bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.1038/s41438-021-00474-6

Genome-wide analysis of changes in miRNA and target gene expression reveals key roles in heterosis for Chinese cabbage biomass
Cited by: 23
Author(s): Pei-Rong Li, Tongbing Su, Deshuang Zhang, Weihong Wang, Xiaoyun Xin, Yangjun Yu, Xiuyun Zhao
Software Mentions: 2
Published: over 5 years ago

10.1038/s41438-020-00458-y

Insights into triterpene synthesis and unsaturated fatty-acid accumulation provided by chromosomal-level genome analysis of Akebia trifoliata subsp. australis
Cited by: 22
Author(s): Hui Huang, Juan Boo Liang, Qian Tan, Lin-Feng Ou, Xin Li, Caihong Zhong, Ian Max Møller, WU Xian-jin, Song-Quan Song
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41438-020-00410-0

Perception of unrelated microbe-associated molecular patterns triggers conserved yet variable physiological and transcriptional changes in Brassica rapa ssp. pekinensis
Cited by: 6
Author(s): Wanhui Kim, Maxim Prokchorchik, Yuan Tian, Seulgi Kim, Hyelim Jeon, Cécile Segonzac
Software Mentions: 2
Published: about 6 years ago

10.1038/s41438-018-0115-1

Wide transcriptional investigation unravel novel insights of the on-tree maturation and postharvest ripening of ‘Abate Fetel’ pear fruit
Cited by: 13
Author(s): Nicola Busatto, Brian Farneti, Alice Tadiello, Vicky Oberkofler, Antonio Cellini, Franco Biasioli, Massimo Delledonne, Alessandro Cestaro, Christos Noutsos, Fabrizio Costa
Software Mentions: 2
Published: over 7 years ago

10.1038/s41438-020-00419-5

The apple DNA-binding one zinc-finger protein MdDof54 promotes drought resistance
Cited by: 23
Author(s): Pengxiang Chen, Minmin Yan, Lei Li, Jieqiang He, Shuangxi Zhou, Zhongxing Li, Chundong Niu, Chana Bao, Fang Zhi, Fengwang Ma, Qingmei Guan
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41438-018-0067-5

The origin and biosynthesis of the naphthalenoid moiety of juglone in black walnut
Cited by: 38
Author(s): Rachel M. McCoy, Sagar M. Utturkar, Joseph W. Crook, Jyothi Thimmapuram, Joshua R. Widhalm
Software Mentions: 2
Published: about 8 years ago

10.1038/hortres.2017.29

An eFP browser for visualizing strawberry fruit and flower transcriptomes
Cited by: 53
Author(s): Charles Hawkins, Julie Caruana, Jiaming Li, Chris Zawora, Omar Darwish, Jun Wu, Nadim W. Alkharouf, Zhongchi Liu
Software Mentions: 2
Published: over 9 years ago

10.1038/s41438-019-0184-9

Multiple quantitative trait loci contribute to resistance to bacterial canker incited by Pseudomonas syringae pv. actinidiae in kiwifruit (Actinidia chinensis)
Cited by: 20
Author(s): Jibran Tahir, S.M. Hoyte, H. Bassett, Cyril Brendolise, Abhishek Chatterjee, Kerry Templeton, Cecilia Deng, Ross N. Crowhurst, Mirco Montefiori, E.R. Morgan, Andrew Wotton, Keith A. Funnell, Claudia Wiedow, Mareike Knaëbel, Duncan I. Hedderley, J. L. Vanneste, John McCallum, Kirsten Hoeata, Amardeep Nath, David Chagné, L. D. Gea, Susan E. Gardiner
Software Mentions: 2
Published: about 7 years ago

10.1002/iid3.349

Multiomic analysis identifies natural intrapatient temporal variability and changes in response to systemic corticosteroid therapy in chronic rhinosinusitis
Cited by: 4
Author(s): Michael Hoggard, Bincy Jacob, David A. Wheeler, Melissa Zoing, Kevin Chang, Kristi Biswas, Martin Middleditch, Richard Douglas, Michael W. Taylor
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.immuni.2017.11.016

Oncogenic RAS Signaling Promotes Tumor Immunoresistance by Stabilizing PD-L1 mRNA
Cited by: 416
Author(s): Matthew A. Coelho, Sophie de Carné Trécesson, Sareena Rana, Davide Zecchin, Christopher Moore, Míriam Molina‐Arcas, Philip East, Bradley Spencer‐Dene, Emma Nye, Karin Barnouin, Ambrosius P. Snijders, Wi S. Lai, Perry J. Blackshear, Julian Downward
Software Mentions: 2
Published: almost 9 years ago

10.1016/j.immuni.2018.04.031

Protein Kinase C-β Dictates B Cell Fate by Regulating Mitochondrial Remodeling, Metabolic Reprogramming, and Heme Biosynthesis
Cited by: 73
Author(s): C. Kimberly Tsui, Núria Martínez, Mauro Gaya, Paula Maldonado, Miriam Llorian, Nathalie Legrave, Merja Rossi, James I. MacRae, Angus J.M. Cameron, Peter J. Parker, Michael Leitges, Andreas Bruckbauer, Facundo D. Batista
Software Mentions: 2
Published: over 8 years ago

