bioconductor: edgeR | Projects | Ecosyste.ms: Papers

10.1128/mSystems.01044-20

Simultaneous Presence of Bacteriochlorophyll and Xanthorhodopsin Genes in a Freshwater Bacterium
Cited by: 9
Author(s): Karel Kopejtka, Jürgen Tomasch, Yonghui Zeng, Vadim Selyanin, Marko Dachev, Kasia Piwosz, Martin Tichý, David Bína, Zdenko Gardian, Boyke Bunk, Henner Brinkmann, Robert Geffers, Rubén Sommaruga, Michal Koblížek
Software Mentions: 2
Published: over 5 years ago

10.1128/mSystems.00049-21

Characterization of the Blood and Cerebrospinal Fluid Microbiome in Children with Bacterial Meningitis and Its Potential Correlation with Inflammation
Cited by: 9
Author(s): Huiping Liao, Yuchao Zhang, Wei Guo, Xi Wang, Hailong Wang, Haocheng Ye, Kai Wu, Yuhang Zhang, Lingyun Guo, Yong Zhu, Yongli Guo, Landian Hu, Gang Liu, Xiangyin Kong
Software Mentions: 2
Published: about 5 years ago

10.1128/mSystems.01186-20

Anaerobic Sulfur Oxidation Underlies Adaptation of a Chemosynthetic Symbiont to Oxic-Anoxic Interfaces
Cited by: 9
Author(s): Gabriela F. Paredes, Tobias Viehboeck, Raymond Lee, Márton Palatinszky, Michaela A. Mausz, Siegfried Reipert, Arno Schintlmeister, Andreas Maier, Jean-Marie Volland, Claudia Hirschfeld, Michael Wagner, David Berry, Stephanie Markert, Silvia Bulgheresi, Lena König
Software Mentions: 2
Published: about 5 years ago

10.1007/s00439-020-02237-0

The relationship between the gut microbiome and host gene expression: a review
Cited by: 61
Author(s): Robert G. Nichols, Emily Davenport
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40246-018-0161-7

Computational analysis of mRNA expression profiling in the inner ear reveals candidate transcription factors associated with proliferation, differentiation, and deafness
Cited by: 9
Author(s): Kobi Perl, Ron Shamir, Karen B. Avraham
Software Mentions: 2
Published: about 8 years ago

10.7554/eLife.29815

Context-dependent deposition and regulation of mRNAs in P-bodies
Cited by: 58
Author(s): Congwei Wang, Fabian Schmich, Sumana Srivatsa, Julie Weidner, Niko Beerenwinkel, Anne Spang
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.07687

Distinct transcriptional responses elicited by unfolded nuclear or cytoplasmic protein in mammalian cells
Cited by: 20
Author(s): Yusuke Miyazaki, Ling-chun Chen, Bernard Chu, Tomek Swigut, Thomas J. Wandless
Software Mentions: 2
Published: about 11 years ago

10.7554/eLife.30506

Chromatin accessibility underlies synthetic lethality of SWI/SNF subunits in ARID1A-mutant cancers
Cited by: 121
Author(s): Timothy W. R. Kelso, Devin K. Porter, Maria Luisa Amaral, Maxim N. Shokhirev, Chris Benner, Diana C. Hargreaves
Software Mentions: 2
Published: almost 9 years ago

10.7554/eLife.62232

Failures of nerve regeneration caused by aging or chronic denervation are rescued by restoring Schwann cell c-Jun
Cited by: 54
Author(s): Laura Wagstaff, Jose A. Gomez-Sanchez, Shaline V. Fazal, G. Otto, Alastair M. Kilpatrick, Kirolos Michael, Liam Y.N. Wong, Ki H., Mark Turmaine, John Svaren, Tessa Gordon, Peter Arthur‐Farraj, Sergio Velasco-Avilés, Hugo Cabedo, Cristina Benito, Rhona Mirsky, Kristján R. Jessen
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.56883

KDM5A mutations identified in autism spectrum disorder using forward genetics
Cited by: 23
Author(s): Lauretta El Hayek, İslam Oğuz Tuncay, Nadine Nijem, Jamie L. Russell, Sara Ludwig, Kiran Kaur, Xiaohong Li, Priscilla Anderton, Miao Tang, Amanda Gerard, Anja Heinze, Pia Zacher, Hessa S. Alsaif, Abolfazl Rad, Kazem Hassanpour, Mohammad Reza Abbaszadegan, Camerun Washington, Barbara R. DuPont, Raymond J. Louie, Causes Study, Madeline Couse, Maha Faden, R. Curtis Rogers, Rami Abou Jamra, Ellen Roy Elias, Reza Maroofian, Henry Houlden, Anna Lehman, Bruce Beutler, Maria H. Chahrour
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.52558

