bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.3389/fimmu.2019.00589

2D Visualization of the Psoriasis Transcriptome Fails to Support the Existence of Dual-Secreting IL-17A/IL-22 Th17 T Cells
Cited by: 9
Author(s): Stephanie Le, Alexander A. Merleev, Guillaume Luxardi, Michiko Shimoda, Iannis E. Adamopoulos, Lam C. Tsoi, Jenny Z. Wang, Claire Alexanian, S. P. Raychaudhuri, Samuel T Hwang, Jóhann E. Guðjónsson, Alina I. Marusina, Emanual Maverakis
Software Mentions: 2
Published: over 7 years ago

10.3389/fimmu.2021.639489

Transcriptional Profiles of Genes Related to Stress and Immune Response in Rainbow Trout (Oncorhynchus mykiss) Symptomatically or Asymptomatically Infected With Vibrio anguillarum
Cited by: 8
Author(s): Zhi-Shuai Hou, Yuan-Ru Xin, Xiaodong Yang, Chu Zeng, Hong-Kui Zhao, Meng-Qun Liu, Mei-Zhao Zhang, Jeffrey G. Daniel, Jifang Li, Haishen Wen
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-019-6344-3

Comparison of the molecular and cellular phenotypes of common mouse syngeneic models with human tumors
Cited by: 87
Author(s): Wenyan Zhong, Jeremy S. Myers, Fang Wang, Kai Wang, Justin Lucas, Edward Rosfjord, Judy Lucas, Andrea T. Hooper, Sharon Yang, Lu Anna Lemon, Magali Guffroy, Chad May, Jadwiga Bienkowska, Paul A. Rejto
Software Mentions: 2
Published: almost 7 years ago

10.1242/bio.048652

Perturbation of maternal PIASy abundance disrupts zygotic genome activation and embryonic development via SUMOylation pathway
Cited by: 12
Author(s): Chika Higuchi, Masanobu Yamamoto, Seung Wook Shin, Kazuaki Miyamoto, Kazuya Matsumoto
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0246063

Multi-tissue transcriptomic analysis reveals that L-methionine supplementation maintains the physiological homeostasis of broiler chickens than D-methionine under acute heat stress
Cited by: 2
Author(s): Mingyung Lee, Hyesun Park, Jung Min Heo, Hyun Joon Choi, Seongwon Seo
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0195102

Vertically distinct microbial communities in the Mariana and Kermadec trenches
Cited by: 55
Author(s): Logan M. Peoples, Sierra Donaldson, Oladayo Osuntokun, Qing Xia, Alex Nelson, Jessica M. Blanton, Eric E. Allen, Matthew J. Church, Douglas H. Bartlett
Software Mentions: 2
Published: over 8 years ago

10.3389/fimmu.2020.00453

Tissue-Specific Factors Differentially Regulate the Expression of Antigen-Processing Enzymes During Dendritic Cell Ontogeny
Cited by: 9
Author(s): Karim Mahiddine, Chervin Hassel, Claire Murat, Maeva Girard, Sylvie Guerder
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-021-07461-0

Analysis of temporal gene regulation of Listeria monocytogenes revealed distinct regulatory response modes after exposure to high pressure processing
Cited by: 4
Author(s): Bahareh Nikparvar, Margarita Andreevskaya, Ilhan Cem Duru, Florentina Ionela Bucur, Leontina Grigore‐Gurgu, Daniela Borda, Anca Ioana Nicolau, Christian U. Riedel, Petri Auvinen, Nadav Bar
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2020.01470

An RNA-seq Based Machine Learning Approach Identifies Latent Tuberculosis Patients With an Active Tuberculosis Profile
Cited by: 23
Author(s): Olivia Estévez, Luis Anibarro, Elina Garet, Ángeles Pallarés, Laura Barcia, Laura Calviño, Cremildo Maueia, Tufária Mussá, Florentino Fdez-Riverola, Daniel Glez-Peña, Miguel Reboiro-Jato, Hugo López-Fernández, Nuno A. Fonseca, Rajko Reljić, África González-Fernández
Software Mentions: 2
Published: over 6 years ago

10.3389/fimmu.2021.679184

RUVBL1/2 Complex Regulates Pro-Inflammatory Responses in Macrophages via Regulating Histone H3K4 Trimethylation
Cited by: 5
Author(s): Rui Zhang, Chris Cheung, Sang Uk Seo, Hang Liu, Lakhansing Pardeshi, Koon Ho Wong, Larry M. C. Chow, Mary P. Chau, Yixiang Wang, Ah Ra Lee, Woon Yong Kwon, Sheng Chen, Bill Kwan wai Chan, Kenneth Wong, Richard Choy, Ben C.B. Ko
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2019.00261

Aberrant Expressions of Co-stimulatory and Co-inhibitory Molecules in Autoimmune Diseases
Cited by: 11
Author(s): Wei He, Bin Wang, Qian Li, Qiuming Yao, Xi Jia, Ronghua Song, Sheli Li, Jinan Zhang
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-019-5454-2

Genome-wide characterization and expression profiling of SWEET genes in cabbage (Brassica oleracea var. capitata L.) reveal their roles in chilling and clubroot disease responses
Cited by: 43
Author(s): Wei Zhang, Shenyun Wang, Fangwei Yu, Jun Tang, Shibo Xi, Kan Bao, Li Yu, Hong Wang, Zhangjun Fei, Jianbin Li
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pgen.1006552

