Ecosyste.ms: Papers

10.1038/s42003-021-02412-7

From the first touch to biofilm establishment by the human pathogen Candida glabrata: a genome-wide to nanoscale view
Cited by: 7
Author(s): Mafalda Cavalheiro, Diana Pereira, Cécile Formosa-Dague, Carolina Leitão, Pedro Pais, Easter Ndlovu, Romeu Viana, Andreia I. Pimenta, Rui Santos, Azusa Takahashi‐Nakaguchi, Michiyo Okamoto, Mihaela Ola, Hiroji Chibana, Arsénio M. Fialho, Geraldine Butler, Étienne Dague, Miguel C. Teixeira
Software Mentions: 3
Published: over 3 years ago

10.1016/j.dib.2019.104893

Dataset on the formation of Thioredoxin interacting protein (Txnip) containing redox sensitive high molecular weight nucleoprotein complexes
Cited by: 1
Author(s): Cristiane Lumi Hirata, Shinji Ito, Hiroshi Masutani
Software Mentions: 3
Published: about 5 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: over 4 years ago

10.1038/s42003-018-0089-4

De novo genome assembly of Oryza granulata reveals rapid genome expansion and adaptive evolution
Cited by: 19
Author(s): Zhigang Wu, Dongming Fang, Rui Yang, Fei Gao, Xingyu An, Xiaoxuan Zhuo, Yafei Li, Chuandeng Yi, Tao Zhang, Chengzhi Liang, Peng Cui, Zhukuan Cheng, Qiong Luo
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.62312

A Non-stop identity complex (NIC) supervises enterocyte identity and protects from premature aging
Cited by: 4
Author(s): Neta Erez, Lena Israitel, Eliya Bitman-Lotan, Wing Hing Wong, Gal Raz, Dayanne V Cornelio-Parra, Salwa Danial, Na’ama Flint Brodsly, Elena Belova, Oksana Maksimenko, Pavel Georgiev, Todd E. Druley, Ryan D. Mohan, Amir Orian
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.01630

A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells
Cited by: 123
Author(s): Tony Ly, Yasmeen Ahmad, Adam Shlien, Dominique N. Soroka, Allie Mills, Michael J. Emanuele, Michael R. Stratton, Angus I. Lamond
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0128041

Transcriptome Profiling of the Potato (Solanum tuberosum L.) Plant under Drought Stress and Water-Stimulus Conditions
Cited by: 85
Author(s): Lei Gong, Hongxia Zhang, Xiaoyan Gan, Li Zhang, Yuchao Chen, Fengjie Nie, Lei Shi, Miao Li, Zhiqian Guo, Guohui Zhang, Song Yao
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0192362

Transporter genes identified in landraces associated with high zinc in polished rice through panicle transcriptome for biofortification
Cited by: 21
Author(s): C. N. Neeraja, Kalyani S. Kulkarni, P. Madhu Babu, D. N. Rao, K. Surekha, V. Ravindra Babu
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2164-15-955

Comparative transcriptomics reveals striking similarities between the bovine and feline isolates of Tritrichomonas foetus: consequences for in silico drug-target identification
Cited by: 34
Author(s): Victoria Morin-Adeline, Rodrigo Lomas, Denis O’Meally, Colin M. Stack, Ana Conesa, Jan Šlapeta
Software Mentions: 3
Published: over 10 years ago

10.7554/eLife.48767

Induction of Sertoli-like cells from human fibroblasts by NR5A1 and GATA4
Cited by: 35
Author(s): Jianlin Liang, Nan Wang, Jing He, Jian Du, Yin Guo, Lin Li, Wenbo Wu, Chencheng Yao, Zheng Li, Kehkooi Kee
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0245749

Effects of Chinese wolfberry and Astragalus extract on the antioxidant capacity of Tibetan pig liver
Cited by: 6
Author(s): Zhuang Hao, Zhen Li, Jinjin Huo, Jiandong Li, Peng Yin
Software Mentions: 3
Published: about 4 years ago

10.1186/s12915-020-00897-y

Long-term experimental evolution reveals purifying selection on piRNA-mediated control of transposable element expression
Cited by: 7
Author(s): Ulfar Bergthorsson, Caroline J. Sheeba, Anke Konrad, Tony Bélicard, Toni Beltran, Vaishali Katju, Peter Sarkies
Software Mentions: 3
Published: over 4 years ago

10.1186/s12870-021-02825-w

Transcriptional and proteomic insights into phytotoxic activity of interspecific potato hybrids with low glycoalkaloid contents
Cited by: 5
Author(s): Katarzyna Szajko, Jarosław Ciekot, Iwona Wasilewicz‐Flis, Waldemar Marczewski, Dorota Sołtys‐Kalina
Software Mentions: 3
Published: about 4 years ago

