Hidenori Tani, Jun-ichi Takeshita, Hiroshi Aoki, Kaoru Nakamura, Ryosuke Abe, Akinobu Toyoda, Yasunori Endo, Sadaaki Miyamoto, Masashi Gamo, Hiroaki Sato, Masaki Takasu
Software Mentions: 1
Published: about 9 years ago

10.1186/1756-8935-6-19

Smchd1 regulates a subset of autosomal genes subject to monoallelic expression in addition to being critical for X inactivation
Cited by: 87
Author(s): Arne W. Mould, Zhenyi Pang, Miha Pakusch, Ian D. Tonks, Mitchell Stark, Dianne Carrie, Pamela Mukhopadhyay, Annica Seidel, Jonathan Ellis, Janine E. Deakin, Matthew J. Wakefield, Lutz Krause, Marnie E. Blewitt, Graham F. Kay
Software Mentions: 1
Published: over 13 years ago

10.1038/s41598-020-77604-y

Effects of dietary n-3-PUFA supplementation, post-insemination plane of nutrition and pregnancy status on the endometrial transcriptome of beef heifers
Cited by: 4
Author(s): Carla Surlis, Paul Cormican, Sinéad M. Waters, Patrick Lonergan, Kate Keogh, David Noel Doyle, David A. Kenny
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13072-018-0183-3

Genome-wide analysis of gene regulation mechanisms during Drosophila spermatogenesis
Cited by: 10
Author(s): Petr P. Laktionov, Daniil A. Maksimov, Stanislav E. Romanov, Polina A. Antoshina, Olga V. Posukh, Helen White-Cooper, Dmitry E. Koryakov, Stepan N. Belyakin
Software Mentions: 1
Published: over 8 years ago

10.1186/s13072-016-0101-5

Insights into long noncoding RNAs of naked mole rat (Heterocephalus glaber) and their potential association with cancer resistance
Cited by: 16
Author(s): Jianjun Jiang, Lehua Cheng, Huan Wu, Yonghan He, Qing‐Peng Kong
Software Mentions: 1
Published: almost 10 years ago

10.1186/1756-8935-5-6

A genome-wide screen in human embryonic stem cells reveals novel sites of allele-specific histone modification associated with known disease loci
Cited by: 16
Author(s): James Prendergast, Pin Tong, David C. Hay, Susan M. Farrington, Colin A. Semple
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0190935

Relaxin reverses inflammatory and immune signals in aged hearts
Cited by: 25
Author(s): Brian Martin, Beth A Gabris-Weber, Rajiv P. Reddy, Guillermo Romero, Ansuman Chattopadhyay, Guy Salama
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0170609

Transcriptome Sequencing Reveals Key Pathways and Genes Associated with Cisplatin Resistance in Lung Adenocarcinoma A549 Cells
Cited by: 25
Author(s): Yani Fang, Cheng Zhang, Tong Wu, Qi Wang, Jinhui Liu, Peng Dai
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0140487

Alternative Splicing in Next Generation Sequencing Data of Saccharomyces cerevisiae
Cited by: 36
Author(s): Konrad Schreiber, Gergely Csaba, Martin Haslbeck, Ralf Zimmer
Software Mentions: 1
Published: almost 11 years ago

10.1186/1756-8935-6-36

Aging is associated with highly defined epigenetic changes in the human epidermis
Cited by: 69
Author(s): Günter Raddatz, Sabine Hagemann, Dvir Aran, Jörn Söhle, Pranav P Kulkarni, Lars Kaderali, Asaf Hellman, Marc Winnefeld, Frank Lyko
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0158279

Transcriptome Profiling Reveals the Antitumor Mechanism of Polysaccharide from Marine Algae Gracilariopsis lemaneiformis
Cited by: 26
Author(s): Yani Kang, Hua Li, Jun Wu, Xiaoting Xu, Xue Sun, Xiaodong Zhao, Nianjun Xu
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0112964