SBDS-Deficient Cells Have an Altered Homeostatic Equilibrium due to Translational Inefficiency Which Explains their Reduced Fitness and Provides a Logical Framework for Intervention
Cited by: 31
Author(s): Piera Calamita, Annarita Miluzio, Andrew F. Russo, Elisa Pesce, Sara Ricciardi, Farhat L. Khanim, Cristina Cheroni, Roberta Alfieri, Marilena Mancino, Chiara Gorrini, Grazisa Rossetti, Ilaria Peluso, Massimiliano Pagani, Diego L. Medina, Johanna M. Rommens, Stefano Biffo
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0250349

Genome-wide analysis of gibberellin-dioxygenases gene family and their responses to GA applications in maize
Cited by: 6
Author(s): Jiabin Ci, Xingyang Wang, Qi Wang, Fuxing Zhao, Wei Yang, Cui Xueyu, Lan Jiang, Xuejiao Ren, Weiguang Yang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-016-3110-7

Short- and long-term effects of 56Fe irradiation on cognition and hippocampal DNA methylation and gene expression
Cited by: 47
Author(s): Soren Impey, Timothy Jopson, Carl Pelz, Amanuel Tafessu, Fatema Fareh, Damian G. Zuloaga, Tessa Marzulla, Lara Kirstie Riparip, Blair Stewart, Susanna Rosi, Mitchell S. Turker, Jacob Raber
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0216120

Copy number variants in kiwifruit ETHYLENE RESPONSE FACTOR/APETALA2 (ERF/AP2)-like genes show divergence in fruit ripening associated cold and ethylene responses in C-REPEAT/DRE BINDING FACTOR-like genes
Cited by: 16
Author(s): Kularajathevan Gunaseelan, Peter A. McAtee, Simona Nardozza, P. Pidakala, Ruiling Wang, Karine David, J. Burdon, Robert J. Schaffer
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1009589

Transcriptomic characterization of cancer-testis antigens identifies MAGEA3 as a driver of tumor progression in hepatocellular carcinoma
Cited by: 9
Author(s): Amanda Craig, Teresa García‐Lezana, Marina Ruiz de Galarreta, Carlos Villacorta‐Martin, Edgar Kozlova, Sebastião N. Martins-Filho, Johann von Felden, Mehmet Eren Ahsen, Erin Bresnahan, Gabriela Hernandez-Meza, Ismaïl Labgaa, Delia D’Avola, Myron Schwartz, Josep M. Llovet, Daniela Sia, Swan N. Thung, Bojan Losic, Amaia Lujambio, Augusto Villanueva
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-021-07572-8

Genome-scale analyses of transcriptional start sites in Mycobacterium marinum under normoxic and hypoxic conditions
Cited by: 3
Author(s): Shuo Huang, Wei Zhou, Wei Tang, Yong Zhang, Yangbo Hu, Shiyun Chen
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2021.699633

IRF7-Associated Immunophenotypes Have Dichotomous Responses to Virus/Allergen Coexposure and OM-85-Induced Reprogramming
Cited by: 3
Author(s): Emma de Jong, Jean-François Lauzon-Joset, Jonatan Leffler, Michael Serralha, Alexander N. Larcombe, Claus T. Christophersen, Patrick G. Holt, Deborah H. Strickland, Anthony Bosco
Software Mentions: 2
Published: over 5 years ago

10.1063/5.0054639

High shear stress enhances endothelial permeability in the presence of the risk haplotype at 9p21.3
Cited by: 3
Author(s): Evan L. Teng, Evan Masutani, Benjamin Yeoman, Jessica Fung, Rachel Lian, Brenda Ngo, Aditya Kumar, Jesse K. Placone, Valentina Lo Sardo, Adam J. Engler
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2021.757231

Ubiquitin Ligases CBL and CBL-B Maintain the Homeostasis and Immune Quiescence of Dendritic Cells
Cited by: 2
Author(s): Haijun Tong, Xin Li, Jinping Zhang, Liying Gong, Weili Sun, Virginie Calderon, Xiaochen Zhang, Yue Li, Adeline Gadzinski, Wallace Y. Langdon, Boris Reizis, Yong-Rui Zou, Hua Gu
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0232994

GeneTEFlow: A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data
Cited by: 1
Author(s): Xiaochuan Liu, Jadwiga Bienkowska, Wenyan Zhong
Software Mentions: 2
Published: about 6 years ago

10.3389/fimmu.2021.690817

Impact of Interleukin 10 Deficiency on Intestinal Epithelium Responses to Inflammatory Signals
Cited by: 9
Author(s): Σταματια Παπουτσοπουλου, Liam Pollock, Catherine Walker, William D. Tench, Sakim Shakh Samad, François Bergey, Luca Lenzi, Raheleh Sheibani-Tezerji, P Rosenstiel, Mohammad Tauqeer Alam, Vítor A. P. Martins dos Santos, Werner Müller, Barry J. Campbell
Software Mentions: 2
Published: over 5 years ago

10.18632/aging.101747

Transcriptome analysis reveals immune-related gene expression changes with age in giant panda (Ailuropoda melanoleuca) blood
Cited by: 16
Author(s): Lianming Du, Qin Liu, Fang Shen, Zhenxin Fan, Rong Hou, Bisong Yue, Xiuyue Zhang
Software Mentions: 2
Published: almost 8 years ago