10.7554/eLife.29518

Unique molecular events during reprogramming of human somatic cells to induced pluripotent stem cells (iPSCs) at naïve state
Cited by: 32
Author(s): Yixuan Wang, Chengchen Zhao, Zhenzhen Hou, Yuanyuan Yang, Yan Bi, Hong Wang, Yong Zhang, Shaorong Gao
Software Mentions: 3
Published: about 7 years ago

10.1038/s42003-021-02242-7

A human isogenic iPSC-derived cell line panel identifies major regulators of aberrant astrocyte proliferation in Down syndrome
Cited by: 11
Author(s): Keiji Kawatani, Toshihiko Nambara, Nobutoshi Nawa, Hidetaka Yoshimatsu, Haruna Kusakabe, Katsuya Hirata, Akira Tanave, Kenta Sumiyama, Kimihiko Banno, Hidetoshi Taniguchi, Hitomi Arahori, Keiichi Ozono, Yasuji Kitabatake
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.49808

Extracellular matrix-inducing Sox9 promotes both basal progenitor proliferation and gliogenesis in developing neocortex
Cited by: 26
Author(s): Ayse Güven, Nereo Kalebic, Katherine R. Long, Marta Florio, Samir Vaid, Holger Brandl, Denise Stenzel, Wieland B. Huttner
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0177814

ANK1 is up-regulated in laser captured microglia in Alzheimer’s brain; the importance of addressing cellular heterogeneity
Cited by: 35
Author(s): Diego Mastroeni, Shobana Sekar, Jennifer Nolz, Elaine Delvaux, Katie Lunnon, Jonathan Mill, Winnie S. Liang, Paul D. Coleman
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.44306

PAX8 regulon in human ovarian cancer links lineage dependency with epigenetic vulnerability to HDAC inhibitors
Cited by: 31
Author(s): Kaixuan Shi, Xiang Yin, Mei-Chun Cai, Yan Yan, Chenqiang Jia, Ping Ma, Shengzhe Zhang, Zhenfeng Zhang, Zhenyu Gu, Meiying Zhang, Wen Di, Guanglei Zhuang
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0234029

An investigation into the beneficial effects and molecular mechanisms of humic acid on foxtail millet under drought conditions
Cited by: 8
Author(s): Jie Shen, Meijun Guo, Yuguo Wang, Xiangyang Yuan, Shuqi Dong, Xi-e Song, Peng Guo
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.08954

The splicing regulators Esrp1 and Esrp2 direct an epithelial splicing program essential for mammalian development
Cited by: 110
Author(s): Thomas W. Bebee, Juw Won Park, Katherine I Sheridan, Claude C. Warzecha, Benjamin Cieply, Alex M Rohacek, Yi Xing, Russ P. Carstens
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0184003

Honokiol induces superoxide production by targeting mitochondrial respiratory chain complex I in Candida albicans
Cited by: 38
Author(s): Libo Sun, Kai Liao, Dayong Wang
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-15-406

Differential gene expression between functionally specialized polyps of the colonial hydrozoan Hydractinia symbiolongicarpus (Phylum Cnidaria)
Cited by: 43
Author(s): Steven M. Sanders, Mariya Shcheglovitova, Paulyn Cartwright
Software Mentions: 3
Published: about 11 years ago

10.7554/eLife.08527

Protein biogenesis machinery is a driver of replicative aging in yeast
Cited by: 149
Author(s): Georges E. Janssens, Anne C Meinema, Javier González, Justina C. Wolters, Alexander Schmidt, Victor Guryev, Rainer Bischoff, Ernst Wit, Liesbeth M. Veenhoff, Matthias Heinemann
Software Mentions: 3
Published: about 9 years ago

10.7554/eLife.63731

CEP78 functions downstream of CEP350 to control biogenesis of primary cilia by negatively regulating CP110 levels
Cited by: 24
Author(s): André Gonçalves, Sarah Kirstine Hasselbalch, Beinta Biskopstø Joensen, Sebastian Patzke, Pernille Martens, Signe Krogh Ohlsen, Mathieu Quinodoz, Konstantinos Nikopoulos, Reem Suleiman, Magnus Per Damsø Jeppesen, Catja Weiss, Søren Tvorup Christensen, Carlo Rivolta, Jens S. Andersen, Pietro Farinelli, Lotte B. Pedersen
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0162402

Comprehensive Transcriptome Analyses of the Fructose-Fed Syrian Golden Hamster Liver Provides Novel Insights into Lipid Metabolism
Cited by: 8
Author(s): Ziyang Li, Chaoliang Xiong, Suo Mo, Haiying Tian, Mengqian Yu, Tingting Mao, Qian Chen, Huai‐Rong Luo, Quan-Zhen Li, Jianxin Lü, Yi Zhao, Wei Li
Software Mentions: 3
Published: over 8 years ago

10.1186/s13148-020-00916-3

The fusiform gyrus exhibits an epigenetic signature for Alzheimer’s disease
Cited by: 11
Author(s): Dingailu Ma, Irfete S. Fetahu, Mei Wang, Rui Fang, Jia-hui Li, Huan Liu, Tobin Gramyk, Isabella Iwanicki, Sophie Zhaotao Gu, Winnie Xu, Li Tan, Feizhen Wu, Yujiang Geno Shi
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.61406