10.1016/j.immuni.2018.12.018

The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages
Cited by: 543
Author(s): Julie Schulthess, Sumeet Pandey, Melania Capitani, Kévin Rue-Albrecht, Isabelle C. Arnold, Fanny Franchini, Agnieszka Chomka, Nicholas E. Ilott, Daniel Johnston, Elisabete Pires, James McCullagh, Stephen N. Sansom, Carolina V. Arancibia‐Cárcamo, Holm H. Uhlig, Fiona Powrie
Software Mentions: 2
Published: almost 8 years ago

10.1186/s40168-018-0589-y

Specialisation events of fungal metacommunities exposed to a persistent organic pollutant are suggestive of augmented pathogenic potential
Cited by: 16
Author(s): Celso Martins, Adélia Varela, Céline C. Leclercq, Óscar Núñez, Tomáš Větrovský, Jenny Renaut, Petr Baldrián, Cristina Silva Pereira
Software Mentions: 2
Published: almost 8 years ago

10.1097/MD.0000000000012018

Gene co-expression network analysis identifies the hub genes associated with immune functions for nocturnal hemodialysis in patients with end-stage renal disease
Cited by: 11
Author(s): Hongwei Dai, Jiao Zhou, Bo Zhu
Software Mentions: 2
Published: about 8 years ago

10.3390/ijms22105079

Implication of a Key Region of Six Bacillus cereus Genes Involved in Siroheme Synthesis, Nitrite Reductase Production and Iron Cluster Repair in the Bacterial Response to Nitric Oxide Stress
Cited by: 3
Author(s): Constance Porrini, Cyprien Guérin, Seav-Ly Tran, Rozenn Dervyn, Pierre Nicolas, Nalini Ramarao
Software Mentions: 2
Published: over 5 years ago

10.1097/MD.0000000000026271

Bioinformatics analysis of the key potential ceRNA biomarkers in human thymic epithelial tumors
Cited by: 4
Author(s): Kegong Chen, Long Bai, Lin Ji, Libo Wu, Guanghua Li
Software Mentions: 2
Published: over 5 years ago

10.1111/imcb.12371

Time‐resolved mRNA and miRNA expression profiling reveals crucial coregulation of molecular pathways involved in epithelial–pneumococcal interactions
Cited by: 3
Author(s): Haiyan Li, Li Lin, Chong Lei, Shu-Ge Gu, Shunhang Wen, Gang Yu, Xin Hu, Lin Dong, Hailin Zhang, Changchong Li
Software Mentions: 2
Published: over 6 years ago

10.20900/immunometab20210025

oxLDL-Induced Trained Immunity Is Dependent on Mitochondrial Metabolic Reprogramming
Cited by: 19
Author(s): Laszlo Groh, Anaísa V Ferreira, Leonie Helder, Charlotte D C C van der Heijden, Boris Novakovic, Els van de Westerlo, Vasiliki Matzaraki, Simone J.C.F.M. Moorlag, L. Charlotte de Bree, Valerie A C M Koeken, Vera P. Mourits, Samuel T. Keating, Jelmer H. van Puffelen, Alexander Hoischen, Leo A. B. Joosten, Mihai G. Netea, Werner J.H. Koopman, Niels P. Riksen
Software Mentions: 2
Published: over 5 years ago

10.1128/IAI.00161-15

Interaction of Salmonella enterica Serovar Typhimurium with Intestinal Organoids Derived from Human Induced Pluripotent Stem Cells
Cited by: 214
Author(s): Jessica L. Forbester, David Goulding, Ludovic Vallier, Nicholas R.F. Hannan, Christine Hale, Derek Pickard, Subhankar Mukhopadhyay, Gordon Dougan
Software Mentions: 2
Published: over 11 years ago

10.1128/IAI.00041-18

Adipocyte Model of Mycobacterium tuberculosis Infection Reveals Differential Availability of Iron to Bacilli in the Lipid-Rich Caseous Environment
Cited by: 10
Author(s): Aditya Nandy, Anupam Mondal, Rajesh Pandey, Prakash Arumugam, Stanzin Dawa, Neetika Jaisinghani, Vittal Rao, Debasis Dash, Sheetal Gandotra
Software Mentions: 2
Published: over 8 years ago

10.1007/s00011-020-01326-0

Novel adipokine associated with OA: retinol binding protein 4 (RBP4) is produced by cartilage and is correlated with MMPs in osteoarthritis patients
Cited by: 17
Author(s): Morena Scotece, Anna Koskinen-Kolasa, Antti Pemmari, Tiina Leppänen, Mari Hämäläinen, Teemu Moilanen, Eeva Moilanen, Katriina Vuolteenaho
Software Mentions: 2
Published: over 6 years ago

10.3390/insects11020090

Transcriptome Profiling Revealed Potentially Critical Roles for Digestion and Defense-Related Genes in Insects’ Use of Resistant Host Plants: A Case Study with Sitobion Avenae
Cited by: 4
Author(s): Da Wang, Xiaoqin Shi, Deguang Liu, Yujing Yang, Zheming Shang
Software Mentions: 2
Published: almost 7 years ago