10.3389/fimmu.2020.559332

Polyunsaturated Fatty Acids Influence LPS-Induced Inflammation of Fish Macrophages Through Differential Modulation of Pathogen Recognition and p38 MAPK/NF-κB Signaling
Cited by: 14
Author(s): Qingfei Li, Kun Chen, Mengjiao Wu, Dan Xu, Kangsen Mai, Qinghui Ai
Software Mentions: 2
Published: about 6 years ago

10.3389/fimmu.2021.661437

Expression of Human Endogenous Retroviruses in Systemic Lupus Erythematosus: Multiomic Integration With Gene Expression
Cited by: 11
Author(s): Nathaniel Stearrett, Tyson Dawson, Ali Rahnavard, Prathyusha Bachali, Matthew L. Bendall, Chen Zeng, Roberto Caricchio, Marcos Pérez‐Losada, Amrie C. Grammer, Peter E. Lipsky, Keith A. Crandall
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-017-3986-x

Nutrient supply affects the mRNA expression profile of the porcine skeletal muscle
Cited by: 17
Author(s): Tainã Figueiredo Cardoso, Raquel Quintanilla, J. Tibau, Marta Gil, Emilio Mármol-Sánchez, Olga González‐Rodríguez, Rayner González-Prendes, Marcel Amills
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0194881

Variation in the microbiome of the urogenital tract of Chlamydia-free female koalas (Phascolarctos cinereus) with and without ‘wet bottom’
Cited by: 7
Author(s): Alistair R. Legione, Jemima Amery-Gale, Michael Lynch, Leesa Haynes, James R. Gilkerson, Fiona M. Sansom, Joanne M. Devlin
Software Mentions: 2
Published: over 8 years ago

10.3389/fimmu.2021.724662

Activated γδ T Cells With Higher CD107a Expression and Inflammatory Potential During Early Pregnancy in Patients With Recurrent Spontaneous Abortion
Cited by: 10
Author(s): Yu Liu, Yang Zhang, Jun Xiong, Jianjun Li, Ying Zhang, Qi Kang, Pan Zhi, Qiang Wang, Hui Wang, Wanjiang Zeng, Yafei Huang
Software Mentions: 2
Published: about 5 years ago

10.3389/fimmu.2021.621744

In Vitro Culture Expansion Shifts the Immune Phenotype of Human Adipose-Derived Mesenchymal Stem Cells
Cited by: 25
Author(s): Richard Jeske, Xuegang Yuan, Qin Fu, Bruce A. Bunnell, Timothy M. Logan, Yan Li
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-019-5632-2

Genome-wide identification and expression profiling of trihelix gene family under abiotic stresses in wheat
Cited by: 40
Author(s): Jie Xiao, Rui Hu, Tao Gu, Jiapeng Han, Ding Qiu, Peipei Su, Jialu Feng, Junli Chang, Guangxiao Yang, Guoqing He
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1007932

Lysine 27 of replication-independent histone H3.3 is required for Polycomb target gene silencing but not for gene activation
Cited by: 34
Author(s): Mary Leatham-Jensen, Christopher M. Uyehara, Brian D. Strahl, A. Gregory Matera, Robert J. Duronio, Daniel J. McKay
Software Mentions: 2
Published: almost 8 years ago

10.3389/fimmu.2020.607048

Bacterial and Fungal Toll-Like Receptor Activation Elicits Type I IFN Responses in Mast Cells
Cited by: 11
Author(s): Lisa Kornstädt, Sandra Pierre, Andreas Weigert, Stefanie Ebersberger, Tim J. Schäufele, Anja Kolbinger, Tobias Schmid, Jennifer Cohnen, Dominique Thomas, Nerea Ferreirós, Bernhard Brüne, Ingo Ebersberger, Klaus Scholich
Software Mentions: 2
Published: almost 6 years ago

10.3389/fimmu.2021.627926

uhrf1 and dnmt1 Loss Induces an Immune Response in Zebrafish Livers Due to Viral Mimicry by Transposable Elements
Cited by: 14
Author(s): Elena Magnani, Filippo Macchi, Bhavani P. Madakashira, Chi Zhang, Fatima AlAydaroos, Kirsten C. Sadler
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2020.01327

Rhinovirus Infection Drives Complex Host Airway Molecular Responses in Children With Cystic Fibrosis
Cited by: 12
Author(s): Kak-Ming Ling, Luke W. Garratt, Erin E. Gill, Ahwon Lee, Ana Patrícia, Erika N. Sutanto, Thomas Iosifidis, Tim Rosenow, Stuart E. Turvey, Timo Lassmann, Robert E. W. Hancock, Anthony Kicic, Stephen M. Stick
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0224646

THAP11F80L cobalamin disorder-associated mutation reveals normal and pathogenic THAP11 functions in gene expression and cell proliferation
Cited by: 7
Author(s): Harmonie Dehaene, Viviane Praz, Philippe Lhôte, Maykel Lopes, Winship Herr
Software Mentions: 2
Published: almost 7 years ago