Mitochondrial pyruvate carrier is required for optimal brown fat thermogenesis
Cited by: 41
Author(s): Vanja Panic, Stephanie Pearson, James Banks, Trevor S. Tippetts, Jesse N. Velasco-Silva, Sanghoon Lee, Judith Simcox, Gisela Geoghegan, Claire Bensard, Tyler Van Ry, Will L Holland, Scott A. Summers, James E. Cox, Gregory S. Ducker, Jared Rutter, Claudio J. Villanueva
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.00473

Accurate timekeeping is controlled by a cycling activator in Arabidopsis
Cited by: 160
Author(s): Polly Yingshan Hsu, Upendra Kumar Devisetty, Stacey L. Harmer
Software Mentions: 2
Published: over 13 years ago

10.7554/eLife.61630

Loss of FLCN-FNIP1/2 induces a non-canonical interferon response in human renal tubular epithelial cells
Cited by: 11
Author(s): Iris E. Glykofridis, Jaco C. Knol, Jesper A. Balk, Denise Westland, Thang V. Pham, Sander R. Piersma, Sinéad M. Lougheed, Sepide Derakhshan, Puck Veen, Martin A. Rooimans, Saskia E. van Mil, Franziska Böttger, Pino J. Poddighe, Irma van de Beek, Jarno Drost, Fried Zwartkruis, Renée X. de Menezes, Hanne Meijers-Heijboer, Arjan C. Houweling, Connie R. Jiménez, Rob M. F. Wolthuis
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.58641

Optogenetic investigation of BMP target gene expression diversity
Cited by: 29
Author(s): Katherine W. Rogers, Mohammad ElGamacy, Benjamin M Jordan, Patrick Müller
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.07378

Mitotic fidelity requires transgenerational action of a testis-restricted HP1
Cited by: 16
Author(s): Mia T. Levine, Helen Vander Wende, Harmit S. Malik
Software Mentions: 2
Published: about 11 years ago

10.7554/eLife.66050

Multiplexed mRNA assembly into ribonucleoprotein particles plays an operon-like role in the control of yeast cell physiology
Cited by: 14
Author(s): Rohini R. Nair, Dmitry Zabezhinsky, Rita Gelin-Licht, Brian J. Haas, Michael Ca Dyhr, Hannah Sabeth Sperber, Chad Nusbaum, Jeffrey E. Gerst
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.30918

The somatically generated portion of T cell receptor CDR3α contributes to the MHC allele specificity of the T cell receptor
Cited by: 17
Author(s): Philippa Marrack, S. Harsha Krovi, Daniel Silberman, Janicé White, Eleanor Kushnir, Maki Nakayama, J. Crooks, Thomas Danhorn, Sonia M. Leach, Randy Anselment, James Scott‐Browne, Laurent Gapin, John W. Kappler
Software Mentions: 2
Published: almost 9 years ago

10.7554/eLife.48448

Neutrophils promote CXCR3-dependent itch in the development of atopic dermatitis
Cited by: 74
Author(s): Carolyn M. Walsh, Rose Z. Hill, Jamie Schwendinger-Schreck, Jacques Deguine, Emily C. Brock, Natalie Kucirek, Ziad Rifi, Jessica Wei, Karsten Gronert, Rachel B. Brem, Gregory M. Barton, Diana M. Bautista
Software Mentions: 2
Published: almost 7 years ago

10.7554/eLife.32496

Codon usage bias controls mRNA and protein abundance in trypanosomatids
Cited by: 72
Author(s): Laura Jeacock, Joana Faria, David Horn
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.27192

Extensive alternative splicing transitions during postnatal skeletal muscle development are required for calcium handling functions
Cited by: 56
Author(s): Amy E. Brinegar, Zheng Xia, James A. Loehr, Wei Li, George G. Rodney, Thomas A. Cooper
Software Mentions: 2
Published: about 9 years ago

