bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1038/s41396-019-0580-z

Phage-specific metabolic reprogramming of virocells
Cited by: 118
Author(s): Cristina Howard-Varona, Morgan Lindback, G. Eric Bastien, Natalie Solonenko, Ahmed A. Zayed, Ho Bin Jang, Bill Andreopoulos, Heather M. Brewer, Tijana Glavina del Rio, Joshua N. Adkins, Subhadeep Paul, Matthew B. Sullivan, Melissa B. Duhaime
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13046-018-0873-5

Integrated genomic analyses in PDX model reveal a cyclin-dependent kinase inhibitor Palbociclib as a novel candidate drug for nasopharyngeal carcinoma
Cited by: 20
Author(s): Cheng Lung Hsu, Kar Wai Lui, Ming Liu, Yung Chia Kuo, Yin‐Kai Chao, Chun‐Nan Yeh, Li Yu Lee, Yen‐Lin Huang, Tsan-Shiun Lin, Mei Yuan Huang, Yi Ru Lai, Yuan Ming Yeh, Hsien Chi Fan, An Chi Lin, Yen Jung Lu, Chia Hsun Hsieh, Kai Ping Chang, Ngan Ming Tsang, Hung Ming Wang, Alex Y. Chang, Yu Sun Chang, Hsin Pai Li
Software Mentions: 2
Published: about 8 years ago

10.1186/s13046-020-01624-9

Long non-coding RNA CASC9 promotes tumor growth and metastasis via modulating FZD6/Wnt/β-catenin signaling pathway in bladder cancer
Cited by: 29
Author(s): Yonghao Zhan, Lianghao Zhang, Shuanbao Yu, Jianguo Wen, Yuchen Liu, Xuepei Zhang
Software Mentions: 2
Published: over 6 years ago

10.1186/s13046-020-01807-4

Cell surface GRP78 regulates BACE2 via lysosome-dependent manner to maintain mesenchymal phenotype of glioma stem cells
Cited by: 16
Author(s): Zihang Chen, Huizhi Wang, Zongpu Zhang, Jianye Xu, Yanhua Qi, Hao Xue, Zijie Gao, Rongrong Zhao, Shaobo Wang, Shouji Zhang, Wei Qiu, Xing Guo, Gang Li
Software Mentions: 2
Published: almost 6 years ago

10.1084/jem.20161418

Niche-mediated depletion of the normal hematopoietic stem cell reservoir by Flt3-ITD–induced myeloproliferation
Cited by: 39
Author(s): Adam J. Mead, Wen Hao Neo, Nikolaos Barkas, Satoshi Matsuoka, Alice Giustacchini, R Facchini, Supat Thongjuea, Lauren E. Jamieson, Christopher A.G. Booth, Nicholas Fordham, Cristina Di Genua, Deborah Atkinson, Onima Chowdhury, Emmanouela Repapi, Nicola E. Gray, Shabnam Kharazi, Clark S-A., Tiphaine Bouriez, Petter Woll, Toshio Suda, Claus Nerlov, Sten Eirik W. Jacobsen
Software Mentions: 2
Published: over 9 years ago

10.1084/jem.20181762

Immune homeostasis and regulation of the interferon pathway require myeloid-derived Regnase-3
Cited by: 23
Author(s): Matthias von Gamm, Annalisa Schaub, Alisha N Jones, Christine Wolf, Gesine Behrens, Johannes Lichti, Katharina Essig, Anna Macht, Joachim Pircher, Andreas Ehrlich, Kathrin Davari, Dhruv Chauhan, Benjamin Busch, Wolfgang Wurst, Regina Feederle, Annette Feuchtinger, Matthias H. Tschöp, Caroline C. Friedel, Stefanie M. Hauck, Michael Sattler, Arie Geerlof, Veit Hornung, Vigo Heissmeyer, Christian Schulz, Mathias Heikenwälder, Elke Glasmacher
Software Mentions: 2
Published: over 7 years ago

10.1084/jem.20190493

Regulatory roles of IL-10–producing human follicular T cells
Cited by: 60
Author(s): Pablo F. Cañete, Rebecca A. Sweet, Paula González-Figueroa, Ilenia Papa, Naganari Ohkura, Holly A. Bolton, Jonathan A. Roco, Marta Cuenca, Katharine Bassett, İsmail Sayin, Emma F. Barry, Angel F. Lopez, David H. Canaday, Michael Meyer‐Hermann, Claudio Doglioni, Barbara Fazekas de St Groth, Shimon Sakaguchi, Matthew C. Cook, Carola G. Vinuesa
Software Mentions: 2
Published: over 7 years ago

10.1084/jem.20170807

In vivo single cell analysis reveals Gata2 dynamics in cells transitioning to hematopoietic fate
Cited by: 31
Author(s): Christina Eich, Jochen Arlt, Chris S. Vink, Parham Solaimani Kartalaei, Polynikis Kaimakis, Samanta A. Mariani, Reinier van der Linden, Wiggert A. van Cappellen, Elaine Dzierzak
Software Mentions: 2
Published: almost 9 years ago

10.1002/ijc.32643

Multiscale network analysis reveals molecular mechanisms and key regulators of the tumor microenvironment in gastric cancer
Cited by: 14
Author(s): Won‐Min Song, Xiandong Lin, Xuehong Liao, Dan Hu, Jianhua Lin, Umut Sarpel, Yunbin Ye, Yael Feferman, Daniel M. Labow, Martin J. Walsh, Xiongwei Zheng, Bin Zhang
Software Mentions: 2
Published: about 7 years ago