10.3389/fimmu.2021.743030

NOX2-Deficient Neutrophils Facilitate Joint Inflammation Through Higher Pro-Inflammatory and Weakened Immune Checkpoint Activities
Cited by: 7
Author(s): Yi‐Chu Liao, Szu‐Yu Wu, Ya‐Fang Huang, Pei‐Chi Lo, Tzu‐Yi Chan, Chih-An Chen, Chun-Hsin Wu, Che-Chia Hsu, Chia Liang Yen, Peng Chen, Chi‐Chang Shieh
Software Mentions: 2
Published: about 5 years ago

10.7554/eLife.27450

Molecular conservation of marsupial and eutherian placentation and lactation
Cited by: 28
Author(s): Michael W Guernsey, Edward B. Chuong, Guillaume Cornelis, Marilyn B. Renfree, Julie C. Baker
Software Mentions: 2
Published: about 9 years ago

10.1186/s12864-021-07400-z

Genome-wide identification and gene-editing of pigment transporter genes in the swallowtail butterfly Papilio xuthus
Cited by: 6
Author(s): Guichun Liu, Wei Liu, Ruoping Zhao, Jinwu He, Zhiwei Dong, Lei Chen, Wenting Wan, Zhou Chang, Wen Wang, Xueyan Li
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2018.02282

Parasitic Nematodes Exert Antimicrobial Activity and Benefit From Microbiota-Driven Support for Host Immune Regulation
Cited by: 52
Author(s): Sebastian Rausch, Ankur Midha, Mathias Kuhring, Nicole Affinass, Aleksandar Radonić, Anja A. Kühl, André Bleich, Bernhard Y. Renard, Susanne Hartmann
Software Mentions: 2
Published: about 8 years ago

10.18632/oncotarget.24862

ONC201 kills breast cancer cells<i>in vitro</i>by targeting mitochondria
Cited by: 70
Author(s): Yoshimi Endo Greer, Natalie Porat-Shliom, Kunio Nagashima, Christina H. Stuelten, Dan Crooks, Vishal N. Kopardé, Sarah L. Gilbert, Celia Islam, Ashley Ubaldini, Yun Ji, Luca Gattinoni, Ferri Soheilian, Xiantao Wang, Markus Hafner, Jyoti Shetty, Bao Tran, Parthav Jailwala, Maggie Cam, Martin Lang, Donna Voeller, William C. Reinhold, Vinodh N. Rajapakse, Yves Pommier, Roberto Weigert, W. Marston Linehan, Stanley Lipkowitz
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-019-6265-1

Infection and RNA-seq analysis of a zebrafish tlr2 mutant shows a broad function of this toll-like receptor in transcriptional and metabolic control and defense to Mycobacterium marinum infection
Cited by: 18
Author(s): Wanbin Hu, Shuxin Yang, Yasuhito Shimada, Magnus M. Münch, Rubén Marín-Juez, Annemarie H. Meijer, Herman P. Spaink
Software Mentions: 2
Published: almost 7 years ago

10.3389/fimmu.2021.667136

Transcriptomic Analysis of the Effect of GAT-2 Deficiency on Differentiation of Mice Naïve T Cells Into Th1 Cells In Vitro
Cited by: 5
Author(s): Xueyan Ding, Yajie Chang, Siquan Wang, Dong Yan, Jiakui Yao, Guoqiang Zhu
Software Mentions: 2
Published: over 5 years ago

10.1186/s13062-015-0045-x

An atlas of mouse CD4+ T cell transcriptomes
Cited by: 75
Author(s): Michael J. T. Stubbington, Bidesh Mahata, Valentine Svensson, Andrew Deonarine, Jesper K. Nissen, Alexander G. Betz, Sarah A. Teichmann
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pgen.1006932

Control of RUNX-induced repression of Notch signaling by MLF and its partner DnaJ-1 during Drosophila hematopoiesis
Cited by: 18
Author(s): Marion S. Miller, Aichun Chen, Vanessa Gobert, Benoît Augé, Mathilde Beau, Odile Burlet‐Schiltz, Marc Haenlin, Lucas Waltzer
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0141836

Transcriptomic Changes Due to Cytoplasmic TDP-43 Expression Reveal Dysregulation of Histone Transcripts and Nuclear Chromatin
Cited by: 40
Author(s): Alexandre Amlie‐Wolf, Paul Ryvkin, Rui Tong, Isabelle Dragomir, EunRan Suh, Yan Xu, Vivianna M. Van Deerlin, Brian D. Gregory, Linda K. Kwong, John Q. Trojanowski, Virginia Man-Yee Lee, Li-San Wang, Edward B. Lee
Software Mentions: 2
Published: about 11 years ago

10.1155/2019/3526407

A Simple Competing Endogenous RNA Network Identifies Novel mRNA, miRNA, and lncRNA Markers in Human Cholangiocarcinoma
Cited by: 10
Author(s): Cheng Zhang, Chunlin Ge
Software Mentions: 2
Published: over 7 years ago

10.3389/fmed.2020.624576

Molecular Analysis of IL-5 Receptor Subunit Alpha as a Possible Pharmacogenetic Biomarker in Asthma
Cited by: 7
Author(s): Sandra Elena Pérez, D.H. Heredero Jung, Asunción Garcı́a-Sánchez, Miguel Estravís, Marı́a Jesús Martı́n, Jacinto Ramos‐González, Juan Carlos Triviño, María Isidoro‐García, Catalina Sanz, Ignacio Dávila
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.53174