Global Characterization of Differential Gene Expression Profiles in Mouse Vγ1+ and Vγ4+ γδ T Cells
Cited by: 14
Author(s): Peng Dong, Siya Zhang, Mengli Cai, Ning Kang, Yu Hu, Lianxian Cui, Jianmin Zhang, He Wang
Software Mentions: 1
Published: almost 12 years ago

10.1186/s13072-017-0134-4

Genomic imprinting does not reduce the dosage of UBE3A in neurons
Cited by: 15
Author(s): Paul Hillman, Sarah Christian, Ryan Doan, Noah D. Cohen, Kranti Konganti, Kory C. Douglas, Xiaozhu Wang, Paul B. Samollow, Scott V. Dindot
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0078190

Genome-Wide Transcriptional Effects of the Anti-Cancer Agent Camptothecin
Cited by: 29
Author(s): Artur Veloso, Benjamin Biewen, Michelle T. Paulsen, Nathaniel K. Berg, Leonardo Carmo de Andrade Lima, J.K. Prasad, Karan Bedi, Brian Magnuson, Thomas E. Wilson, Mats Ljungman
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0100088

Fed State Prior to Hemorrhagic Shock and Polytrauma in a Porcine Model Results in Altered Liver Transcriptomic Response
Cited by: 7
Author(s): Charles Determan, Rebecca Cogwell Anderson, Aaron Becker, Nancy E. Witowski, Elizabeth R. Lusczek, Kristine E. Mulier, Greg J. Beilman
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0184581

Transcriptional responses in the hepatopancreas of Eriocheir sinensis exposed to deltamethrin
Cited by: 12
Author(s): Zhengfu Yang, Yiliu Zhang, Yingying Jiang, Fengjiao Zhu, Lingfeng Zeng, Yulan Wang, Xiaoqing Lei, Yi Yao, Yujie Hou, Xu Liu, Chengliang Xiong, Xianle Yang, Kun Hu
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0028585

EZH2 Codon 641 Mutations are Common in BCL2-Rearranged Germinal Center B Cell Lymphomas
Cited by: 106
Author(s): Russell J.H. Ryan, Mai Nitta, Darrell R. Borger, Lawrence Zukerberg, Judith A. Ferry, Nancy L. Harris, A. John Iafrate, B Bernstein, Aliyah R. Sohani, Long P. Le
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-15-159

Polysome profiling reveals broad translatome remodeling during endoplasmic reticulum (ER) stress in the pathogenic fungus Aspergillus fumigatus
Cited by: 20
Author(s): Karthik Krishnan, Zhaowei Ren, Liliana Losada, William C. Nierman, Long Lu, David Askew
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0147625

ABA Is Required for Plant Acclimation to a Combination of Salt and Heat Stress
Cited by: 211
Author(s): Nobuhiro Suzuki, Elias Bassil, J. F. Hamilton, Madhuri A. Inupakutika, Sara I. Zandalinas, Deesha Tripathy, Yuting Luo, Erin Dion, Ginga Fukui, Ayana Kumazaki, Ruka Nakano, Rosa M. Rivero, Guido F. Verbeck, Rajeev K. Azad, Eduardo Blumwald, Ron Mittler
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0134057

Vitamin D Modulates Expression of the Airway Smooth Muscle Transcriptome in Fatal Asthma
Cited by: 32
Author(s): Blanca E. Himes, Cynthia Koziol‐White, Martin Johnson, Christina Nikolos, William F. Jester, Barbara J. Klanderman, Augusto A. Litonjua, Kelan G. Tantisira, Kevin Truskowski, Kevin Macdonald, Reynold A. Panettieri, Scott T. Weiss
Software Mentions: 1
Published: about 11 years ago

10.1186/s13072-016-0069-1

Abnormal X chromosome inactivation and sex-specific gene dysregulation after ablation of FBXL10
Cited by: 18
Author(s): Mathieu Boulard, John Edwards, Timothy H. Bestor
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0168744