10.1155/2015/528395

Transcriptomes That Confer to Plant Defense against Powdery Mildew Disease inLagerstroemia indica
Cited by: 7
Author(s): Xinwang Wang, Weibing Shi, Timothy A. Rinehart
Software Mentions: 2
Published: almost 12 years ago

10.1155/2015/265791

Analysis of theThinopyrum elongatumTranscriptome under Water Deficit Stress
Cited by: 7
Author(s): Yongjun Shu, Jun Zhang, You Ao, Lili Song, Changhong Guo
Software Mentions: 2
Published: almost 12 years ago

10.1155/2019/7859121

Gene Expression Pattern and Regulatory Network of α-Toxin Treatment in Bombyx mori
Cited by: 0
Author(s): Tieshan Feng, Ping Lin, Jiao Gong, Chen Dong, Xi Yang, Quan Zhang, Tingcai Cheng
Software Mentions: 2
Published: over 7 years ago

10.1155/2016/2895303

Differential Gene Expression during Larval Metamorphic Development in the Pearl Oyster,Pinctada fucata, Based on Transcriptome Analysis
Cited by: 8
Author(s): Haimei Li, Bo Zhang, Guiju Huang, Bao-Suo Liu, Sigang Fan, Dongling Zhang, Dahui Yu
Software Mentions: 2
Published: almost 11 years ago

10.1155/2018/8084032

Transcriptomic Profiling of Fruit Development in Black Raspberry Rubus coreanus
Cited by: 5
Author(s): Qing Chen, Xunju Liu, Yun Hu, Bo Sun, Yaodong Hu, Xiaorong Wang, Haoru Tang, Yan Wang
Software Mentions: 2
Published: almost 9 years ago

10.1155/2020/7434737

Nomogram Based on microRNA Signature Contributes to Improve Survival Prediction of Clear Cell Renal Cell Carcinoma
Cited by: 7
Author(s): Enfa Zhao, Xiaofang Bai
Software Mentions: 2
Published: over 6 years ago

10.1155/2015/527054

Genome-Wide Identification of Genes Probably Relevant to the Uniqueness of Tea Plant (Camellia sinensis) and Its Cultivars
Cited by: 2
Author(s): Yan Wei, Jing Wang, Youxiang Zhou, Mingming Zhao, Yan Gong, Hua Ding, Lijun Peng, HU Ding-jin
Software Mentions: 2
Published: almost 12 years ago

10.7150/ijms.57504

Roles of the miR-139-5p/CCT5 axis in hepatocellular carcinoma: a bioinformatic analysis
Cited by: 7
Author(s): Jingjing Xu, Yuan Zhang, Cheng Liu, Ping Yan, Zongguo Yang
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41366-020-0561-3

Impact of maternal obesity on placental transcriptome and morphology associated with fetal growth restriction in mice
Cited by: 19
Author(s): Daniela de Barros Mucci, Laura C. Kusinski, Phoebe Wilsmore, Elena Loche, Lucas Carminatti Pantaleão, Tom Ashmore, Heather L. Blackmore, Denise S. Fernandez‐Twinn, Maria das Graças Tavares do Carmo, Susan E. Ozanne
Software Mentions: 2
Published: over 6 years ago

10.1186/s13045-021-01045-x

The construction, expression, and enhanced anti-tumor activity of YM101: a bispecific antibody simultaneously targeting TGF-β and PD-L1
Cited by: 90
Author(s): Ming Yi, Jing Zhang, An‐Ping Li, Mengke Niu, Yongxiang Yan, Yanmei Jiao, Suxia Luo, Pengfei Zhou, Kongming Wu
Software Mentions: 2
Published: over 5 years ago

10.1093/jhered/esaa021

X-Linked Signature of Reproductive Isolation in Humans is Mirrored in a Howler Monkey Hybrid Zone
Cited by: 6
Author(s): Marcella D. Baiz, Priscilla K. Tucker, Jacob L. Mueller, Liliana Cortés‐Ortiz
Software Mentions: 2
Published: over 6 years ago

10.1186/s40425-019-0503-6

Combined treatment with HMGN1 and anti-CD4 depleting antibody reverses T cell exhaustion and exerts robust anti-tumor effects in mice
Cited by: 8
Author(s): Chang Yu Chen, Satoshi Ueha, Yoichi Ishiwata, Shoji Yokochi, De Yang, Joost J. Oppenheim, Haru Ogiwara, Shigeyuki Shichino, Shungo Deshimaru, Francis H.W. Shand, Sotaro Shibayama, Kouji Matsushima
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41388-020-01593-5

C-terminal truncated HBx initiates hepatocarcinogenesis by downregulating TXNIP and reprogramming glucose metabolism
Cited by: 45
Author(s): Yu Zhang, Qian Yan, Lanqi Gong, Hang Xu, Beilei Liu, Xiaona Fang, Dandan Yu, Lei Li, Ting Wei, Ying Wang, Ching Ngar Wong, Zhaojie Lyu, Ying Tang, Pak C. Sham, Xin‐Yuan Guan
Software Mentions: 2
Published: almost 6 years ago

10.1038/oncsis.2017.30

Epigenetic pathway inhibitors represent potential drugs for treating pancreatic and bronchial neuroendocrine tumors
Cited by: 33
Author(s): Kate E Lines, Mark Stevenson, P. Filippakopoulos, Susanne Müller, Helen Lockstone, Benjamin Wright, Simona Grozinsky‐Glasberg, Ashley Grossman, S. Knapp, David Buck, C. Bountra, R V Thakker
Software Mentions: 2
Published: over 9 years ago