10.1155/2017/5047403

Comparison of Oropharyngeal Microbiota from Children with Asthma and Cystic Fibrosis
Cited by: 29
Author(s): Sébastien Boutin, Martin Depner, Mirjam Stahl, Simon Y. Graeber, S Dittrich, Antje Legatzki, Erika von Mutius, Marcus Mall, Alexander H. Dalpke
Software Mentions: 2
Published: almost 10 years ago

10.3390/insects12080704

Transcriptional Profiles of Diploid Mutant Apis mellifera Embryos after Knockout of csd by CRISPR/Cas9
Cited by: 4
Author(s): Xiuxiu Wang, Yan Lin, Liqiang Liang, Haiyang Geng, Meng Zhang, Hongyi Nie, Songkun Su
Software Mentions: 2
Published: over 5 years ago

10.1186/s40635-019-0271-0

The peripheral blood transcriptome in septic cardiomyopathy: an observational, pilot study
Cited by: 5
Author(s): Meghan M. Cirulis, Sarah J. Beesley, Emily L. Wilson, Chris Stubben, Troy D. Olsen, Eliotte L. Hirshberg, Lane M. Smith, Michael J. Lanspa, Theodore P. Abraham, Colin K. Grissom, Matthew T. Rondina
Software Mentions: 2
Published: about 7 years ago

10.1001/jamanetworkopen.2019.5394

Prevalence of Periodontal Disease and Periodontopathic Bacteria in Anti–Cyclic Citrullinated Protein Antibody–Positive At-Risk Adults Without Arthritis
Cited by: 69
Author(s): Kulveer Mankia, Ziyang Cheng, Thuy Do, Laura Hunt, Josephine L. Meade, Jing Kang, V. Clerehugh, A F Speirs, Aradhna Tugnait, Elizabeth M A Hensor, Jackie Nam, Deirdre DeVine, Paul Emery
Software Mentions: 2
Published: over 7 years ago

10.1002/jbm4.10171

The Osteocyte Transcriptome Is Extensively Dysregulated in Mouse Models of Osteogenesis Imperfecta
Cited by: 28
Author(s): Sarah M. Zimmerman, Milena Dimori, Melissa E. Heard‐Lipsmeyer, Roy Morello
Software Mentions: 2
Published: almost 8 years ago

10.1172/jci.insight.121144

The TAB1-p38α complex aggravates myocardial injury and can be targeted by small molecules
Cited by: 15
Author(s): G.F. De Nicola, Rekha Bassi, C. Blake Nichols, Mariana Fernández-Caggiano, Pelin Golforoush, Dibesh Thapa, Rosaleen J. Anderson, Eva Denise Martin, Sharwari Verma, Jens Kleinjung, Adam Laing, Jonathan P. Hutchinson, Philip Eaton, James E. Clark, Michael Marber
Software Mentions: 2
Published: about 8 years ago

10.1172/jci.insight.94716

Molecular characterization of the transition from acute to chronic kidney injury following ischemia/reperfusion
Cited by: 190
Author(s): Jing Liu, Sanjeev Kumar, Egor Dolzhenko, Gregory F. Alvarado, Jinjin Guo, Can Lü, Yibu Chen, Meng Li, Mark C. Dessing, Riana K. Parvez, Pietro E Cippà, A. Michaela Krautzberger, Gohar Saribekyan, Andrew D. Smith, Andrew P. McMahon
Software Mentions: 2
Published: about 9 years ago

10.1172/jci.insight.93739

Neonatal and adult recent thymic emigrants produce IL-8 and express complement receptors CR1 and CR2
Cited by: 43
Author(s): Marcin Ł. Pękalski, Arcadio Rubio Garćıa, Ricardo C. Ferreira, Daniel B. Rainbow, Deborah J. Smyth, Meghavi Mashar, Jane Brady, Natalia Savinykh, Xaquín Castro Dopico, Sumiyya Mahmood, Simon Duley, Helen Stevens, Neil Walker, Antony J. Cutler, Frank Waldron‐Lynch, David B. Dunger, Claire Shannon-Lowe, Alasdair Coles, Joanne L. Jones, Chris Wallace, John A. Todd, Linda S. Wicker
Software Mentions: 2
Published: about 9 years ago

10.1172/jci.insight.97422

Mutant p53R270H drives altered metabolism and increased invasion in pancreatic ductal adenocarcinoma
Cited by: 24
Author(s): Heather Schofield, Jörg Zeller, Carlos Espinoza, Christopher J. Halbrook, Annachiara del Vecchio, Brian Magnuson, Tania Fabo, Ayse Ece Cali Daylan, Ilya Kovalenko, Ho‐Joon Lee, Wei Yan, Ying Feng, Saadia A. Karim, Daniel M. Kremer, Chandan Kumar-Sinha, Costas A. Lyssiotis, Mats Ljungman, Jennifer P. Morton, Stefanie Galbán, Eric R. Fearon, Marina Pasca di Magliano
Software Mentions: 2
Published: almost 9 years ago