The kinase PDK1 is critical for promoting T follicular helper cell differentiation
Cited by: 12
Author(s): Zhen Sun, Yingpeng Yao, Menghao You, Jingjing Liu, Wenhui Guo, Zhihong Qi, Zhao Wang, Fang Wang, Weiping Yuan, Shuyang Yu
Software Mentions: 3
Published: about 4 years ago

10.3390/cells10030635

Genome-Wide Identification of U-To-C RNA Editing Events for Nuclear Genes in Arabidopsis thaliana
Cited by: 12
Author(s): Ruchika, Chisato Okudaira, Matomo Sakari, Toshifumi Tsukahara
Software Mentions: 3
Published: almost 4 years ago

10.3390/cells9010025

Depolarization-Associated CircRNA Regulate Neural Gene Expression and in Some Cases May Function as Templates for Translation
Cited by: 28
Author(s): Elena Mahmoudi, Dylan Kiltschewskij, Chantel Fitzsimmons, Murray J. Cairns
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2164-15-570

Comparing reference-based RNA-Seq mapping methods for non-human primate data
Cited by: 33
Author(s): Ashlee M. Benjamin, Marshall Nichols, Thomas W. Burke, Geoffrey S. Ginsburg, Joseph E. Lucas
Software Mentions: 3
Published: about 11 years ago

10.7554/eLife.30809

The role of microglia and their CX3CR1 signaling in adult neurogenesis in the olfactory bulb
Cited by: 73
Author(s): R. Reshef, Elena Kudryavitskaya, Haran Shani-Narkiss, Batya Isaacson, Neta Rimmerman, Adi Mizrahi, Raz Yirmiya
Software Mentions: 3
Published: about 7 years ago

10.3390/cells9010090

PP2A Deficiency Enhances Carcinogenesis of Lgr5+ Intestinal Stem Cells Both in Organoids and In Vivo
Cited by: 3
Author(s): Yu–Ting Yen, May B. Chien, Yung-Chih Lai, Dao-Peng Chen, Cheng‐Ming Chuong, Mien‐Chie Hung, Shih‐Chieh Hung
Software Mentions: 3
Published: about 5 years ago

10.1128/AAC.00554-20

Candida glabrata Transcription Factor Rpn4 Mediates Fluconazole Resistance through Regulation of Ergosterol Biosynthesis and Plasma Membrane Permeability
Cited by: 18
Author(s): Pedro Pais, Raquel Califórnia, Mónica Galocha, Romeu Viana, Mihaela Ola, Mafalda Cavalheiro, Azusa Takahashi‐Nakaguchi, Hiroji Chibana, Geraldine Butler, Miguel C. Teixeira
Software Mentions: 3
Published: over 4 years ago

10.1530/JME-15-0119

Gene expression changes in subcutaneous adipose tissue due to Cushing's disease
Cited by: 24
Author(s): Irit Hochberg, Innocence Harvey, Quynh Tran, Erin J. Stephenson, Ariel L. Barkan, Alan R. Saltiel, William F. Chandler, Dave Bridges
Software Mentions: 3
Published: over 9 years ago

10.7554/eLife.46045

Circulating T cell-monocyte complexes are markers of immune perturbations
Cited by: 60
Author(s): Julie G. Burel, Mikhail Pomaznoy, Cecilia S. Lindestam Arlehamn, Daniela Weiskopf, Ricardo da Silva Antunes, Youngmo Jung, Mariana Babor, Véronique Schulten, Grégory Seumois, Jason A. Greenbaum, Sunil Premawansa, Gayani Premawansa, Ananda Wijewickrama, Dhammika Vidanagama, Bandu Gunasena, Rashmi Tippalagama, Aruna Dharshan De Silva, Robert H. Gilman, Mayuko Saito, Randy Taplitz, Klaus Ley, Pandurangan Vijayanand, Alessandro Sette, Bjoern Peters
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0174236

Enhancement of Arabidopsis growth characteristics using genome interrogation with artificial transcription factors
Cited by: 7
Author(s): Niels van Tol, Martijn Rolloos, Johan E. Pinas, Christiaan V. Henkel, Dieuwertje Augustijn, Paul J. J. Hooykaas, Bert J. van der Zaal
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-016-3009-3

Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat
Cited by: 79
Author(s): Siyuan Zhan, Yao Dong, Wei Zhao, Jiazhong Guo, Tao Zhong, Linjie Wang, Li Li, Hongping Zhang
Software Mentions: 3
Published: over 8 years ago

10.1038/s41388-020-01614-3

Comprehensive characterisation of intronic mis-splicing mutations in human cancers
Cited by: 20
Author(s): Hyunchul Jung, Kang Seon Lee, Jung Kyoon Choi
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0242970