10.1007/s10911-017-9385-8

Menin Modulates Mammary Epithelial Cell Numbers in Bovine Mammary Glands Through Cyclin D1
Cited by: 6
Author(s): Kerong Shi, Xue Li, Honghui Li, Xueyan Lin, Zhiying Yan, Qiaoqiao Cao, Meng Zhao, Zhongjin Xu, Zhonghua Wang
Software Mentions: 2
Published: almost 9 years ago

10.1007/s00239-020-09951-3

Spatial Patterns of Gene Expression in Bacterial Genomes
Cited by: 13
Author(s): Daniella F. Lato, G. Brian Golding
Software Mentions: 2
Published: over 6 years ago

10.1007/s00109-020-02020-8

3D culture conditions support Kaposi’s sarcoma herpesvirus (KSHV) maintenance and viral spread in endothelial cells
Cited by: 10
Author(s): Tatyana Dubich, Anne Dittrich, Kristine Bousset, Robert Geffers, Guntram Büsche, Mario Köster, Hansjörg Hauser, Thomas F. Schulz, Dagmar Wirth
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.34114

Transcriptomic analyses reveal rhythmic and CLOCK-driven pathways in human skeletal muscle
Cited by: 81
Author(s): Laurent Perrin, Ursula Loizides‐Mangold, Stéphanie Chanon, Cédric Gobet, Nicolas Hulo, Laura Isenegger, Benjamin D. Weger, Eugenia Migliavacca, Aline Charpagne, James A. Betts, Jean–Philippe Walhin, Iain Templeman, Keith Stokes, Dylan Thompson, Kostas Tsintzas, M. Robert, Cédric Howald, Howard Riezman, Jérôme N. Feige, Leonidas G. Karagounis, Jeanne D. Johnston, Emmanouil T. Dermitzakis, Frédéric Gachon, Étienne Lefai, Charna Dibner
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.52063

The genetic basis of aneuploidy tolerance in wild yeast
Cited by: 59
Author(s): James Hose, Leah E. Escalante, Katie J. Clowers, H Auguste Dutcher, DeElegant Robinson, Venera Bouriakov, Joshua J. Coon, Evgenia Shishkova, Audrey P. Gasch
Software Mentions: 2
Published: almost 7 years ago

10.7554/eLife.59795

Amino acid synthesis loss in parasitoid wasps and other hymenopterans
Cited by: 0
Author(s): Xinhai Ye, Shijiao Xiong, Ziwen Teng, Yi Yang, Jiale Wang, Kaili Yu, Huizi Wu, Mei Yang, Zhichao Yan, Sammy Cheng, Chuanlin Yin, Fang Wang, Hongwei Yao, Qi Fang, Qisheng Song, John H. Werren, Gōngyín Yè, Fēi Li
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.55744

Host-induced spermidine production in motile Pseudomonas aeruginosa triggers phagocytic uptake
Cited by: 5
Author(s): Sebastian Felgner, Matthias Preuße, Ulrike Beutling, Stephanie Stahnke, Vinay Pawar, Manfred Rohde, Mark Brönstrup, Theresia E. B. Stradal, Susanne Häußler
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.53159

FoxO suppresses endoplasmic reticulum stress to inhibit growth of Tsc1-deficient tissues under nutrient restriction
Cited by: 4
Author(s): Avantika Gupta, Hugo Stocker
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.20607

Transcriptional signatures of somatic neoblasts and germline cells in Macrostomum lignano
Cited by: 40
Author(s): Magda Grudniewska, Stijn Mouton, Daniil Simanov, Frank W. Beltman, Margriet Grelling, Katrien De Mulder, Wibowo Arindrarto, Philipp M. Weissert, Stefan van der Elst, Eugène Berezikov
Software Mentions: 2
Published: almost 10 years ago

10.3390/ijms21217858

Meta-Analysis of Transcriptome Data Detected New Potential Players in Response to Dioxin Exposure in Humans
Cited by: 3
Author(s): Е. А. Ощепкова, Yana Sizentsova, Daniil S. Wiebe, В. В. Миронова, Nikolay А. Kolchanov
Software Mentions: 2
Published: about 6 years ago

10.3390/ijms21218170

Whole-Transcriptome Sequencing-Based Analysis of DAZL and Its Interacting Genes during Germ Cells Specification and Zygotic Genome Activation in Chickens
Cited by: 6
Author(s): Deivendran Rengaraj, Sohyoung Won, Jong Won Han, DongAhn Yoo, Heebal Kim, Jae Yong Han
Software Mentions: 2
Published: about 6 years ago

10.3390/ijms21239182

Oxidative Stress Impact on the Transcriptome of Differentiating Neuroblastoma Cells: Implication for Psychiatric Disorders
Cited by: 1
Author(s): Behnaz Khavari, Elena Mahmoudi, Michael Geaghan, Murray J. Cairns
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms21249359

Identification of the 3-lncRNA Signature as a Prognostic Biomarker for Colorectal Cancer
Cited by: 42
Author(s): Shuzhen Liu, Qing Cao, Guoyan An, Bianbian Yan, Lei Lei
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms22010289

Whole-Transcriptome RNA Sequencing Reveals the Global Molecular Responses and CeRNA Regulatory Network of mRNAs, lncRNAs, miRNAs and circRNAs in Response to Salt Stress in Sugar Beet (Beta vulgaris)
Cited by: 39
Author(s): Junliang Li, Jie Cui, Chunhua Dai, Tianjiao Liu, Dansong Cheng, Chen Luo
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms22020619