10.1172/jci.insight.139179

Reduced left atrial cardiomyocyte PITX2 and elevated circulating BMP10 predict atrial fibrillation after ablation
Cited by: 37
Author(s): Jasmeet S. Reyat, Winnie Chua, Victor Roth Cardoso, Anika Witten, Peter Kastner, S. Nashitha Kabir, Moritz F. Sinner, Robin Wesselink, Andrew P. Holmes, Davor Pavlović, Monika Stoll, Stefan Kääb, Georgios V. Gkoutos, Joris R. de Groot, Paulus Kirchhof, Larissa Fabritz
Software Mentions: 2
Published: about 6 years ago

10.1172/jci.insight.137926

Human Tregs at the materno-fetal interface show site-specific adaptation reminiscent of tumor Tregs
Cited by: 19
Author(s): Judith Wienke, Laura Brouwers, Leone M. van der Burg, Michal Mokrý, Rianne C. Scholman, Floris Groenendaal, Bas B. van Rijn, Femke van Wijk
Software Mentions: 2
Published: about 6 years ago

10.1172/jci.insight.138215

PPP2R2D suppresses IL-2 production and Treg function
Cited by: 12
Author(s): Wenliang Pan, Amir Sharabi, Andrew Ferretti, Yinfeng Zhang, Catalina Burbano, Norimitsu Yoshida, Maria Tsokos, George C. Tsokos
Software Mentions: 2
Published: about 6 years ago

10.1172/jci.insight.139163

ROS-producing immature neutrophils in giant cell arteritis are linked to vascular pathologies
Cited by: 42
Author(s): Lihui Wang, Zhichao Ai, Tariq E. Khoyratty, Kristina Zec, Hayley L. Eames, Erinke van Grinsven, Alison Hudak, Susan Morris, David Ahern, Claudia Monaco, Evgeniy Eruslanov, Raashid Luqmani, Irina A. Udalova
Software Mentions: 2
Published: about 6 years ago

10.3390/ijms22115448

MMP-9 Deletion Attenuates Arteriovenous Fistula Neointima through Reduced Perioperative Vascular Inflammation
Cited by: 10
Author(s): Yu Chung Shih, Po Yuan Chen, Tai Ming Ko, Po Hsun Huang, Hsu Ma, Der Cherng Tarng
Software Mentions: 2
Published: over 5 years ago

10.1172/jci.insight.140940

Meta-analysis of the gut microbiota in predicting response to cancer immunotherapy in metastatic melanoma
Cited by: 71
Author(s): Angelo Limeta, Boyang Ji, Max Levin, Francesco Gatto, Jens Nielsen
Software Mentions: 2
Published: almost 6 years ago

10.1172/jci.insight.139452

Prenatal inflammation enhances antenatal corticosteroid–induced fetal lung maturation
Cited by: 10
Author(s): Augusto F. Schmidt, Paranthaman Senthamaraikannan, James P. Bridges, Pietro Presicce, Courtney M. Jackson, Lisa Miller, Suhas G. Kallapur, Claire Chougnet, Alan H. Jobe
Software Mentions: 2
Published: almost 6 years ago

10.1007/s00395-020-0793-3

The endocannabinoid anandamide has an anti-inflammatory effect on CCL2 expression in vascular smooth muscle cells
Cited by: 15
Author(s): Beatrice Pflüger‐Müller, James A. Oo, Jan Heering, Timothy Warwick, Ewgenij Proschak, Stefan Günther, Mario Looso, Flávia Rezende, Christian Fork, Gerd Geißlinger, Dominique Thomas, Robert Gurke, Dieter Steinhilber, Marcel H. Schulz, Matthias Leisegang, Ralf P. Brandes
Software Mentions: 2
Published: over 6 years ago

10.1172/jci.insight.144955

Modulation of ATXN1 S776 phosphorylation reveals the importance of allele-specific targeting in SCA1
Cited by: 9
Author(s): Larissa Nitschke, Stephanie L. Coffin, Eder Xhako, Dany B. El-Najjar, James P. Orengo, Elizabeth Alcala, Yun Dai, Ying Wan, Zhandong Liu, Harry T. Orr, Huda Y. Zoghbi
Software Mentions: 2
Published: almost 6 years ago

10.1172/jci.insight.143465

Reversible cardiac disease features in an inducible CUG repeat RNA–expressing mouse model of myotonic dystrophy
Cited by: 10
Author(s): Ashish N. Rao, Hannah M. Campbell, Xiangnan Guan, Tarah A. Word, Xander H.T. Wehrens, Zheng Xia, Thomas A. Cooper
Software Mentions: 2
Published: over 5 years ago

10.1172/jci.insight.148425

Molecular signatures of labor and non-labor myometrium with parsimonious classification from two calcium transporter genes
Cited by: 2
Author(s): William E. Ackerman, Catalin S. Buhimschi, Ali Snedden, Taryn Summerfield, Guomao Zhao, Irina A. Buhimschi
Software Mentions: 2
Published: over 5 years ago