Chronic IL-1 exposure drives LNCaP cells to evolve androgen and AR independence
Cited by: 8
Author(s): Haley Dahl, Mohammed Kanchwala, Shayna E. Thomas‐Jardin, Amrit Sandhu, Preethi Kanumuri, Afshan F. Nawas, Chao Xing, Chenchu Lin, Daniel E. Frigo, Nikkí A. Delk
Software Mentions: 3
Published: about 4 years ago

10.1016/j.stem.2018.09.008

Stage-Specific Transcription Factors Drive Astrogliogenesis by Remodeling Gene Regulatory Landscapes
Cited by: 67
Author(s): Neha Tiwari, Abhijeet Pataskar, Sophie Péron, Sudhir Thakurela, Sanjeeb Kumar Sahu, María Figueres-Oñate, Nicolás Marichal, Laura López‐Mascaraque, Vijay Tiwari, Benedikt Berninger
Software Mentions: 3
Published: over 6 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: almost 8 years ago

10.1038/s41389-019-0178-3

Repression of transcription factor AP-2 alpha by PPARγ reveals a novel transcriptional circuit in basal-squamous bladder cancer
Cited by: 21
Author(s): Haruo Yamashita, Yuka Imamura Kawasawa, Lauren Shuman, Zongyu Zheng, Tracy S. Tran, Vonn Walter, Joshua I. Warrick, Guoli Chen, Hikmat Al‐Ahmadie, Matthew Kaag, Pak Kin Wong, Jay D. Raman, David J. DeGraff
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0195132

RNA-Seq reveals differentially expressed genes affecting polyunsaturated fatty acids percentage in the Huangshan Black chicken population
Cited by: 15
Author(s): Shaohua Yang, Ying Wāng, Lulu Wang, Zhaoyuan Shi, Xiaoqian Ou, Dan Wu, Xinmiao Zhang, Hao Hu, Yuan Jia, Wei Wang, Fu-Hu Cao, Guoqing Liu
Software Mentions: 3
Published: almost 7 years ago

10.1155/2020/8831331

Differential Expression and PAH Degradation: What <i>Burkholderia vietnamiensi</i>s G4 Can Tell Us?
Cited by: 7
Author(s): Guilherme Pinto Cauduro, Ana Lusia Leal, Tiago Falcón Lopes, Marcela Marmitt, Victor Hugo Valiati
Software Mentions: 3
Published: over 4 years ago

10.1155/2016/1562041

Transcript Polymorphism Rates in Soybean Seed Tissue Are Increased in a Single Transformant of Glycine max
Cited by: 2
Author(s): Kevin Lambirth, Adam M. Whaley, Jessica A. Schlueter, Kenneth J. Piller, Kenneth L. Bost
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pntd.0005461

Modulation of the immune response by Fonsecaea pedrosoi morphotypes in the course of experimental chromoblastomycosis and their role on inflammatory response chronicity
Cited by: 26
Author(s): Isaque Medeiros Siqueira, Raffael Júnio Araújo de Castro, Luiza Chaves de Miranda Leonhardt, Márcio Sousa Jerônimo, A.J.M. Soares, Tainá Raiol, Christiane Nishibe, Nalvo F. Almeida, Aldo Henrique Tavares, Christian Hoffmann, Anamélia Lorenzetti Bocca
Software Mentions: 3
Published: almost 8 years ago

10.1186/1471-2164-14-818

Exploration of the gene fusion landscape of glioblastoma using transcriptome sequencing and copy number data
Cited by: 67
Author(s): Nameeta Shah, Michael Lankerovich, Hwahyung Lee, Jae-Geun Yoon, Brett Schroeder, Greg Foltz
Software Mentions: 3
Published: about 12 years ago

10.1155/2015/206937

Comprehensive Analysis of Transcriptome Sequencing Data in the Lung Tissues of COPD Subjects
Cited by: 52
Author(s): Woo Jin Kim, Jae Hyun Lim, Jae Seung Lee, Sang Do Lee, Ju Han Kim, Yeon Mok Oh
Software Mentions: 3
Published: about 10 years ago

10.1016/j.celrep.2020.108154

Protein Stability Buffers the Cost of Translation Attenuation following eIF2α Phosphorylation
Cited by: 15
Author(s): Kim Schneider, Geoffrey M. Nelson, J. P. Watson, Jörg Morf, Maximillian M. Dalglish, Laura M. Luh, Annika Weber, Anne Bertolotti
Software Mentions: 3
Published: over 4 years ago

10.1186/s40478-019-0712-8

Inhibition of mitochondrial respiration prevents BRAF-mutant melanoma brain metastasis
Cited by: 30
Author(s): Terje Sundstrøm, Lars Prestegarden, Francisco Azuaje, Synnøve Nymark Aasen, Gro Vatne Røsland, Jobin K. Varughese, Marzieh Bahador, Simon Bernatz, Yannick Braun, Patrick N. Harter, Kai Ove Skaftnesmo, Elizabeth S. Ingham, Lisa M. Mahakian, Sarah Tam, Clifford G. Tepper, Kjell Petersen, Katherine W. Ferrara, Karl Johan Tronstad, Morten Lund‐Johansen, Rudi Beschorner, Rolf Bjerkvig, Frits Thorsen
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pntd.0007589