Signatures of Crested Ibis MHC Revealed by Recombination Screening and Short-Reads Assembly Strategy
Cited by: 2
Author(s): Liao Chang, Shiyang He, Danqing Mao, Yuanhong Liu, Zijun Xiong, Deliang Fu, Bo Li, Shuguang Wei, Xun Xu, Shengbin Li, Hui Yuan
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0217461

Transcriptome profiling of longissimus thoracis muscles identifies highly connected differentially expressed genes in meat type sheep of India
Cited by: 18
Author(s): Reena Arora, Shakti Kumar, Sunil Sudarshan, Mohamed Nadeem Fairoze, Manpreet Kaur, Anju Sharma, Yashila Girdhar, R. M. Sreesujatha, Suresh Devatkal, Sonika Ahlawat, R. K. Vijh, Shilpa Manjunatha
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0105267

Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome
Cited by: 127
Author(s): Patrick T. West, Qing Li, Lexiang Ji, Steven R. Eichten, Jawon Song, Matthew Vaughn, Robert J. Schmitz, Nathan M. Springer
Software Mentions: 1
Published: about 12 years ago

10.1186/s12864-020-6566-4

Presence–absence polymorphisms of single-copy genes in the stony coral Acropora digitifera
Cited by: 6
Author(s): Shiho Takahashi-Kariyazono, Kazuhiko Sakai, Yohey Terai
Software Mentions: 1
Published: over 6 years ago

10.18632/aging.202550

LncRNA Sirt1-AS upregulates Sirt1 to attenuate aging related deep venous thrombosis
Cited by: 12
Author(s): Zhenkai Lou, Jinwen Zhu, Xing Li, Xingguo Li, Kaili Du, Bing Wang, Fan Zhang, Chi Zhang
Software Mentions: 1
Published: over 5 years ago

10.1038/s12276-019-0254-y

AMPK alleviates high uric acid-induced Na+-K+-ATPase signaling impairment and cell injury in renal tubules
Cited by: 22
Author(s): Jing Xiao, Sibo Zhu, Haochen Guan, Yuqi Zheng, Fengqin Li, Xiaoli Zhang, Hui Guo, Xiaojun Wang, Zhibin Ye
Software Mentions: 1
Published: over 7 years ago

10.12688/f1000research.6735.1

Questioned validity of Gene Expression Dysregulated Domains in Down's Syndrome
Cited by: 16
Author(s): Henry W. Long, William C. Mobley, Nishant Singhal
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0108670

Foxp3 Expression in Macrophages Associated with RENCA Tumors in Mice
Cited by: 21
Author(s): Christel Devaud, Carmen S. Yong, Liza B. John, Jennifer A. Westwood, Connie P.M. Duong, Colin M. House, Delphine Denoyer, Jason Li, Phillip K. Darcy, Michael H. Kershaw
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0161256

The Genome-Wide Analysis of Carcinoembryonic Antigen Signaling by Colorectal Cancer Cells Using RNA Sequencing
Cited by: 16
Author(s): Olga Bajenova, А. В. Горбунова, Igor Evsyukov, Mikhail Rayko, Svetlana Gapon, Ekaterina Bozhokina, A.A. Shishkin, Stephen J. O’Brien
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0090989

Deep RNA Sequencing Reveals Hidden Features and Dynamics of Early Gene Transcription in Paramecium bursaria Chlorella Virus 1
Cited by: 37
Author(s): Guillaume Blanc, Michael Mozar, Irina V. Agarkova, James R. Gurnon, Giane M. Yanai-Balser, Janet M. Rowe, Yuannan Xia, Jean-Jack M. Riethoven, David D. Dunigan, James L. Van Etten
Software Mentions: 1
Published: over 12 years ago

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Papers Mentioning TopHat 5,017