10.1172/jci.insight.141486

CD109-GP130 interaction drives glioblastoma stem cell plasticity and chemoresistance through STAT3 activity
Cited by: 21
Author(s): Pauliina Filppu, Jayendrakishore Tanjore Ramanathan, Kirsi J. Granberg, Erika Gucciardo, Hannu Haapasalo, Kaisa Lehti, Matti Nykter, Vadim Le Joncour, Pirjo Laakkonen
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1008105

Proteasomal inhibition triggers viral oncoprotein degradation via autophagy-lysosomal pathway
Cited by: 8
Author(s): Chandrima Gain, Samaresh Malik, Shaoni Bhattacharjee, Arijit Ghosh, Erle S. Robertson, Benu Brata Das, Abhik Saha
Software Mentions: 2
Published: over 6 years ago

10.1007/s10126-020-09980-5

Red and White Chinook Salmon (Oncorhynchus tshawytscha): Differences in the Transcriptome Profile of Muscle, Liver, and Pylorus
Cited by: 14
Author(s): Angelico Madaro, Ole Torrissen, Paul Whatmore, Santosh P. Lall, Jerome Schmeisser, Viviane Verlhac Trichet, Rolf Erik Olsen
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1008446

Transcytosis subversion by M cell-to-enterocyte spread promotes Shigella flexneri and Listeria monocytogenes intracellular bacterial dissemination
Cited by: 24
Author(s): Camille Rey, Yuen-Yan Chang, Patricia Latour-Lambert, Hugo Varet, Caroline Proux, Rachel Legendre, Jean‐Yves Coppée, Jost Enninga
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1008390

Human cytomegalovirus long noncoding RNA4.9 regulates viral DNA replication
Cited by: 29
Author(s): Julie Tai-Schmiedel, Sharon Karniely, Betty Lau, Adi Ezra, Erez Eliyahu, Aharon Nachshon, Karen Kerr, Nicolás M. Suárez, Michal Schwartz, Andrew J. Davison, Noam Stern-Ginossar
Software Mentions: 2
Published: over 6 years ago

10.1186/s12974-021-02232-w

Anti-AQP4 autoantibodies promote ATP release from astrocytes and induce mechanical pain in rats
Cited by: 18
Author(s): Teruyuki Ishikura, Makoto Kinoshita, Mikito Shimizu, Yoshiaki Yasumizu, Daisuke Motooka, Daisuke Okuzaki, Kazuya Yamashita, Hisashi Murata, Shohei Beppu, Toru Koda, Satoru Tada, Naoyuki Shiraishi, Yoshihiro Sugiyama, Katsuichi Miyamoto, Susumu Kusunoki, Tomoyuki Sugimoto, Atsushi Kumanogoh, Tatsusada Okuno, Hideki Mochizuki
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.ppat.1008555

Rapid in vitro generation of bona fide exhausted CD8+ T cells is accompanied by Tcf7 promotor methylation
Cited by: 33
Author(s): Manzhi Zhao, Caoimhe H. Kiernan, Christopher J. Stairiker, Jennifer L. Hope, Leticia G. León, Marjan van Meurs, Inge Brouwers-Haspels, Ruben Boers, Joachim Boers, Joost Gribnau, Wilfred F. J. van IJcken, Eric Bindels, Remco M. Hoogenboezem, Stefan J. Erkeland, Yvonne M. Mueller, Peter D. Katsikis
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1008528

Head-to-head comparisons of Toxoplasma gondii and its near relative Hammondia hammondi reveal dramatic differences in the host response and effectors with species-specific functions
Cited by: 6
Author(s): Zhee Sheen Wong, Sarah L. Sokol-Borrelli, Philipp Olias, J. P. Dubey, Jon P. Boyle
Software Mentions: 2
Published: over 6 years ago

10.1186/s12936-021-03598-1

In silico identification of novel open reading frames in Plasmodium falciparum oocyte and salivary gland sporozoites using proteogenomics framework
Cited by: 1
Author(s): Sophie Gunnarsson, Sudhakaran Prabakaran
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.ppat.1008821

Innate, non-cytolytic CD8+ T cell-mediated suppression of HIV replication by MHC-independent inhibition of virus transcription
Cited by: 21
Author(s): Michelle Zanoni, David Palesch, Claudia Pinacchio, Maura Statzu, Gregory K. Tharp, Mirko Paiardini, Ann Chahroudi, Steven E. Bosinger, Jack Yoon, Bryan Cox, Guido Silvestri, Deanna A. Kulpa
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.ppat.1008904

The transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress
Cited by: 19
Author(s): Crispín Zavala-Alvarado, Odile Sismeiro, Rachel Legendre, Hugo Varet, Giovanni Bussotti, Jan Bayram, Samuel G. Huete, Guillaume Rey, Jean‐Yves Coppée, Mathieu Picardeau, Nadia Benaroudj
Software Mentions: 2
Published: about 6 years ago