NHR-8 and P-glycoproteins uncouple xenobiotic resistance from longevity in chemosensory C. elegans mutants
Cited by: 4
Author(s): Gabriel A Guerrero, Maxime Derisbourg, Felix A.M.C. Mayr, Laura E Wester, Marco Giorda, J Eike Dinort, Matías D. Hartman, Klara Schilling, María José Alonso-De Gennaro, Rong Lu, Bérénice A. Benayoun, Martin S. Denzel
Software Mentions: 2
Published: about 5 years ago

10.3389/fmed.2021.664045

Comparative Transcriptomics of IBD Patients Indicates Induction of Type 2 Immunity Irrespective of the Disease Ideotype
Cited by: 2
Author(s): Miguel Gonzalez Acera, Jay V. Patankar, Leonard Diemand, Britta Siegmund, Markus F. Neurath, Stefan Wirtz, Christoph Becker
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2020.01771

Exposure of the Opportunistic Marine Pathogen Photobacterium damselae subsp. damselae to Human Body Temperature Is a Stressful Condition That Shapes the Transcriptome, Viability, Cell Morphology, and Virulence
Cited by: 8
Author(s): Xosé M. Matanza, Carlos R. Osorio
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2018.00217

Verticillium dahliae-Arabidopsis Interaction Causes Changes in Gene Expression Profiles and Jasmonate Levels on Different Time Scales
Cited by: 29
Author(s): Sandra S. Scholz, Wolfgang Schmidt‐Heck, Reinhard Guthke, Alexandra C. U. Furch, Michael Reichelt, Jonathan Gershenzon, Ralf Oelmüller
Software Mentions: 2
Published: almost 9 years ago

10.7554/eLife.44392

A de novo evolved gene in the house mouse regulates female pregnancy cycles
Cited by: 31
Author(s): Chen Xie, Cemalettin Bekpen, Sven Künzel, Maryam Keshavarz, Rebecca Krebs-Wheaton, Neva Škrabar, Kristian K. Ullrich, Diethard Tautz
Software Mentions: 2
Published: about 7 years ago

10.3389/fmicb.2020.00530

Substrate-Dependent Fermentation of Bamboo in Giant Panda Gut Microbiomes: Leaf Primarily to Ethanol and Pith to Lactate
Cited by: 6
Author(s): Alberto Scoma, Way Cern Khor, Marta Coma, Robert Heyer, Ruben Props, Jonas Schoelynck, Tim Bouts, Dirk Benndorf, Desheng Li, Hemin Zhang, Korneel Rabaey
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0217978

Social status regulates the hepatic miRNAome in rainbow trout: Implications for posttranscriptional regulation of metabolic pathways
Cited by: 14
Author(s): Daniel J. Kostyniuk, David Zhang, Christopher J. Martyniuk, Kathleen M. Gilmour, Jan A. Mennigen
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-015-1654-6

Partial depletion of yolk during zebrafish embryogenesis changes the dynamics of methionine cycle and metabolic genes
Cited by: 7
Author(s): Yunxian Huang, Sam E.V. Linsen
Software Mentions: 2
Published: over 11 years ago

10.3389/fmicb.2020.588906

Chitin Attenuates Expression of Listeria monocytogenes Virulence Genes in vitro
Cited by: 0
Author(s): Miguel Villoria Recio, Bo-Hyung Lee, Eva Maria Sternkopf Lillebæk, Birgitte H. Kallipolitis, Cormac G. M. Gahan, Hanne Ingmer, Mona Larsen
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2021.705326

Effects of NaCl Concentrations on Growth Patterns, Phenotypes Associated With Virulence, and Energy Metabolism in Escherichia coli BW25113
Cited by: 14
Author(s): Fen Li, Xue-Song Xiong, Yingying Yang, Jun‐Jiao Wang, Mengmeng Wang, Jia-Wei Tang, Qinghua Liu, Liang Wang, Bing Gu
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1009642

Repeated evolution of circadian clock dysregulation in cavefish populations
Cited by: 22
Author(s): Katya L. Mack, James B. Jaggard, Jenna Persons, Emma Y. Roback, Courtney N. Passow, Bethany A. Stanhope, Estephany Ferrufino, Dai Tsuchiya, Sarah E. Smith, Brian D. Slaughter, Johanna E. Kowalko, Nicolas Rohner, Alex C. Keene, Suzanne E. McGaugh
Software Mentions: 2
Published: over 5 years ago

10.18632/oncotarget.25239

The cyclin-dependent kinase inhibitor flavopiridol (alvocidib) inhibits metastasis of human osteosarcoma cells
Cited by: 30
Author(s): Loredana Zocchi, Stephanie Wu, Jie Wu, Ken Hayama, Claudia A. Benavente
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-020-07059-y

SWI/SNF complexes act through CBP-1 histone acetyltransferase to regulate acute functional tolerance to alcohol
Cited by: 5
Author(s): Laura D. Mathies, Jonathan H. Lindsay, Amal P. Handal, GinaMari G. Blackwell, Andrew G. Davies, Jill C. Bettinger
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0198575

Inferring the presence of aflatoxin-producing Aspergillus flavus strains using RNA sequencing and electronic probes as a transcriptomic screening tool
Cited by: 13
Author(s): Andrés S. Espíndola, William L. Schneider, Kitty F. Cardwell, Yisel Carrillo, Peter R. Hoyt, Stephen M. Marek, H. A. Melouk, Carla D. Garzón
Software Mentions: 2
Published: about 8 years ago