CXCR4 Regulates Temporal Differentiation via PRC1 Complex in Organogenesis of Epithelial Glands
Cited by: 0
Author(s): Jun Chul Kim, Sang‐Woo Lee, Kyungpyo Park
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms22052737

Different miRNA Profiles in Plasma Derived Small and Large Extracellular Vesicles from Patients with Neurodegenerative Diseases
Cited by: 33
Author(s): Daisy Sproviero, Stella Gagliardi, Susanna Zucca, Maddalena Arigoni, Marta Giannini, Maria Garofalo, Martina Olivero, Michela Dell’Orco, Orietta Pansarasa, Stefano Bernuzzi, Micol Avenali, Matteo Cotta Ramusino, Luca Diamanti, Brigida Minafra, Giulia Perini, Roberta Zangaglia, Alfredo Costa, Mauro Ceroni, Nora I. Perrone‐Bizzozero, Raffaele Calogero, Cristina Cereda
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22073531

Differential Response of Grapevine to Infection with ‘Candidatus Phytoplasma solani’ in Early and Late Growing Season through Complex Regulation of mRNA and Small RNA Transcriptomes
Cited by: 10
Author(s): Marina Dermastia, Blaž Škrlj, Rebeka Strah, Barbara Anžič, Špela Tomaž, Maja Križnik, Christina Schönhuber, Monika Riedle‐Bauer, Živa Ramšak, Marko Petek, Aleš Kladnik, Nada Lavrač, Kristina Gruden, Thomas Roitsch, Günter Brader, Maruša Pompe-Novak
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22083896

Prolyl 3-Hydroxylase 2 Is a Molecular Player of Angiogenesis
Cited by: 1
Author(s): Paola Pignata, Ivana Apicella, Valeria Cicatiello, Caterina Puglisi, Sara Magliacane Trotta, Remo Sanges, Valeria Tarallo, Sandro De Falco
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22084204

Multi–Omics Analysis of Key microRNA–mRNA Metabolic Regulatory Networks in Skeletal Muscle of Obese Rabbits
Cited by: 6
Author(s): Yanhong Li, Jie Wang, Mauricio A. Elzo, Mingchuan Gan, Tao Tang, Jiahao Shao, Tianfu Lai, Yuan Ma, Xianbo Jia, Songjia Lai
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22084290

Out-of-Field Hippocampus from Partial-Body Irradiated Mice Displays Changes in Multi-Omics Profile and Defects in Neurogenesis
Cited by: 3
Author(s): Simonetta Pazzaglia, Barbara Tanno, Francesca Antonelli, Paola Giardullo, Gabriele Babini, Prabal Subedi, Omid Azimzadeh, Zohaib Nisar Khan, Kateryna Oleksenko, Fabian Metzger, Christine von Toerne, Damien Traynor, Dinesh Medipally, Aidan D. Meade, Munira Kadhim, Fiona M. Lyng, Soile Tapio, Anna Saran, Mariateresa Mancuso
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22094372

Single Cell Gene Expression Analysis in a 3D Microtissue Liver Model Reveals Cell Type-Specific Responses to Pro-Fibrotic TGF-β1 Stimulation
Cited by: 4
Author(s): Catherine Jane Messner, Lmar Babrak, Gaia Titolo, Michaela Caj, Enkelejda Miho, Laura Suter‐Dick
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22094414

Integrative Analysis of Transcriptome and Metabolome Reveals Salt Stress Orchestrating the Accumulation of Specialized Metabolites in Lycium barbarum L. Fruit
Cited by: 10
Author(s): Shuang Lin, Shaohua Zeng, A Biao, Xiaoman Yang, Tianshun Yang, Guodi Zheng, Guilian Mao, Ying Wang
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22095031

Candida Administration in Bilateral Nephrectomy Mice Elevates Serum (1→3)-β-D-glucan That Enhances Systemic Inflammation Through Energy Augmentation in Macrophages
Cited by: 21
Author(s): Jiraphorn Issara-Amphorn, Cong Phi Dang, Wilasinee Saisorn, Kavee Limbutara, Asada Leelahavanichkul
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22126537

Expression Profiling and Bioinformatics Analysis of CircRNA in Mice Brain Infected with Rabies Virus
Cited by: 8
Author(s): Wen Zhao, Jingyin Su, Ningning Wang, Naiyu Zhao, Shuo Su
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22137164

Transcriptional Modulation of the Hippo Signaling Pathway by Drugs Used to Treat Bipolar Disorder and Schizophrenia
Cited by: 9
Author(s): Bruna Panizzutti, Chiara C. Bortolasci, Briana Spolding, Srisaiyini Kidnapillai, Timothy Connor, Mark F. Richardson, Trang T. T. Truong, Zoe Liu, Gerwyn Morris, Laura J. Gray, Jee Hyun Kim, Olivia Dean, Michael Berk, Ken Walder
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22147537

Genome-Wide Identification and Analysis of the Polycomb Group Family in Medicago truncatula
Cited by: 4
Author(s): Yuanyuan Zhao, Junchao Zhang, Zhanmin Sun, Yixiong Tang, Yihan Wu
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22147508

4-Acetyl-Antroquinonol B Improves the Sensitization of Cetuximab on Both Kras Mutant and Wild Type Colorectal Cancer by Modulating the Expression of Ras/Raf/miR-193a-3p Signaling Axis
Cited by: 7
Author(s): Yi Cheng Chu, Tung Yao Tsai, Vijesh Kumar Yadav, Li Deng, Chun Chih Huang, Yew Min Tzeng, Chi Tai Yeh, Ming‐Yao Chen
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22157905