10.1186/s12974-016-0644-1

Transcriptome sequencing reveals that LPS-triggered transcriptional responses in established microglia BV2 cell lines are poorly representative of primary microglia
Cited by: 91
Author(s): Amitabh Das, Sun Hwa Kim, Sarder Arifuzzaman, Tae-Ho Yoon, Jin Choul Chai, Young Seek Lee, Kyoung Sun Park, Kyoung Hwa Jung, Young Gyu Chai
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.ppat.1008748

Extensive proteomic and transcriptomic changes quench the TCR/CD3 activation signal of latently HIV-1 infected T cells
Cited by: 6
Author(s): Eric Carlin, Braxton D. Greer, Kelsey E. Lowman, Alexandra Duverger, Frederic H. Wagner, David C. Moylan, Alexander Dalecki, Shekwonya Samuel, Mildred D. Perez, Steffanie Sabbaj, Olaf Kutsch
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12917-020-02707-7

Equine synovial fluid small non-coding RNA signatures in early osteoarthritis
Cited by: 16
Author(s): Catarina Castanheira, Panagiotis Balaskas, Charlotte Falls, Yalda Ashraf Kharaz, Peter Clegg, Kim Burke, Yongxiang Fang, Philip Dyer, Tim J. M. Welting, Mandy J. Peffers
Software Mentions: 2
Published: almost 6 years ago

10.26508/lsa.201800084

Role of Cnot6l in maternal mRNA turnover
Cited by: 37
Author(s): Filip Horvat, Helena Fulka, Radek Jankele, Radek Malı́k, Jun Ma, Katerina Solcova, Radislav Sedláček, Kristian Vlahoviček, Richard M. Schultz, Petr Svoboda
Software Mentions: 2
Published: over 8 years ago

10.26508/lsa.202000924

Identification and characterization of distinct brown adipocyte subtypes in C57BL/6J mice
Cited by: 12
Author(s): Ruth Karlina, Dominik Lutter, Viktorian Miok, David Fischer, Irem Altun, Theresa Schöttl, Kenji Schorpp, Andreas Israel, Cheryl Cero, James W. Johnson, Ingrid Kapser-Fischer, Anika Böttcher, Susanne Keipert, Annette Feuchtinger, Elisabeth Graf, Tim M. Strom, Axel Walch, Heiko Lickert, Thomas Walzthoeni, Matthias Heinig, Fabian J. Theis, Cristina García‐Cáceres, Aaron M. Cypess, Siegfried Ussar
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.ppat.1009419

Epstein-Barr virus nuclear antigen 3C (EBNA3C) interacts with the metabolism sensing C-terminal binding protein (CtBP) repressor to upregulate host genes
Cited by: 6
Author(s): Makoto Ohashi, Mitchell Hayes, Kyle G. McChesney, Eric Johannsen
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1009430

Plasmodium falciparum malaria drives epigenetic reprogramming of human monocytes toward a regulatory phenotype
Cited by: 34
Author(s): Rajan Guha, Anna Mathioudaki, Safiatou Doumbo, Didier Doumtabé, Jeff Skinner, Gunjan Arora, Shafiuddin Siddiqui, Shanping Li, Kassoum Kayentao, Aissata Ongoïba, Judith B. Zaugg, Boubacar Traoré, Peter D. Crompton
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1009416

Viral genomic, metagenomic and human transcriptomic characterization and prediction of the clinical forms of COVID-19
Cited by: 23
Author(s): Christophe Rodriguez, Nicolas de Prost, Slim Fourati, Claudie Lamoureux, Guillaume Gricourt, Mélissa N’Debi, Florence Canouï‐Poitrine, Isaac Désveaux, Oriane Picard, Vanessa Démontant, Elisabeth Trawinski, R. Lepeule, Laure Surgers, William Vindrios, Jean‐Daniel Lelièvre, Nicolas Mongardon, Olivier Langeron, José L. Cohen, Armand Mekontso-Dessap, Paul‐Louis Woerther, Jean‐Michel Pawlotsky
Software Mentions: 2
Published: over 5 years ago

10.26508/lsa.201900623

Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling
Cited by: 31
Author(s): Simone Bersini, Nikki K. Lytle, Roberta Schulte, Ling Huang, Geoffrey M. Wahl, Martin W. Hetzer
Software Mentions: 2
Published: almost 7 years ago

10.26508/lsa.201800018

Small RNA-Seq reveals novel miRNAs shaping the transcriptomic identity of rat brain structures
Cited by: 6
Author(s): Anaïs Soula, Mélissa Valere, María-José López-González, Vicky Ury-Thiery, Alexis Groppi, Marc Landry, Macha Nikolski, Alexandre Favereaux
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.ppat.1009565

Mitigation of endemic GI-tract pathogen-mediated inflammation through development of multimodal treatment regimen and its impact on SIV acquisition in rhesus macaques
Cited by: 9
Author(s): Rachele M. Bochart, Kathleen Busman‐Sahay, Stephen Bondoc, David W. Morrow, Alexandra M. Ortiz, Christine M. Fennessey, Miranda Fischer, Oriene Shiel, Tonya Swanson, Christine Shriver-Munsch, Hugh Crank, Kimberly Armantrout, Aaron M Barber-Axthelm, Charlotte A. Langner, Cassandra Rae Moats, Caralyn Labriola, Rhonda MacAllister, Michael K. Axthelm, Jason M. Brenchley, Brandon F. Keele, Jacob D. Estes, Scott G. Hansen, Jeremy Smedley
Software Mentions: 2
Published: over 5 years ago