10.7554/eLife.39381

Zygotic gene activation in the chicken occurs in two waves, the first involving only maternally derived genes
Cited by: 12
Author(s): Young Sun Hwang, Minseok Seo, Sang Kyung Kim, Sohyun Bang, Heebal Kim, Jae Yong Han
Software Mentions: 2
Published: almost 8 years ago

10.7554/eLife.39030

Targeting MYC dependency in ovarian cancer through inhibition of CDK7 and CDK12/13
Cited by: 101
Author(s): Mei Zeng, Nicholas Kwiatkowski, Tinghu Zhang, Behnam Nabet, Mousheng Xu, Yanke Liang, Chunshan Quan, Jinhua Wang, Mingfeng Hao, Sangeetha Palakurthi, Shan Zhou, Qing Zeng, Paul Kirschmeier, Khyati Meghani, Alan L. Leggett, Jun Qi, Geoffrey I. Shapiro, Joyce F. Liu, Ursula A. Matulonis, Charles Y. Lin, Panagiotis A. Konstantinopoulos, Nathanael S. Gray
Software Mentions: 2
Published: almost 8 years ago

10.7554/eLife.70557

3′HS1 CTCF binding site in human β-globin locus regulates fetal hemoglobin expression
Cited by: 5
Author(s): Pamela Himadewi, Xue Qing David Wang, Fan Feng, Haley Gore, Yushuai Liu, Li Yu, Ryo Kurita, Yukio Nakamura, Gerd P. Pfeifer, Jie Liu, Xiaotian Zhang
Software Mentions: 2
Published: almost 5 years ago

10.7554/eLife.46793

Genetic interactions of G-quadruplexes in humans
Cited by: 83
Author(s): Katherine G. Zyner, Darcie S Mulhearn, Santosh Adhikari, Sergio Martínez Cuesta, Marco Di Antonio, Nicolas Erard, Gregory J. Hannon, David Tannahill, Shankar Balasubramanian
Software Mentions: 2
Published: about 7 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: almost 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: almost 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: over 5 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: over 5 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: over 5 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: about 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: about 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: about 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: about 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: about 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: about 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: almost 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: about 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: over 7 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: over 7 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: over 7 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: over 7 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: about 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

10.1155/2019/4010764

LncRNA LEGLTBC Functions as a ceRNA to Antagonize the Effects of miR-34a on the Downregulation of SIRT1 in Glucolipotoxicity-Induced INS-1 Beta Cell Oxidative Stress and Apoptosis
Cited by: 26
Author(s): Kuanhui Xiang, Chongxiao Liu, Guodong Wang, Hui Yang, Xin-ming Yao, Qiang Hua, Xiaoyong Li, Hongmei Zhang, M. Anthony Moody, Qing Su, Kun Lv
Software Mentions: 2
Published: almost 7 years ago

10.1155/2019/3829342

RNA Expression Profile and Alternative Splicing Signatures of Genistein-Treated Breeder Hens Revealed by Hepatic Transcriptomic Analysis
Cited by: 3
Author(s): Fangxiong Shi, Jingle Jiang, Chao Ning, Hongjian Dai, Jihyun Song, Xie Wei, Debing Yu, Fangxiong Shi
Software Mentions: 2
Published: almost 7 years ago

10.1155/2021/8049079

Yixin-Shu Capsules Ameliorated Ischemia-Induced Heart Failure by Restoring Trx2 and Inhibiting JNK/p38 Activation
Cited by: 4
Author(s): Changpei Xiang, Fangbo Zhang, Jinhuan Gao, Feifei Guo, Mao Zhang, Rui Zhou, Junying Wei, Ping Wang, Yi Zhang, Jingjing Zhang, Hongjun Yang
Software Mentions: 2
Published: over 5 years ago

10.1155/2021/9978206

Prognostic Nomogram Based on Circular RNA-Associated Competing Endogenous RNA Network for Patients with Lung Adenocarcinoma
Cited by: 7
Author(s): Yang Li, Ryan Sun, Rui Li, Yonggang Chen, Du He
Software Mentions: 2
Published: about 5 years ago

10.1523/ENEURO.0475-18.2019

Molecular Profiling Defines Evolutionarily Conserved Transcription Factor Signatures of Major Vestibulospinal Neuron Groups
Cited by: 19
Author(s): Anders Lunde, Benjamin W. Okaty, Susan M. Dymecki, Joel C. Glover
Software Mentions: 2
Published: over 7 years ago