Transcriptomic Analysis of the Photosynthetic, Respiration, and Aerenchyma Adaptation Strategies in Bermudagrass (Cynodon dactylon) under Different Submergence Stress
Cited by: 15
Author(s): Zuoqiang Yuan, Xilu Ni, Muhammad Arif, Dong Zhi, Limiao Zhang, Xue Tan, Jiajia Li, Changxiao Li
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22158009

Prenatal Trimethyltin Exposure Induces Long-Term DNA Methylation Changes in the Male Mouse Hippocampus
Cited by: 4
Author(s): Soon-Ae Kim, Chai Junghoon, Eun-Hye Jang
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22168585

Overexpression of ERAP2N in Human Trophoblast Cells Promotes Cell Death
Cited by: 4
Author(s): Kristen Lospinoso, Mikhail G. Dozmorov, Nadine El Fawal, Rhea Raghu, Wook‐Jin Chae, Eun D. Lee
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms22168634

Epidermal PPARγ Is a Key Homeostatic Regulator of Cutaneous Inflammation and Barrier Function in Mouse Skin
Cited by: 2
Author(s): Raymond L. Konger, Ethel Derr‐Yellin, Teresa A. Zimmers, Terrence M. Katona, Xiaoling Xuei, Yunlong Liu, Hongming Zhou, Edward Simpson, Matthew J. Turner
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms22179255

Evidence for the Role of CYP51A and Xenobiotic Detoxification in Differential Sensitivity to Azole Fungicides in Boxwood Blight Pathogens
Cited by: 1
Author(s): Stefanos Stravoravdis, Robert E. Marra, Nicholas LeBlanc, Jo Anne Crouch, Jonathan P. Hulvey
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms22179222

Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants
Cited by: 6
Author(s): Silvia M. Velasquez, Xiaoyuan Guo, Marçal Gallemí, Bibek Aryal, Peter Venhuizen, Elke Barbez, Kai Dünser, Martin Darino, Aleš Pěnčík, Ondřej Novák, Maria Kalyna, Grégory Mouille, Eva Benková, Rishikesh P. Bhalerao, Jozef Mravec, Jürgen Kleine‐Vehn
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms22189877

Genome-Wide Mapping of Cytosine Methylation Revealed Dynamic DNA Methylation Patterns Associated with Sporophyte Development of Saccharina japonica
Cited by: 3
Author(s): Xiaoqi Yang, Xiuliang Wang, Jianting Yao, Delin Duan
Software Mentions: 2
Published: about 5 years ago

10.2196/18387

Personal Health Information Inference Using Machine Learning on RNA Expression Data from Patients With Cancer: Algorithm Validation Study
Cited by: 4
Author(s): Solbi Kweon, Jeong Hoon Lee, Younghee Lee, Yu Rang Park
Software Mentions: 2
Published: about 6 years ago

10.1186/s12951-021-00923-3

Single-cell RNA sequencing reveals the mechanism of sonodynamic therapy combined with a RAS inhibitor in the setting of hepatocellular carcinoma
Cited by: 15
Author(s): Bolin Wu, Yanchi Yuan, Jiayin Liu, Haitao Shang, Jing Dong, Xitian Liang, Dongxu Wang, Yi-Chi Chen, Chunyue Wang, Yang Zhou, Hui Jing, Wen Cheng
Software Mentions: 2
Published: over 5 years ago

10.1186/s12951-018-0439-x

Tri-mannose grafting of chitosan nanocarriers remodels the macrophage response to bacterial infection
Cited by: 15
Author(s): Juan Manuel Coya, Laura De Matteis, Alexandre Giraud-Gatineau, Anne Biton, Inés Serrano‐Sevilla, Anne Danckært, Marie‐Agnès Dillies, Brigitte Gicquel, Jesús M. de la Fuente, Ludovic Tailleux
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12951-020-00591-9

Proteome interrogation using gold nanoprobes to identify targets of arctigenin in fish parasites
Cited by: 7
Author(s): Xiao Tu, Xiaoping Tan, Xiaozhou Qi, Aiguo Huang, Fei Ling, Gao‐Xue Wang
Software Mentions: 2
Published: over 6 years ago

10.1007/s11418-018-1270-2

Identification of potential genes involved in triterpenoid saponins biosynthesis in Gleditsia sinensis by transcriptome and metabolome analyses
Cited by: 11
Author(s): Yusuke Kuwahara, D. Nakajima, Sayaka Shinpo, Michimi Nakamura, Noriaki Kawano, Nobuo Kawahara, Mami Yamazaki, Kazuki Saito, Hideyuki Suzuki, Hideki Hirakawa
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12974-020-02026-6

Crosstalk between microglia and patient-derived glioblastoma cells inhibit invasion in a three-dimensional gelatin hydrogel model
Cited by: 17
Author(s): Jee Wei Emily Chen, Jan Lumibao, Sarah Leary, Jann N. Sarkaria, Andrew J. Steelman, H. Rex Gaskins, Brendan A.C. Harley
Software Mentions: 2
Published: almost 6 years ago

10.1523/JNEUROSCI.2571-18.2019

The Spinal Transcriptome after Cortical Stroke: In Search of Molecular Factors Regulating Spontaneous Recovery in the Spinal Cord
Cited by: 22
Author(s): Julia Kaiser, Martina A. Maibach, Iris Salpeter, Niels Hagenbuch, Vladimir B. C. de Souza, Mark D. Robinson, Martin E. Schwab
Software Mentions: 2
Published: over 7 years ago