10.1186/s12917-021-02955-1

A defect in the NOG gene increases susceptibility to spontaneous superficial chronic corneal epithelial defects (SCCED) in boxer dogs
Cited by: 5
Author(s): Kathryn M. Meurs, Keith W. Montgomery, Steven G. Friedenberg, Brian Williams, Brian C. Gilger
Software Mentions: 2
Published: over 5 years ago

10.26508/lsa.202000808

The chromatin landscape of primary synovial sarcoma organoids is linked to specific epigenetic mechanisms and dependencies
Cited by: 18
Author(s): Gaylor Boulay, Luisa Cironi, Sara P. Garcia, Shruthi Rengarajan, Yu-Hang Xing, Lukuo Lee, Mary E. Awad, Beverly Naigles, Sowmya Iyer, Liliane C. Broye, Tuğba Keskin, Alexandra Cauderay, Carlo Fusco, Igor Letovanec, Ivan Chebib, Petur Nielsen, Stéphane Tercier, Stéphane Cherix, Tu Nguyen-Ngoc, Gregory M. Coté, Edwin Choy, Paolo Provero, Mario L. Suvà, Miguel N. Rivera, Ivan Stamenkovic, Nicolò Riggi
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.ppat.1009709

Transgenic expression of a T cell epitope in Strongyloides ratti reveals that helminth-specific CD4+ T cells constitute both Th2 and Treg populations
Cited by: 7
Author(s): Bonnie Douglas, Yun Wei, Xinshe Li, Annabel A. Ferguson, Li-Yin Hung, Christopher Pastore, Jonathan R. Kurtz, James B. McLachlan, Thomas J. Nolan, James B. Lok, De’Broski R. Herbert
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1009759

Altered microRNA expression in COVID-19 patients enables identification of SARS-CoV-2 infection
Cited by: 98
Author(s): Ryan J. Farr, Christina L. Rootes, Louise C. Rowntree, Thi H. O. Nguyen, Luca Hensen, Łukasz Kędzierski, Allen Cheng, Katherine Kedzierska, Gough G. Au, Glenn A. Marsh, Seshadri S. Vasan, Chwan Hong Foo, Christopher Cowled, Cameron R. Stewart
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

10.1371/journal.ppat.1009351

A unique GCN5 histone acetyltransferase complex controls erythrocyte invasion and virulence in the malaria parasite Plasmodium falciparum
Cited by: 19
Author(s): Jun Miao, Chengqi Wang, Amuza Byaruhanga Lucky, Xiaoying Liang, Hui Min, Swamy Rakesh Adapa, Rays H. Y. Jiang, Kami Kim, Liwang Cui
Software Mentions: 2
Published: about 5 years ago

10.26508/lsa.201900407

Endogenous RNAi pathway evolutionarily shapes the destiny of the antisense lncRNAs transcriptome
Cited by: 7
Author(s): Ugo Szachnowski, Sara Andjus, Dominika Foretek, Antonin Morillon, Maxime Wéry
Software Mentions: 2
Published: about 7 years ago

10.1186/s40813-021-00226-x

Differences in gene expression and variable splicing events of ovaries between large and small litter size in Chinese Xiang pigs
Cited by: 3
Author(s): Xueqin Ran, Hu Fengbin, Ning Mao, Yi-Qi Ruan, Fanli Yi, Xi Niu, Shihui Huang, Sheng Li, Longjiang You, Fuping Zhang, Liang-Ting Tang, Jiafu Wang, Jianfeng Liu
Software Mentions: 2
Published: about 5 years ago

10.1016/j.postharvbio.2020.111420

New insights into the effects of ethylene on ABA catabolism, sweetening and dormancy in stored potato tubers
Cited by: 18
Author(s): Roberta Tosetti, Amanda J. Waters, Gemma A. Chope, Katherine Cools, M. Carmen Alamar, Simon C. McWilliam, Andrew J. Thompson, Leon A. Terry
Software Mentions: 2
Published: over 5 years ago

10.1098/rspb.2015.1746

Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge Sycon ciliatum
Cited by: 16
Author(s): Jon Bråte, Marcin Adamski, Ralf Stefan Neumann, Kamran Shalchian-Tabrizi, Maja Adamska
Software Mentions: 2
Published: almost 11 years ago

10.1073/pnas.1722125115

Histone H3 lysine 4 methylation signature associated with human undernutrition
Cited by: 22
Author(s): Robin Uchiyama, Kristyna Kupkova, Savera J. Shetty, Alicia S. Linford, Marilyn G. Pray-Grant, Lisa E. Wagar, Mark M. Davis, Rashidul Haque, Alban Gaultier, Marty W. Mayo, Patrick A. Grant, William A. Petri, Stefan Bekiranov, David T. Auble
Software Mentions: 2
Published: about 8 years ago