10.3389/fmicb.2017.01042

Co-registered Geochemistry and Metatranscriptomics Reveal Unexpected Distributions of Microbial Activity within a Hydrothermal Vent Field
Cited by: 18
Author(s): H. C. Olins, Daniel R. Rogers, Christina M. Preston, William Ussler, Douglas Pargett, Scott Jensen, Brent Roman, James M. Birch, Christopher A. Scholin, Mohamed Fauzi Haroon, Peter R. Girguis
Software Mentions: 2
Published: over 9 years ago

10.7554/eLife.50561

MicroRNA-934 is a novel primate-specific small non-coding RNA with neurogenic function during early development
Cited by: 11
Author(s): Kanella Prodromidou, Ioannis S. Vlachos, Maria Gaitanou, Georgia Kouroupi, Artemis G. Hatzigeorgiou, Rebecca Matsas
Software Mentions: 2
Published: over 6 years ago

10.1186/s12881-019-0771-5

The CIMP-high phenotype is associated with energy metabolism alterations in colon adenocarcinoma
Cited by: 13
Author(s): Maria S. Fedorova, George S. Krasnov, E. N. Lukyanova, Andrew R. Zaretsky, Alexey A. Dmitriev, Nataliya V. Melnikova, Alexey Moskalev, Sergey L. Kharitonov, Elena A. Pudova, Zulfiya G. Guvatova, Anastasiya A. Kobelyatskaya, Irina A. Ishina, Е. Н. Славнова, Anastasiya V. Lipatova, М. А. Черниченко, Д. В. Сидоров, A. Yu. Popov, Marina V. Kiseleva, А. Д. Каприн, Anastasiya V. Snezhkina, Anna V. Kudryavtseva
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2020.600823

Dinoflagellate Host Chloroplasts and Mitochondria Remain Functional During Amoebophrya Infection
Cited by: 6
Author(s): Ehsan Kayal, Catharina Alves‐de‐Souza, Sarah Farhat, Lourdes Velo‐Suárez, Joanne Monjol, Jeremy Szymczak, Estelle Bigeard, Dominique Marie, Benjamin Noël, Betina M. Porcel, Erwan Corre, Christophe Six, Laure Guillou
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13062-019-0239-8

Robust pathway-based multi-omics data integration using directed random walks for survival prediction in multiple cancer studies
Cited by: 34
Author(s): So Yeon Kim, Hyun-Hwan Jeong, Jae‐Sik Kim, Jeong-Hyeon Moon, Kyung-Ah Sohn
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2018.03037

The AGXX® Antimicrobial Coating Causes a Thiol-Specific Oxidative Stress Response and Protein S-bacillithiolation in Staphylococcus aureus
Cited by: 27
Author(s): Vu Van Loi, Tobias Busche, Thalia Preuß, Jörn Kalinowski, Jörg Bernhardt, Haike Antelmann
Software Mentions: 2
Published: almost 8 years ago

10.1002/advs.202001978

A Fifteen‐Gene Classifier to Predict Neoadjuvant Chemotherapy Responses in Patients with Stage IB to IIB Squamous Cervical Cancer
Cited by: 7
Author(s): Xun Tian, Xin Wang, Zifeng Cui, Jia Liu, Xiaoyuan Huang, Chao Shi, Min Zhang, Ting Liu, Xiaofang Du, Rui Li, Lei Huang, Danni Gong, Rui Tian, Chen Cao, Jin Park, Zhen Zeng, Guangxin Pan, Meng Xia, Hongfeng Zhang, Baoming Luo, Yonghui Xie, Xiaoming Li, Tianye Li, Jun Wu, Qinghua Zhang, Gang Chen, Zheng Hu
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1008369

Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes
Cited by: 18
Author(s): Rahulsimham Vegesna, Marta Tomaszkiewicz, Paul Medvedev, Kateryna D. Makova
Software Mentions: 2
Published: about 7 years ago

10.3389/fmicb.2019.01930

Cas9 Contributes to Group B Streptococcal Colonization and Disease
Cited by: 35
Author(s): Brady L. Spencer, Liwen Deng, Kathryn A. Patras, Zachary M. Burcham, Glenda F. Sanches, Prescilla Emy Nagao, Kelly S. Doran
Software Mentions: 2
Published: about 7 years ago

10.3389/fmicb.2016.00380

Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3
Cited by: 12
Author(s): Adam R. Rivers, Andrew S. Burns, Leong-Keat Chan, Mary Ann Moran
Software Mentions: 2
Published: over 10 years ago

10.1186/s12864-018-4961-x

Virulence-related comparative transcriptomics of infectious and non-infectious chlamydial particles
Cited by: 10
Author(s): Thomas Beder, Hans Peter Saluz
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2019.00755

Campylobacter jejuni Demonstrates Conserved Proteomic and Transcriptomic Responses When Co-cultured With Human INT 407 and Caco-2 Epithelial Cells
Cited by: 17
Author(s): Nicholas M. Negretti, Gérémy Clair, Prabhat K. Talukdar, Christopher R. Gourley, Steven Huynh, Joshua N. Adkins, Craig T. Parker, Colby M Corneau, Michael E. Konkel
Software Mentions: 2
Published: over 7 years ago