The cell fate regulator NUPR1 is induced by Mycobacterium leprae via type I interferon in human leprosy
Cited by: 5
Author(s): Priscila Ribeiro Andrade, Manali Mehta, Jing Lü, Rosane M. B. Teles, Dennis Montoya, Phillip Scumpia, Euzenir Nunes Sarno, Marîa Teresa Ochoa, Feiyang Ma, Matteo Pellegrini, Robert L. Modlin
Software Mentions: 3
Published: over 5 years ago

10.1038/s41388-018-0661-x

Lineage-specific control of TFIIH by MITF determines transcriptional homeostasis and DNA repair
Cited by: 17
Author(s): Marcos Seoane, Sophia Buhs, Pablo A. Iglesias, Julia Strauß, Ann-Christin Puller, Jürgen Müller, Helwe Gerull, Susanne Feldhaus, Malik Alawi, Johanna M. Brandner, Dennis Eggert, Jinyan Du, Jürgen Thomale, Peter J. Wild, Martin Zimmermann, Thomas Sternsdorf, Udo Schumacher, Peter Nollau, David E. Fisher, Martin Horstmann
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.57090

Deep evolutionary origin of gamete-directed zygote activation by KNOX/BELL transcription factors in green plants
Cited by: 23
Author(s): Tetsuya Hisanaga, Shota Fujimoto, Yihui Cui, Katsutoshi Sato, Ryosuke Sano, Shohei Yamaoka, Takayuki Kohchi, Frédéric Berger, Keiji Nakajima
Software Mentions: 3
Published: over 3 years ago

10.1186/s12918-016-0366-0

Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion
Cited by: 87
Author(s): Mingyan Lin, Erika Pedrosa, Anastasia Hrabovsky, Jian Chen, Benjamin R. Puliafito, Stephanie R. Gilbert, Deyou Zheng, Herbert M. Lachman
Software Mentions: 3
Published: over 8 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: over 5 years ago

10.1371/journal.pntd.0007764

Identification of a systemic interferon-γ inducible antimicrobial gene signature in leprosy patients undergoing reversal reaction
Cited by: 20
Author(s): Rosane M. B. Teles, Jing Lü, Maria Tió-Coma, Isabela M. B. Goulart, Sayera Banu, Deanna A. Hagge, Kidist Bobosha, Tom H. M. Ottenhoff, Matteo Pellegrini, Annemieke Geluk, Robert L. Modlin
Software Mentions: 3
Published: over 5 years ago

10.1016/j.celrep.2015.12.012

NIPBL Controls RNA Biogenesis to Prevent Activation of the Stress Kinase PKR
Cited by: 27
Author(s): Kobe Yuen, Baoshan Xu, Ian D. Krantz, Jennifer L. Gerton
Software Mentions: 3
Published: about 9 years ago

10.1186/s12917-017-1279-x

RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars
Cited by: 14
Author(s): Maren van Son, Nina Hårdnes Tremoen, Ann Helen Gaustad, Frøydis Deinboll Myromslien, Dag Inge Våge, Else‐Berit Stenseth, Teklu T Zeremichael, Eli Grindflek
Software Mentions: 3
Published: about 7 years ago

10.1016/j.celrep.2018.07.058

Oral Cavity Squamous Cell Carcinoma Xenografts Retain Complex Genotypes and Intertumor Molecular Heterogeneity
Cited by: 25
Author(s): Katie M. Campbell, Tianxiang Lin, Paul Zolkind, Erica K. Barnell, Zachary L. Skidmore, Ashley E. Winkler, Jonathan H. Law, Elaine R. Mardis, Lukas D. Wartman, Douglas R. Adkins, Rebecca D. Chernock, Malachi Griffith, Ravindra Uppaluri
Software Mentions: 3
Published: over 6 years ago

10.1016/j.celrep.2019.05.057

Tumor Heterogeneity Underlies Differential Cisplatin Sensitivity in Mouse Models of Small-Cell Lung Cancer
Cited by: 39
Author(s): Franziska Böttger, Ekaterina A. Semenova, Ji‐Ying Song, Giustina Ferone, Jan van der Vliet, Miranda Cozijnsen, Rajith Bhaskaran, Lorenzo Bombardelli, Sander R. Piersma, Thang V. Pham, Connie R. Jiménez, Anton Berns
Software Mentions: 3
Published: over 5 years ago

10.7150/ijbs.56152

MLKL inhibits intestinal tumorigenesis by suppressing STAT3 signaling pathway
Cited by: 11
Author(s): Qun Zhao, Xinran Cheng, Jian Guo, Yunbo Bi, Li Qing Kuang, Jianhua Ren, Jing Zhong, Longrui Pan, Xudong Zhang, Yang Guo, Yongqiang Liu, S. Jin, Yan Tan, Yu Lei
Software Mentions: 3
Published: about 4 years ago