10.1080/20002297.2019.1653124

Sex-specific differences in the salivary microbiome of caries-active children
Cited by: 24
Author(s): Stephanie Ortiz, Elisa Herrman, Claudia Lyashenko, Anne Purcell, Kareem Raslan, Brandon Khor, Michael Snow, Anna Forsyth, Dong‐Hee Choi, Tom Maier, Curtis A. Machida
Software Mentions: 2
Published: almost 8 years ago

10.1080/20002297.2019.1599670

Metatranscriptomic analysis of an in vitro biofilm model reveals strain-specific interactions among multiple bacterial species
Cited by: 15
Author(s): Yifei Zhang, Wenyu Shi, Yeqing Song, Jinfeng Wang
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13048-019-0494-4

Next-generation sequencing-based genomic profiling analysis reveals novel mutations for clinical diagnosis in Chinese primary epithelial ovarian cancer patients
Cited by: 26
Author(s): Lei Zhang, Min Luo, Hongjiang Yang, Shaoyan Zhu, Xianliang Cheng, Qing Chen
Software Mentions: 2
Published: over 7 years ago

10.1186/s13048-021-00828-7

The LINC00922 aggravates ovarian cancer progression via sponging miR-361-3p
Cited by: 9
Author(s): Liping Wang, Chen Ren, Yan Xu, Yang Li, Yannan Chen, Yuanhang Zhu
Software Mentions: 2
Published: over 5 years ago

10.18632/oncotarget.3731

Integrated genomic analyses identify frequent gene fusion events and VHL inactivation in gastrointestinal stromal tumors
Cited by: 26
Author(s): Gyu-Hong Kang, Hong Seok Yun, Chuanbowen Sun, Inho Park, Seungmook Lee, Jekeun Kwon, In‐Gu Do, Min Eui Hong, Michael Van Vrancken, Jeeyun Lee, Joon Oh Park, Jeonghee Cho, Kyoung Mee Kim, Tae Sung Sohn
Software Mentions: 2
Published: over 11 years ago

10.18632/oncotarget.7781

Identification of a six microRNA signature as a novel potential prognostic biomarker in patients with head and neck squamous cell carcinoma
Cited by: 27
Author(s): Hao Shi, Jian Chen, Yuncheng Li, Guojun Li, Rong Zhong, Dandan Du, Mengqi Wang, Weijia Kong, Meixia Lü
Software Mentions: 2
Published: over 10 years ago

10.18632/oncotarget.8124

Non-invasive prostate cancer detection by measuring miRNA variants (isomiRs) in urine extracellular vesicles
Cited by: 108
Author(s): Danijela Koppers-Lalić, Michael Hackenberg, Renée X. de Menezes, Branislav Mišovic, Magda Wąchalska, Albert A. Geldof, Nicoletta Zini, Theo de Reijke, Thomas Würdinger, Andrè N. Vis, Jeroen van Moorselaar, D. Michiel Pegtel, Irene V. Bijnsdorp
Software Mentions: 2
Published: over 10 years ago

10.3390/ijms22063156

Megalocytivirus Induces Complicated Fish Immune Response at Multiple RNA Levels Involving mRNA, miRNA, and circRNA
Cited by: 11
Author(s): Qian Wu, Xianhui Ning, Li Sun
Software Mentions: 1
Published: over 5 years ago

10.3389/fphys.2019.00631

Mixed Diets Reduce the Oxidative Stress of Common Carp (Cyprinus carpio): Based on MicroRNA Sequencing
Cited by: 9
Author(s): Song Yang, Jie Luo, Yalan Long, Jie Du, Gaosi Xu, Zongjun Du, Wei Luo, Yan Wang, Zhi He
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-19200-9

Maternal whole blood cell miRNA-340 is elevated in gestational diabetes and inversely regulated by glucose and insulin
Cited by: 37
Author(s): Laura Stirm, Peter Huypens, Steffen Sass, Richa Batra, Louise Fritsche, Sara Y. Brucker, Harald Abele, Anita M. Hennige, Fabian J. Theis, Johannes Beckers, Martin Hrabé de Angelis, Andreas Fritsche, Hans‐Ulrich Häring, Harald Staiger
Software Mentions: 1
Published: almost 9 years ago

10.1111/pbi.12960

Transgenic creeping bentgrass overexpressing Osa‐miR393a exhibits altered plant development and improved multiple stress tolerance
Cited by: 63
Author(s): Junlong Zhao, Shuangrong Yuan, Man Zhou, Nannan Yuan, Zhigang Li, Qian Hu, Frank Bethea, Haibo Liu, Shigui Li, Hong Luo
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-19837-6

Persistent activation of interlinked type 2 airway epithelial gene networks in sputum-derived cells from aeroallergen-sensitized symptomatic asthmatics
Cited by: 15
Author(s): Anya C. Jones, Niamh M. Troy, Elisha White, Elysia M. Hollams, Alexander M. Gout, Kak-Ming Ling, Anthony Kicic, Stephen M. Stick, Peter D. Sly, Patrick G. Holt, Graham L. Hall, Anthony Bosco
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-018-19954-2

Different milk diets have substantial effects on the jejunal mucosal immune system of pre-weaning calves, as demonstrated by whole transcriptome sequencing
Cited by: 18
Author(s): H.M. Hammon, D. Frieten, C. Gerbert, Christian Koch, G. Dusel, Rosemarie Weikard, Christa Kühn
Software Mentions: 1
Published: almost 9 years ago