10.7554/eLife.30919

ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2
Cited by: 118
Author(s): Devanshi Jain, M. Rhyan Puno, Cem Meydan, Nathalie Lailler, Christopher E. Mason, Christopher D. Lima, Kathryn V. Anderson, Scott Keeney
Software Mentions: 2
Published: almost 9 years ago

10.3389/fmicb.2019.02987

Applying a New REFINE Approach in Zymomonas mobilis Identifies Novel sRNAs That Confer Improved Stress Tolerance Phenotypes
Cited by: 4
Author(s): Katie Haning, Sean M Engels, Paige Williams, Margaret Arnold, Lydia M. Contreras
Software Mentions: 2
Published: almost 7 years ago

10.3389/fmicb.2018.00249

Transcriptional Response of Staphylococcus aureus to Sunlight in Oxic and Anoxic Conditions
Cited by: 6
Author(s): Jill S. McClary, Alexandria B. Boehm
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0140111

Food Deprivation Affects the miRNome in the Lactating Goat Mammary Gland
Cited by: 23
Author(s): Lenha Mobuchon, Sylvain Marthey, Sandrine Le Guillou, Dénis Laloë, Fabienne Le Provost, Christine Leroux
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0162237

RNAseq Transcriptional Profiling following Whip Development in Sugarcane Smut Disease
Cited by: 43
Author(s): Patrícia Dayane Carvalho Schaker, Aristides Palhares, Lucas Mitsuo Taniguti, Leila Priscila Peters, Silvana Creste, Karen S. Aitken, Marie‐Anne Van Sluys, João Paulo Kitajima, Maria Lúcia Carneiro Vieira, Cláudia Barros Monteiro-Vitorello
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0253555

Environmental responsiveness of flowering time in cassava genotypes and associated transcriptome changes
Cited by: 4
Author(s): Deborah N. Oluwasanya, Andreas Gisel, Livia Stavolone, Tim L. Setter
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2018.02362

A Comparison of Techniques for Collecting Skin Microbiome Samples: Swabbing Versus Tape-Stripping
Cited by: 57
Author(s): Kazuhiro Ogai, Satoshi Nagase, Kanae Mukai, Terumi Iuchi, Yosai Mori, Miki Matsue, Kayo Sugitani, Junko Sugama, Shigefumi Okamoto
Software Mentions: 2
Published: about 8 years ago

10.1186/s13059-020-02189-8

A DNA methylation state transition model reveals the programmed epigenetic heterogeneity in human pre-implantation embryos
Cited by: 3
Author(s): Chengchen Zhao, Naiqian Zhang, Yalin Zhang, Nuermaimaiti Tuersunjiang, Shaorong Gao, Wenqiang Liu, Yong Zhang
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pgen.1007241

Atf3 links loss of epithelial polarity to defects in cell differentiation and cytoarchitecture
Cited by: 23
Author(s): Colin D. Donohoe, Gábor Csordás, Andreia Correia, Marek Jindra, Corinna Klein, Bianca Habermann, Mirka Uhlířová
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1008139

Functional robustness of adult spermatogonial stem cells after induction of hyperactive Hras
Cited by: 5
Author(s): Mika Yamada, Cai Winson, L. A. Martin, Thierry N’Tumba-Byn, Marco Seandel
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1009243

Locus-specific paramutation in Zea mays is maintained by a PICKLE-like chromodomain helicase DNA-binding 3 protein controlling development and male gametophyte function
Cited by: 6
Author(s): Natalie C. Deans, Brian Giacopelli, Jay B. Hollick
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pgen.1006570

Anaerobically Grown Escherichia coli Has an Enhanced Mutation Rate and Distinct Mutational Spectra
Cited by: 64
Author(s): Sonal Shewaramani, Thomas J. Finn, Sinead C. Leahy, Rees Kassen, Paul B. Rainey, Christina D. Moon
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pgen.1006024

Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States
Cited by: 72
Author(s): Konrad L. M. Rudolph, Bianca M Schmitt, Diego Villar, Robert J. White, John C. Marioni, Claudia Kutter, Duncan T. Odom
Software Mentions: 1
Published: over 10 years ago

10.1038/s41396-018-0077-1

Peatland Acidobacteria with a dissimilatory sulfur metabolism
Cited by: 121
Author(s): Bela Hausmann, Claus Pelikan, Craig W. Herbold, Stephan Köstlbacher, Mads Albertsen, Stephanie A. Eichorst, Tijana Glavina del Rio, Martin Huemer, Per Halkjær Nielsen, Thomas Rattei, Ulrich Stingl, Susannah G. Tringe, Daniela Trojan, Cécilia Wentrup, Dagmar Woebken, Michael Pester, Alexander Loy
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1007749

Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors
Cited by: 145
Author(s): François Rousset, Lun Cui, Elise Siouve, Christophe Bécavin, Florence Depardieu, David Bikard
Software Mentions: 1
Published: about 8 years ago

10.1155/2019/2951427

Transcriptome Analysis Reveals the Effect of Long Intergenic Noncoding RNAs on Pig Muscle Growth and Fat Deposition
Cited by: 9
Author(s): Guoting Chen, Xiangdong Cheng, Gaoli Shi, Cheng Zou, Lin Chen, Jingxuan Li, Mengxun Li, Fang Cui, Changchun Li
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1006808