10.1523/ENEURO.0397-19.2019

Identification of a Sacral, Visceral Sensory Transcriptome in Embryonic and Adult Mice
Cited by: 18
Author(s): Casey J. A. Smith-Anttila, Elizabeth A. Mason, Christine Wells, Bruce J. Aronow, Peregrine B. Osborne, Janet R. Keast
Software Mentions: 2
Published: over 6 years ago

10.1186/s12986-019-0339-6

Dietary iron interacts with genetic background to influence glucose homeostasis
Cited by: 7
Author(s): Mario A. Miranda, Celine L. St. Pierre, Juan F Macias-Velasco, Harrison P. Nguyen, Heather Schmidt, Lucian T. Agnello, Jessica P Wayhart, Heather A. Lawson
Software Mentions: 2
Published: over 7 years ago

10.3390/nu11061347

Chrysanthemum Leaf Ethanol Extract Prevents Obesity and Metabolic Disease in Diet-Induced Obese Mice via Lipid Mobilization in White Adipose Tissue
Cited by: 11
Author(s): Ri Ryu, Eun‐Young Kwon, Jiyoung Choi, Jong Cheol Shon, Kwang-Hyeon Liu, Myung‐Sook Choi
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pgen.1004845

Association Mapping across Numerous Traits Reveals Patterns of Functional Variation in Maize
Cited by: 172
Author(s): Jason G. Wallace, Peter J. Bradbury, Nengyi Zhang, Yves Gibon, Mark Stitt, Edward S. Buckler
Software Mentions: 1
Published: almost 12 years ago

10.1534/g3.114.010744

Fighting a Losing Battle: Vigorous Immune Response Countered by Pathogen Suppression of Host Defenses in the Chytridiomycosis-Susceptible FrogAtelopus zeteki
Cited by: 90
Author(s): Amy Ellison, Anna E. Savage, Graziella V. DiRenzo, Penny F. Langhammer, Karen R. Lips, Kelly R. Zamudio
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pgen.1005959

MicroProtein-Mediated Recruitment of CONSTANS into a TOPLESS Trimeric Complex Represses Flowering in Arabidopsis
Cited by: 116
Author(s): Moritz Graeff, Daniel Straub, Tenai Eguen, Ulla Dolde, Vandasue Rodrigues, Ronny Brandt, Stephan Wenkel
Software Mentions: 1
Published: over 10 years ago

10.1534/g3.114.010553

Rapid Evolution of Phenotypic Plasticity and Shifting Thresholds of Genetic Assimilation in the NematodeCaenorhabditis remanei
Cited by: 65
Author(s): Kristin L. Sikkink, Rose M. Reynolds, Catherine M. Ituarte, William A. Cresko, Patrick C. Phillips
Software Mentions: 1
Published: over 12 years ago

10.1534/g3.112.004119

Identification of Gene Expression Changes Associated With Long-Term Memory of Courtship Rejection in Drosophila Males
Cited by: 28
Author(s): Ari Winbush, Danielle R. Reed, Peter L. Chang, Sergey V. Nuzhdin, Lisa C. Lyons, Michelle N. Arbeitman
Software Mentions: 1
Published: almost 14 years ago

10.1007/s10142-019-00708-w

Comparative analysis of integument transcriptomes identifies genes that participate in marking pattern formation in three allelic mutants of silkworm, Bombyx mori
Cited by: 0
Author(s): Xin Ding, Junxia Liu, Xiaoling Tong, Songyuan Wu, Chunlin Li, Jun‐Ho Song, Hai Hu, Tan D, Fangyin Dai
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-020-74594-9

Involvement of neutrophils in machineries underlying the rupture of intracranial aneurysms in rats
Cited by: 19
Author(s): Mika Kushamae, Haruka Miyata, Makoto Shirai, Kampei Shimizu, Mieko Oka, Hirokazu Koseki, Yu Abekura, Isao Ono, Kazuhiko Nozaki, Tohru Mizutani, Tomohiro Aoki
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12983-020-00356-y

Transcriptome analysis of the response provided by Lasiopodomys mandarinus to severe hypoxia includes enhancing DNA repair and damage prevention
Cited by: 10
Author(s): Qianqian Dong, Zishi Wang, Mengwan Jiang, Hong Sun, Xuqin Wang, Yangwei Li, Yifeng Zhang, Han Cheng, Yurong Chai, Tian Shao, Luye Shi, Zhenlong Wang
Software Mentions: 1
Published: over 6 years ago