10.1128/mSphere.00028-18

Dal81 Regulates Expression of Arginine Metabolism Genes in Candida parapsilosis
Cited by: 9
Author(s): Siobhán A. Turner, Qinxi Ma, Mihaela Ola, Kontxi Martinez de San Vicente, Geraldine Butler
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pgen.1006108

Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles
Cited by: 148
Author(s): Raúl Castanera, Leticia López-Varas, Alessandra Borgognone, Kurt LaButti, Alla Lapidus, Jeremy Schmutz, Jane Grimwood, Gúmer Pérez, Antonio G. Pisabarro, Igor V. Grigoriev, Jason E. Stajich, Lucı́a Ramı́rez
Software Mentions: 3
Published: over 8 years ago

10.1128/mBio.00768-21

Duplication and Functional Divergence of Branched-Chain Amino Acid Biosynthesis Genes in Aspergillus nidulans
Cited by: 7
Author(s): Joel T Steyer, Damien J. Downes, Cameron C. Hunter, Pierre Migeon, Richard B. Todd
Software Mentions: 3
Published: over 3 years ago

10.1128/mBio.02217-17

Deregulation of HDAC5 by Viral Interferon Regulatory Factor 3 Plays an Essential Role in Kaposi's Sarcoma-Associated Herpesvirus-Induced Lymphangiogenesis
Cited by: 15
Author(s): Hye‐Ra Lee, Fan Li, Un Yung Choi, Hye Ryun Yu, Grace M. Aldrovandi, Pinghui Feng, Shou‐Jiang Gao, Young‐Kwon Hong, Jae U. Jung
Software Mentions: 3
Published: almost 7 years ago

10.1016/j.celrep.2019.03.044

Transcriptomics-Based Screening Identifies Pharmacological Inhibition of Hsp90 as a Means to Defer Aging
Cited by: 56
Author(s): Georges E. Janssens, Xin-Xuan Lin, Lluís Millán-Ariño, Alan Kavšek, Ilke Sen, Renée I. Seinstra, Nicholas Stroustrup, Ellen A. A. Nollen, Christian G. Riedel
Software Mentions: 3
Published: almost 6 years ago

10.1128/mBio.02684-19

Contextual Flexibility in Pseudomonas aeruginosa Central Carbon Metabolism during Growth in Single Carbon Sources
Cited by: 49
Author(s): Stephen K. Dolan, Michael Kohlstedt, Stephen Trigg, Pedro P. Vallejo Ramirez, Clemens F. Kaminski, Christoph Wittmann, Martin Welch
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13046-019-1092-4

LPCAT1 promotes brain metastasis of lung adenocarcinoma by up-regulating PI3K/AKT/MYC pathway
Cited by: 86
Author(s): Chunhua Wei, Xiaomin Dong, Hui Lü, Fan Tong, Lingjuan Chen, Ruiguang Zhang, Jing Dong, Yu Hu, Gang Wu, Xiaorong Dong
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-67482-9

miRNA–mRNA network regulation in the skeletal muscle fiber phenotype of chickens revealed by integrated analysis of miRNAome and transcriptome
Cited by: 20
Author(s): Yifan Liu, Ming Zhang, Yanju Shan, Gaige Ji, Xiaojun Ju, Yan Tu, Zhongwei Sheng, Jing Xie, Jianmin Zou, Shu JingTing
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-69389-x

A high-quality reference genome for cabbage obtained with SMRT reveals novel genomic features and evolutionary characteristics
Cited by: 22
Author(s): Honghao Lv, Yong Wang, Fengqing Han, Jialei Ji, Zhiyuan Fang, Mu Zhuang, Zhansheng Li, Yangyong Zhang, Limei Yang
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-61305-7

Root transcriptome reveals efficient cell signaling and energy conservation key to aluminum toxicity tolerance in acidic soil adapted rice genotype
Cited by: 12
Author(s): Wricha Tyagi, Julia S. Yumnam, Debashish Sen, Mayank Rai
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-020-64938-w

Gene expression trajectories during male and female reproductive development in balsam poplar (Populus balsamifera L.)
Cited by: 10
Author(s): Quentin Cronk, Raju Soolanayakanahally, Katharina Bräutigam
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-020-66939-1

Soluble silica stimulates osteogenic differentiation and gap junction communication in human dental follicle cells
Cited by: 17
Author(s): Pamela Uribe, Anders Johansson, Ravin Jugdaohsingh, Jonathan J. Powell, Catarina Magnusson, Marcela Dávila, Anna Westerlund, Maria Ransjö
Software Mentions: 3
Published: over 4 years ago