10.3389/fphys.2021.687654

Airway Epithelial Cells Drive Airway Smooth Muscle Cell Phenotype Switching to the Proliferative and Pro-inflammatory Phenotype
Cited by: 6
Author(s): Michael J. O’Sullivan, Jinho Jang, Alice Panariti, Amina Bedrat, Gijs Ijpma, Bernardo Lemos, J. A. Park, Anne‐Marie Lauzon, James G. Martin
Software Mentions: 1
Published: over 5 years ago

10.1111/pbi.12754

Genomewide analysis of the lateral organ boundaries domain gene family in Eucalyptus grandis reveals members that differentially impact secondary growth
Cited by: 40
Author(s): Qiang Lu, Fenjuan Shao, Colleen MacMillan, Iain W. Wilson, Karen Van der Merwe, Steven G. Hussey, Alexander Andrew Myburg, Xiaomei Dong, Deyou Qiu
Software Mentions: 1
Published: over 9 years ago

10.3389/fphys.2017.00056

Increased Hemodynamic Load in Early Embryonic Stages Alters Endocardial to Mesenchymal Transition
Cited by: 27
Author(s): Madeline Midgett, Clàudia López, Larry L. David, Alina Maloyan, Sandra Rugonyi
Software Mentions: 1
Published: over 9 years ago

10.3389/fphys.2018.00429

Circulating miRNAs as Putative Biomarkers of Exercise Adaptation in Endurance Horses
Cited by: 9
Author(s): Katia Cappelli, Stefano Capomaccio, A. Viglino, Maurizio Silvestrelli, Francesca Beccati, Livia Moscati, Elisabetta Chiaradia
Software Mentions: 1
Published: over 8 years ago

10.1111/pbi.12913

Transcriptome reprogramming due to the introduction of a barley telosome into bread wheat affects more barley genes than wheat
Cited by: 27
Author(s): Elodie Rey, Michaël Abrouk, Gabriel Keeble‐Gagnère, Miroslava Karafiátová, Jan Vrána, Sandrine Balzergue, Ludivine Soubigou‐Taconnat, Véronique Brunaud, Marie‐Laure Martin‐Magniette, Takashi R. Endo, Jan Bartoš, R. Appels, Jaroslav Doležel
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-21525-4

Molecular characterization of colorectal adenomas with and without malignancy reveals distinguishing genome, transcriptome and methylome alterations
Cited by: 35
Author(s): Brooke R. Druliner, Panwen Wang, Taejeong Bae, Saurabh Baheti, Seth W. Slettedahl, Douglas W. Mahoney, Nikolaos Vasmatzis, Hang Xu, Min‐Soo Kim, Matthew A. Bockol, Daniel R. O’Brien, Diane E. Grill, Nathaniel D. Warner, Miguel Munoz-Gomez, Kimberlee Kossick, Ruth A. Johnson, Mohamad Mouchli, Donna Felmlee-Devine, Jill Washechek-Aletto, Thomas C. Smyrk, Ann L. Oberg, Junwen Wang, Nicholas Chia, Alexej Abyzov, David A. Ahlquist, Lisa A. Boardman
Software Mentions: 1
Published: over 8 years ago

10.3389/fphys.2016.00170

Gene Expression Changes during the Gummosis Development of Peach Shoots in Response to Lasiodiplodia theobromae Infection Using RNA-Seq
Cited by: 22
Author(s): Lei Gao, Yuting Wang, Zhi Li, He Zhang, Junli Ye, Guohuai Li
Software Mentions: 1
Published: over 10 years ago

10.3390/biomedicines9040388

Pharmacological Inhibition of WIP1 Sensitizes Acute Myeloid Leukemia Cells to the MDM2 Inhibitor Nutlin-3a
Cited by: 6
Author(s): Maria Chiara Fontana, Jacopo Nanni, Andrea Ghelli Luserna di Rorà, Elisabetta Petracci, Antonella Padella, Martina Ghetti, Anna Ferrari, Giovanni Marconi, Simona Soverini, Ilaria Iacobucci, Cristina Papayannidis, Antonio Curti, Ernesta Audisio, Maria Benedetta Giannini, Michela Rondoni, Francesco Lanza, Michèle Cavo, Giovanni Martinelli, Giorgia Simonetti
Software Mentions: 1
Published: over 5 years ago

10.1155/2017/4352450

The miRNA Expression Profile in Acute Myocardial Infarct Using Sheep Model with Left Ventricular Assist Device Unloading
Cited by: 4
Author(s): Xiaoqian Yan, Yu Gan, Haibo Chen, Guang-Mao Liu, Shengshou Hu, Jianye Zhou
Software Mentions: 1
Published: almost 10 years ago

10.1038/s41598-018-21371-4

Characterization of gene regulation and protein interaction networks for Matrin 3 encoding mutations linked to amyotrophic lateral sclerosis and myopathy
Cited by: 28
Author(s): María Carolina Gallego Iradi, Judy C. Triplett, James Thomas, Rachel Davila, Anthony M Crown, Hilda Brown, Jada Lewis, Maurice S. Swanson, Guilian Xu, Edgardo Rodríguez-Lebrón, David R. Borchelt
Software Mentions: 1
Published: over 8 years ago