10.3389/fvets.2018.00231

Adrenocortical Challenge Response and Genomic Analyses in Scottish Terriers With Increased Alkaline Phosphate Activity
Cited by: 5
Author(s): Kurt Zimmerman, David L. Panciera, Ina Hoeschele, William E. Monroe, S. Michelle Todd, Stephen R. Werre, Tanya LeRoith, Kellie Fecteau, Bathilda B. Lake
Software Mentions: 1
Published: almost 8 years ago

10.3390/ijms22115877

The miR-106b/NR2F2-AS1/PLEKHO2 Axis Regulates Migration and Invasion of Colorectal Cancer through the MAPK Pathway
Cited by: 4
Author(s): Shuzhen Liu, Guoyan An, Qing Cao, Tong Li, Xinyu Jia, Lei Lei
Software Mentions: 1
Published: over 5 years ago

10.3389/fvets.2021.647153

Integrating miRNA and mRNA Profiling to Assess the Potential miRNA–mRNA Modules Linked With Testicular Immune Homeostasis in Sheep
Cited by: 4
Author(s): Taotao Li, Xia Wang, Ruirui Luo, Xiaopeng An, Yong Zhang, Xingxu Zhao, Youji Ma
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-77177-w

Transcriptome analyses reveals the dynamic nature of oil accumulation during seed development of Plukenetia volubilis L.
Cited by: 6
Author(s): Lu Guo, Zhihua Wu, Peng Yan, Xiuhua Shang, Yi Xie, R. J. Arnold
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-77598-7

Functional characterisation of the transcriptome from leaf tissue of the fluoroacetate-producing plant, Dichapetalum cymosum, in response to mechanical wounding
Cited by: 7
Author(s): Selisha A. Sooklal, Phelelani T. Mpangase, Mihai-Silviu Tomescu, Shaun Aron, Scott Hazelhurst, Robert H. Archer, Karl Rumbold
Software Mentions: 1
Published: almost 6 years ago

10.3389/fpls.2015.00062

Mango (Mangifera indica L.) cv. Kent fruit mesocarp de novo transcriptome assembly identifies gene families important for ripening
Cited by: 52
Author(s): Mitzuko Dautt-Castro, Adrián Ochoa-Leyva, Carmen A. Contreras-Vergara, Magda A. Pacheco-Sánchez, Sergio Casas-Flores, Alejandro Sánchez-Flores, David N. Kuhn, María A. Islas-Osuna
Software Mentions: 1
Published: over 11 years ago

10.3389/fpls.2020.592603

Zucchini Plants Alter Gene Expression and Emission of (E)-β-Caryophyllene Following Aphis gossypii Infestation
Cited by: 7
Author(s): Alessia Vitiello, Donata Molisso, M. Cristina Digilio, Massimo Giorgini, Giuseppe Colla, T. J. A. Bruce, Nunzio D’Agostino, Rosa Rao
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-77293-7

Comparative transcriptome analysis implied a ZEP paralog was a key gene involved in carotenoid accumulation in yellow-fleshed sweetpotato
Cited by: 13
Author(s): Koichi Suematsu, Masaru Tanaka, Rie Kurata, Kai Yu
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms22115959

Nuclear Magnetic Resonance Therapy Modulates the miRNA Profile in Human Primary OA Chondrocytes and Antagonizes Inflammation in Tc28/2a Cells
Cited by: 4
Author(s): Bibiane Steinecker-Frohnwieser, Birgit Lohberger, Nicole Eck, Anda Mann, Cornelia Kratschmann, Andreas Leithner, W. Kullich, Lukas Weigl
Software Mentions: 1
Published: over 5 years ago

10.3389/fpls.2020.00526

MADS-Box and bHLH Transcription Factors Coordinate Transmitting Tract Development in Arabidopsis thaliana
Cited by: 20
Author(s): Maurizio Di Marzo, Irma Roig‐Villanova, Eva Zanchetti, Francesca Caselli, Veronica Gregis, Paola Bardetti, Matteo Chiara, Andrea Guazzotti, Elisabetta Caporali, Marta Adelina Mendes, Lucia Colombo, Martin M. Kater
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-78976-x

Early pregnancy maternal progesterone administration alters pituitary and testis function and steroid profile in male fetuses
Cited by: 13
Author(s): Katarzyna Siemienowicz, Yili Wang, Magda Marečková, Junko Nio‐Kobayashi, Paul A. Fowler, Michael T. Rae, W. Colin Duncan
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-78781-6