10.15252/embj.2019102147

<scp>SLC</scp> 1A3 contributes to L‐asparaginase resistance in solid tumors
Cited by: 40
Author(s): Jianhui Sun, Remco Nagel, Esther A. Zaal, Alejandro P. Ugalde, Ruiqi Han, Natalie Proost, Ji Ying Song, Abhijeet Pataskar, Artur M Burylo, Haigen Fu, Gerrit J. Poelarends, Marieke van de Ven, Olaf van Tellingen, Celia R. Berkers, Reuven Agami
Software Mentions: 3
Published: over 5 years ago

10.18632/aging.101536

A Drosophila model of cigarette smoke induced COPD identifies Nrf2 signaling as an expedient target for intervention
Cited by: 21
Author(s): R. Prange, Marcus Thiedmann, Anita Bhandari, Neha Mishra, Anupam Sinha, Robert Häsler, Philip Rosenstiel, Karin Uliczka, Christina Wagner, Ali Önder Yildirim, Christine Fink, Thomas Roeder
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-57311-z

Landscape of transcriptome variations uncovering known and novel driver events in colorectal carcinoma
Cited by: 16
Author(s): Giovanna Pira, Paolo Uva, Antonio Mario Scanu, Paolo Rocca, Luciano Murgia, Elena Uleri, Claudia Piu, Alberto Porcu, Ciriaco Carru, Alessandra Manca, Ivana Persico, Maria Rosaria Muroni, Francesca Sanges, Caterina Serra, A Dolei, Andrea Angius, Maria Rosaria De Miglio
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-021-07971-x

Unveiling the transcriptomic complexity of Miscanthus sinensis using a combination of PacBio long read- and Illumina short read sequencing platforms
Cited by: 2
Author(s): Yongli Wang, Xia Li, Congsheng Wang, Lu Gao, Yanfang Wu, Xingnan Ni, Jianzhong Sun, Jianxiong Jiang
Software Mentions: 3
Published: over 3 years ago

10.1038/s41419-020-03081-w

The histone H2B ubiquitin ligase RNF40 is required for HER2-driven mammary tumorigenesis
Cited by: 7
Author(s): Florian Wegwitz, Evangelos Prokakis, Anastasija Pejkovska, Robyn Laura Kosinsky, Markus Glatzel, Klaus Pantel, Harriet Wikman, Steven A. Johnsen
Software Mentions: 3
Published: over 4 years ago

10.1038/s41420-020-0264-5

Tet2-mediated epigenetic drive for astrocyte differentiation from embryonic neural stem cells
Cited by: 6
Author(s): Fei He, Hao Wu, Libing Zhou, Qing Lin, Yin Chen, Yi Sun
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-019-57404-9

Comprehensive analysis of circRNAs from cashmere goat skin by next generation RNA sequencing (RNA-seq)
Cited by: 28
Author(s): Yuanyuan Zheng, Taiyu Hui, Yue Chang, Jiaming Sun, Dan Guo, Suling Guo, Shu Guo, Bojiang Li, Zeying Wang, Wenlin Bai
Software Mentions: 3
Published: about 5 years ago

10.1128/mBio.00029-17

The Transcriptome of<i>Leishmania major</i>Developmental Stages in Their Natural Sand Fly Vector
Cited by: 72
Author(s): Ehud Inbar, V. K. Hughitt, Laura A. L. Dillon, Kashinath Ghosh, Najib M. El-Sayed, David L. Sacks
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13046-020-01622-x

Non-coding RNAs in cancer: platforms and strategies for investigating the genomic “dark matter”
Cited by: 110
Author(s): Katia Grillone, Caterina Riillo, Francesca Scionti, Roberta Rocca, Giuseppe Tradigo, Pietro Hiram Guzzi, Stefano Alcaro, Maria Teresa Di Martino, Pierosandro Tagliaferri, Pierfrancesco Tassone
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-45817-5

The Fungal Histone Acetyl Transferase Gcn5 Controls Virulence of the Human Pathogen Candida albicans through Multiple Pathways
Cited by: 34
Author(s): Raju Shivarathri, Michael Tscherner, Florian Zwolanek, Nitesh Kumar Singh, Neeraj Chauhan, Karl Kuchler
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pcbi.1003517

Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson's Leukocytes Identified by RNA Sequencing
Cited by: 145
Author(s): Lilach Soreq, Alessandro Guffanti, Nathan Salomonis, Alon Simchovitz, Zvi Israel, Hagai Bergman, Hermona Soreq
Software Mentions: 3
Published: almost 11 years ago

10.1038/s41598-019-43277-5

Comparative transcriptome profiling of multi-ovary wheat under heterogeneous cytoplasm suppression
Cited by: 1
Author(s): Jialin Guo, Gaisheng Zhang, Yulong Song, Shen Ma, Na Niu, Junwei Wang
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0165823

Transcriptome Profiling of the Phaseolus vulgaris - Colletotrichum lindemuthianum Pathosystem
Cited by: 37
Author(s): Bilal A. Padder, Kelvin Kamfwa, Halima E. Awale
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pcbi.1003323

Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response
Cited by: 26
Author(s): Ashwini Patil, Yutaro Kumagai, Kuo-ching Liang, Yutaka Suzuki, Kenta Nakai
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-019-44305-0