Impact of mutations in Toll-like receptor pathway genes on esophageal carcinogenesis
Cited by: 17
Author(s): Daffolyn Rachael Fels Elliott, Juliane Perner, Xiaodun Li, Martyn F. Symmons, Brett Verstak, Matthew Eldridge, Lawrence Bower, Maria O’Donovan, Rebecca C. Fitzgerald
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1006683

Overlapping SETBP1 gain-of-function mutations in Schinzel-Giedion syndrome and hematologic malignancies
Cited by: 31
Author(s): Rocío Acuña-Hidalgo, Pelagia Derizioti, Marloes Steehouwer, Christian Gilissen, Sarah A. Graham, Sipko van Dam, Julie Hoover‐Fong, Aida Telegrafi, Anne Destrée, Robert Śmigiel, Lindsday A. Lambie, Hülya Kayserili, Umut Altunoğlu, Elisabetta Lapi, Maria Luisa Giovannucci Uzielli, Mariana Aracena, Banu Nur, Ercan Mıhçı, Lília Maria Azevedo Moreira, Viviane Borges Ferreira, Dafne Dain Gandelman Horovitz, Kátia Maria da Rocha, Aleksandra Jezela‐Stanek, Alice S. Brooks, Heiko Reutter, Julie S. Cohen, Ali Fatemi, Martin Smitka, Theresa A. Grebe, Nataliya Di Donato, Charu Deshpande, Anthony Vandersteen, Charles Marques Lourenço, Andreas Dufke, Eva Rossier, Gwenaëlle André, Alessandra Baumer, Careni Spencer, Julie McGaughran, Lude Franke, Joris A. Veltman, Bert B.A. de Vries, Albert Schinzel, Simon E. Fisher, Alexander Hoischen, Bregje W.M. van Bon
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1009098

Loss of the RNA trimethylguanosine cap is compatible with nuclear accumulation of spliceosomal snRNAs but not pre-mRNA splicing or snRNA processing during animal development
Cited by: 9
Author(s): Lin Cheng, Yu Zhang, Yi Zhang, Tao Chen, Yan Xu, Yikang S. Rong
Software Mentions: 1
Published: about 6 years ago

10.1155/2020/2043785

Extraction and Hypolipidemic Activity of Low Molecular Weight Polysaccharides Isolated from Rosa Laevigata Fruits
Cited by: 6
Author(s): Xuejiao Zhang, Hu Y, Chenzhong Jin, Weiguo Wu
Software Mentions: 1
Published: about 6 years ago

10.1038/s41396-020-0715-2

Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation
Cited by: 28
Author(s): Carolina Reyes, Logan H. Hodgskiss, Melina Kerou, Thomas Pribasnig, Sophie S. Abby, Barbara Bayer, Stephan M. Kraemer, Christa Schleper
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1009822

Mitochondrial dysfunction in adult midbrain dopamine neurons triggers an early immune response
Cited by: 7
Author(s): Roberta Filograna, Seungmin Lee, Katarína Tiklová, Mara Mennuni, Viktor Jönsson, Markus Ringnér, Linda Gillberg, Elena Sopova, Oleg Shupliakov, Camilla Koolmeister, Lar̀s Olson, Thomas Perlmann, Nils-Göran Larsson
Software Mentions: 1
Published: about 5 years ago

10.3390/biology10090875

Intersex Plays a Role in Microbial Homeostasis in the Brown Planthopper
Cited by: 1
Author(s): Hou‐Hong Zhang, Hanjing Li, Yuxuan Ye, Ji-Chong Zhuo, Chuan-Xi Zhang
Software Mentions: 1
Published: about 5 years ago

10.18632/aging.103910

Prolonged treatment with Y-27632 promotes the senescence of primary human dermal fibroblasts by increasing the expression of IGFBP-5 and transforming them into a CAF-like phenotype
Cited by: 7
Author(s): Xiangyong Li, Qian Zhou, Shuangshuang Wang, Ping Wang, Juan Li, Zhiwei Xie, Chang Liu, Jie Wen, Xunwei Wu
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pgen.1006239

Comprehensive Analysis of the Transcriptional and Mutational Landscape of Follicular and Papillary Thyroid Cancers
Cited by: 240
Author(s): Seong-Keun Yoo, Seungbok Lee, Su Jin Kim, Hyeon Gun Jee, Byoung Ae Kim, Hyesun Cho, Young Shin Song, Sun Wook Cho, Jae Kyung Won, Jong Yeon Shin, Do Joon Park, Jong‐Il Kim, Kyu Eun Lee, Young Joo Park, Jeong Sun Seo
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1007105

mRNA processing in mutant zebrafish lines generated by chemical and CRISPR-mediated mutagenesis produces unexpected transcripts that escape nonsense-mediated decay
Cited by: 78
Author(s): Jennifer L. Anderson, Timothy S. Mulligan, Meifen Shen, Hui Wang, Catherine Scahill, Frederick J. Tan, Shao Jun Du, Elisabeth M Busch-Nentwich, Steven A. Farber
Software Mentions: 1
Published: almost 9 years ago

Projects: bioconductor: DESeq2

Enhanced Analysis

Science Score: 100/100

Bonuses:

Papers Mentioning DESeq2 9,583