Identifying transcription factors that reduce wood recalcitrance and improve enzymatic degradation of xylem cell wall in Populus
Cited by: 6
Author(s): Chiaki Hori, Naoki Takata, Pui Ying Lam, Yuki Tobimatsu, Soichiro Nagano, Jenny C. Mortimer, Dan Cullen
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22116013

Epithelial Regeneration Ability of Crohn’s Disease Assessed Using Patient-Derived Intestinal Organoids
Cited by: 12
Author(s): Chansu Lee, Sung Noh Hong, Eun Ran Kim, Dong Kyung Chang, Young‐Ho Kim
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1003675

Loss of a Conserved tRNA Anticodon Modification Perturbs Cellular Signaling
Cited by: 184
Author(s): Boris Zinshteyn, Wendy V. Gilbert
Software Mentions: 1
Published: about 13 years ago

10.3389/fpls.2016.00963

Transcriptome Profiling of Light-Regulated Anthocyanin Biosynthesis in the Pericarp of Litchi
Cited by: 43
Author(s): Hongna Zhang, Weicai Li, Huicong Wang, Shengyou Shi, Bo Shu, Liqin Liu, Yongzan Wei
Software Mentions: 1
Published: about 10 years ago

10.3389/fpls.2017.00317

Transcriptome Changes Associated with Boron Deficiency in Leaves of Two Citrus Scion-Rootstock Combinations
Cited by: 12
Author(s): Xiao Liu, Jiawei Zhang, Ling-Xia Guo, Yong-Zhong Liu, Long-Fei Jin, Syed Bilal Hussain, Wei Du, Zhao Deng, Shuang Peng
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-020-80837-6

Transcriptome and phytochemical analyses provide insights into the organic sulfur pathway in Allium hirtifolium
Cited by: 6
Author(s): Aboozar Soorni, Amir Mohammad Akrami, Reza Abolghasemi, Maryam Vahedi
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-80280-7

Comparative transcriptome analysis reveals resistant and susceptible genes in tobacco cultivars in response to infection by Phytophthora nicotianae
Cited by: 15
Author(s): He Meng, Mingming Sun, Zipeng Jiang, Yutong Liu, Yu Sun, Dan Liŭ, Caihong Jiang, Min Ren, Guangdi Yuan, Wenlong Yu, Qi Sheng Feng, Aiguo Yang, Lei Cheng, Yuanying Wang
Software Mentions: 1
Published: over 5 years ago

10.3389/fpls.2015.01179

Transcriptomic Analysis Reveals Key Genes Related to Betalain Biosynthesis in Pulp Coloration of Hylocereus polyrhizus
Cited by: 36
Author(s): Qian Hua, Chengjie Chen, Zhe Chen, Pengkun Chen, Ma Ying, Jingyu Wu, Jian Zheng, Guibing Hu, Jietang Zhao, Yonghua Qin
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1005853

Common and Low Frequency Variants in MERTK Are Independently Associated with Multiple Sclerosis Susceptibility with Discordant Association Dependent upon HLA-DRB1*15:01 Status
Cited by: 29
Author(s): Michele D. Binder, Andrew Fox, Daniel Merlo, Laura Johnson, Lauren Giuffrida, Sarah E. Calvert, Rainer Akkermann, Z. M. Gerry, ANZgene, Ashwyn A Perera, Melissa Gresle, Louise Laverick, Grace M. Foo, Marzena J. Fabis-Pedrini, Timothy Spelman, Margaret A. Jordan, Alan G. Baxter, Simon J. Foote, Helmut Butzkueven, Trevor J. Kilpatrick, Judith Field
Software Mentions: 1
Published: over 10 years ago

10.3389/fpls.2021.713814

The Response of Grain Yield and Root Morphological and Physiological Traits to Nitrogen Levels in Paddy Rice
Cited by: 8
Author(s): Xin Wei, Hualong Liu, Hongwei Zhao, Jingguo Wang, Hongliang Zheng, Yan Jia, Liuqing Yang, Xinpeng Wang, Jiaming Li, Xianwei Li, Lei Lei, Detang Zou
Software Mentions: 1
Published: about 5 years ago

Projects: bioconductor: edgeR

Science Score: 100/100

Bonuses:

Papers Mentioning edgeR 6,568