Variable protein homeostasis in housekeeping and non-housekeeping pathways under mycotoxins stress
Cited by: 6
Author(s): Yu Sun, Jikai Wen, Ruohong Chen, Yiqun Deng
Software Mentions: 3
Published: over 5 years ago

10.1038/s41419-020-2333-3

UHRF1-repressed 5’-hydroxymethylcytosine is essential for the male meiotic prophase I
Cited by: 9
Author(s): Hongjie Pan, Ning Jiang, Shenfei Sun, Hanwei Jiang, Jianze Xu, Xiaohua Jiang, Qian Gao, Liang Li, Haili Wu, Huajun Zheng, Qi Qi, Tianqi Li, Meixing Zhang, Lingling Zhang, Xiaofeng Wan, Xinhua Lin, Jiemin Wong, Qinghua Shi, Li R
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-017-3663-0

Transcriptome analysis of the two unrelated fungal β-lactam producers Acremonium chrysogenum and Penicillium chrysogenum: Velvet-regulated genes are major targets during conventional strain improvement programs
Cited by: 22
Author(s): Dominik Terfehr, Tim A. Dahlmann, Ulrich Kück
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-019-43075-z

A universal transcriptomic signature of age reveals the temporal scaling of Caenorhabditis elegans aging trajectories
Cited by: 35
Author(s): Andrei E. Tarkhov, Ramani Alla, Srinivas Ayyadevara, Mikhail A. Pyatnitskiy, L. I. Men’shikov, Robert J. Shmookler Reis, П. О. Федичев
Software Mentions: 3
Published: almost 6 years ago

10.1038/cddis.2017.48

Inactivation of Lsd1 triggers senescence in trophoblast stem cells by induction of Sirt4
Cited by: 30
Author(s): Josefina Castex, Dominica Willmann, Toufike Kanouni, Laura Arrigoni, Yan Li, Marcel Friedrich, Michael Schleicher, Simon Wöhrle, Mark Pearson, Norbert Kraut, Michaël Méret, Thomas Manke, Eric Metzger, Roland Schüle, Thomas Günther
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-016-3170-8

Numerous genetic loci identified for drought tolerance in the maize nested association mapping populations
Cited by: 52
Author(s): Chunhui Li, Bo Sun, Yongxiang Li, Cheng Liu, Xun Wu, Dengfeng Zhang, Yunsu Shi, Yi Song, Edward S. Buckler, Zhiwu Zhang, Tianyu Wang, Yu Liu
Software Mentions: 3
Published: over 8 years ago

10.3389/fmicb.2020.535673

Transcriptome and miRNome Analysis Provide New Insight Into Host Lipid Accumulation, Innate Immunity, and Viral Persistence in Hepatitis C Virus Infection in vitro
Cited by: 5
Author(s): Chong Li, Lungen Lu, Zhongtian Qi, Yaping Zhu, Fengtao Su, Ping Zhao
Software Mentions: 3
Published: over 4 years ago

10.1038/s41419-020-02963-3

EZH2 reduction is an essential mechanoresponse for the maintenance of super-enhancer polarization against compressive stress in human periodontal ligament stem cells
Cited by: 9
Author(s): Qian Li, Xiwen Sun, Yunyi Tang, Yanan Qu, Yanheng Zhou, Yu Zhang
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1006786

Spatial clustering and common regulatory elements correlate with coordinated gene expression
Cited by: 23
Author(s): Jingyu Zhang, Hengyu Chen, Ruoyan Li, David A. Taft, Guang Yao, Fan Bai, Jianhua Xing
Software Mentions: 3
Published: almost 6 years ago

10.1038/cddis.2017.426

Common microRNA–mRNA interactions exist among distinct porcine iPSC lines independent of their metastable pluripotent states
Cited by: 8
Author(s): Shiqiang Zhang, Youlong Xie, Hongxia Cao, Huayan Wang
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-42608-w

Gene co-expression networks contributing to the expression of compensatory growth in metabolically active tissues in cattle
Cited by: 9
Author(s): Kate Keogh, David A. Kenny, Sinéad M. Waters
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-019-42686-w

Enhanced early-life nutrition upregulates cholesterol biosynthetic gene expression and Sertoli cell maturation in testes of pre-pubertal Holstein bulls
Cited by: 12
Author(s): Chinju Johnson, Alysha Dance, Igor Kovalchuk, John P. Kastelic, Jacob C. Thundathil
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-019-50220-1

Drivers of AR indifferent anti-androgen resistance in prostate cancer cells
Cited by: 41
Author(s): Florian Handle, Stefan Prekovic, Christine Helsen, Thomas Van den Broeck, Elien Smeets, Lisa Moris, Roy Eerlings, Sarah El Kharraz, Alfonso Urbanucci, Ian G. Mills, Steven Joniau, Gerhardt Attard, Frank Claessens
Software Mentions: 3
Published: over 5 years ago