10.3389/fphys.2020.579296

Extracellular Vesicles From High Glucose-Treated Podocytes Induce Apoptosis of Proximal Tubular Epithelial Cells
Cited by: 9
Author(s): Ying Huang, Ruizhao Li, Li Zhang, Yuanhan Chen, Wei Dong, Xingchen Zhao, Huan Yang, Shu Zhang, Zhiyong Xie, Zhiming Ye, Weidong Wang, Chunling Li, Zhilian Li, Shuangxin Liu, Zheng Dong, Xueqing Yu, Xinling Liang
Software Mentions: 1
Published: almost 6 years ago

10.3389/fphar.2021.647084

Research on the Species Difference of the Hepatotoxicity of Medicine Based on Transcriptome
Cited by: 11
Author(s): Ziying Xu, Qianjun Kang, Zihui Yu, Lichun Tian, Jingxuan Zhang, Ting Wang
Software Mentions: 1
Published: over 5 years ago

10.1007/s00425-020-03424-z

The identification of differentially expressed genes in male and female gametophytes of simple thalloid liverwort Pellia endiviifolia sp. B using an RNA-seq approach
Cited by: 3
Author(s): Izabela Sierocka, Sylwia Alaba, Artur Jarmołowski, Wojciech M. Karłowski, Zofia Szweykowska-Kulińska
Software Mentions: 1
Published: over 6 years ago

10.3389/fphar.2018.00619

Antibacterial Activity and Mechanism of Action of Aspidinol Against Multi-Drug-Resistant Methicillin-Resistant Staphylococcus aureus
Cited by: 24
Author(s): Xin Hua, Qin Yang, Wanjiang Zhang, Zhimin Dong, Shen-Ye Yu, Štefan Schwarz, Siguo Liu
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-23714-7

Vitamin C promotes apoptosis in breast cancer cells by increasing TRAIL expression
Cited by: 61
Author(s): David W. Sant, Sushmita Mustafi, Christopher B. Gustafson, Joshua Chen, Joyce M. Slingerland, Gaofeng Wang
Software Mentions: 1
Published: over 8 years ago

10.3389/fphar.2020.621054

HIF Prolyl Hydroxylase Inhibitors for COVID-19 Treatment: Pros and Cons
Cited by: 17
Author(s): Andrey Poloznikov, Stepan Nersisyan, Dmitry M. Hushpulian, Eliot H. Kazakov, Alexander G. Tonevitsky, С. В. Казаков, В.И. Вечорко, С. В. Никулин, J. A. Makarova, Irina G. Gazaryan
Software Mentions: 1
Published: almost 6 years ago

10.3389/fphar.2019.00150

Analysis of lncRNA-Mediated ceRNA Crosstalk and Identification of Prognostic Signature in Head and Neck Squamous Cell Carcinoma
Cited by: 27
Author(s): Yunbao Pan, Guohong Liu, Dujuan Wang, Yirong Li
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms22083882

Comparative Transcriptomes of the Body Wall of Wild and Farmed Sea Cucumber Isostichopus badionotus
Cited by: 2
Author(s): Roberto Martín‐Hernández, Rossanna Rodríguez-Canul, Nuvia Kantún-Moreno, Miguel A. Olvera‐Novoa, Óscar Medina-Contreras, Cristobal Garikoitz-Legarda, Juan Carlos Triviño, Jesús Alejandro Zamora‐Briseño, Víctor May-Solis, Alicia Poot-Salazar, Juan Antonio Pérez-Vega, Judit Gil-Zamorano, George Grant, Alberto Dávalos, Leticia Olivera‐Castillo
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-018-24284-4

Measurement of metabolite variations and analysis of related gene expression in Chinese liquorice (Glycyrrhiza uralensis) plants under UV-B irradiation
Cited by: 33
Author(s): Xiao Zhang, Xiaoli Ding, Yaxi Ji, Shouchuang Wang, Yingying Chen, Jie Luo, Yingbai Shen, Peng Li
Software Mentions: 1
Published: over 8 years ago

10.1186/s13048-021-00814-z

Plasma-derived exosomal miR-4732-5p is a promising noninvasive diagnostic biomarker for epithelial ovarian cancer
Cited by: 28
Author(s): Jingjing Liu, Ji Geun Yoo, Jung Ho, Yoon Young Jung, Sanha Lee, Soo Young Hur, Youn Jin Choi
Software Mentions: 1
Published: over 5 years ago

10.3389/fphar.2019.00986

Transcriptional Analysis of the Effects of Gambogic Acid and Neogambogic Acid on Methicillin-Resistant Staphylococcus aureus
Cited by: 13
Author(s): Xin Hua, Yue Jia, Qin Yang, Wanjiang Zhang, Zhimin Dong, Siguo Liu
Software Mentions: 1
Published: about 7 years ago

10.3389/fphar.2021.607379

17β-Estradiol Promotes Apoptosis of HepG2 Cells Caused by Oxidative Stress by Increasing Foxo3a Phosphorylation
Cited by: 5
Author(s): Yusheng Guo, Xiangsheng Cai, Hong-Yang Lu, Qiqi Li, Ying Zheng, Zefang Lin, Zexiong Cheng, Maoxiang Yang, Li Zhang, Lei Xiang, Xiaorong Yang
Software Mentions: 1
Published: over 5 years ago

10.3389/fphar.2020.529553

The Target MicroRNAs and Potential Underlying Mechanisms of Yiqi-Bushen-Tiaozhi Recipe against‐Non-Alcoholic Steatohepatitis
Cited by: 9
Author(s): Hong Wang, Songsong Li, Yan Cai, Tingting Zhang, Qingrou Yang, Beihui He, Jianshun Yu, Zhiyun Chen
Software Mentions: 1
Published: almost 6 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568