10.1073/pnas.1820556116

Molecular insights into an ancient form of Paget’s disease of bone
Cited by: 23
Author(s): Barry Shaw, Carla L. Burrell, Darrell Green, Ana Navarro-Martinez, Daniel C. Scott, Anna Daroszewska, R. van ’t Hof, Lynn Smith, Frank Hargrave, Sharad Mistry, Andrew R. Bottrill, Benedikt M. Kessler, Román Fischer, Archana Archana, Tamás Dalmay, William D. Fraser, Kirstin Henneberger, Turi King, Silvia González, Robert Layfield
Software Mentions: 2
Published: over 7 years ago

10.1073/pnas.1911497117

Fibroblast rejuvenation by mechanical reprogramming and redifferentiation
Cited by: 47
Author(s): Bibhas Roy, Luezhen Yuan, Yaelim Lee, Aradhana Bharti, Aditi Mitra, G. V. Shivashankar
Software Mentions: 2
Published: over 6 years ago

10.1073/pnas.2012288117

Phosphoglycolate salvage in a chemolithoautotroph using the Calvin cycle
Cited by: 27
Author(s): Nico J. Claassens, Giovanni Scarinci, Axel Fischer, Avi I. Flamholz, William R. Newell, Stefan Frielingsdorf, Oliver Lenz, Arren Bar‐Even
Software Mentions: 2
Published: about 6 years ago

10.1073/pnas.2125016118

CRISPR-based targeting of DNA methylation in Arabidopsis thaliana by a bacterial CG-specific DNA methyltransferase
Cited by: 33
Author(s): Basudev Ghoshal, Colette L. Picard, Brandon Vong, Suhua Feng, Steven E. Jacobsen
Software Mentions: 2
Published: over 5 years ago

10.1073/pnas.2023050118

Molecular design of the γδT cell receptor ectodomain encodes biologically fit ligand recognition in the absence of mechanosensing
Cited by: 7
Author(s): Robert J. Mallis, Jonathan S. Duke‐Cohan, Dibyendu Das, Aoi Akitsu, Adrienne Luoma, Debasis Banik, Hannah M. Stephens, Paul W. Tetteh, Caitlin D. Castro, Sophie Krahnke, Rebecca E. Hussey, Brian Lawney, Kristine N. Brazin, Pedro A. Reche, Wonmuk Hwang, Erin J. Adams, Matthew J. Lang, Ellis L. Reinherz
Software Mentions: 2
Published: over 5 years ago

10.1007/s13238-018-0560-5

CRISPR/Cas9-mediated gene knockout reveals a guardian role of NF-κB/RelA in maintaining the homeostasis of human vascular cells
Cited by: 17
Author(s): Ping Wang, Zunpeng Liu, Xiaoqian Zhang, Jingyi Li, Liang Sun, Zhenyu Ju, Jian Li, Piu Chan, Guanghui Liu, Weiqi Zhang, Moshi Song, Jing Qu
Software Mentions: 2
Published: over 8 years ago

10.1007/s13238-019-0608-1

Modeling CADASIL vascular pathologies with patient-derived induced pluripotent stem cells
Cited by: 38
Author(s): Ling Chen, Zunpeng Liu, Moshi Song, Weiqi Zhang, Si Wang, Xiaoqian Liu, Shuai Ma, Shuhui Sun, Ling Fu, Qun Chu, Juan Carlos Izpisúa Belmonte, Zhaoxia Wang, Jing Qu, Yun Yuan, Guang Hui Liu
Software Mentions: 2
Published: over 7 years ago

10.1007/s13238-018-0567-y

Chemical screen identifies a geroprotective role of quercetin in premature aging
Cited by: 78
Author(s): Li Geng, Zunpeng Liu, Weiqi Zhang, Wei Li, Zeming Wu, Wei Wang, Rui Ren, Yao Su, Peichang Wang, Liang Sun, Zhenyu Ju, Piu Chan, Moshi Song, Jing Qu, Guanghui Liu
Software Mentions: 2
Published: over 8 years ago

10.3390/proteomes7020014

Extracellular Vesicle Integrins Distinguish Unique Cancers
Cited by: 43
Author(s): Stephanie N. Hurwitz, David G. Meckes
Software Mentions: 2
Published: over 7 years ago

10.26508/lsa.201800024

CHRAC/ACF contribute to the repressive ground state of chromatin
Cited by: 24
Author(s): Alessandro Scacchetti, Laura Brueckner, Dhawal Jain, Tamás Schauer, Xu Zhang, Frank Schnorrer, Bas van Steensel, Tobias Straub, Peter B. Becker
Software Mentions: 2
Published: almost 9 years ago

10.1177/2045894021996190

Extracellular matrix degradation pathways and fatty acid metabolism regulate distinct pulmonary vascular cell types in pulmonary arterial hypertension
Cited by: 8
Author(s): Sharon Mumby, Frédèric Perros, Chee‐Kin Hui, Bo Xu, Weiqing Xu, Vahid Elyasigomari, Aurélie Hautefort, Grégoire Manaud, Marc Humbert, Kian Fan Chung, SJ Wort, Ian M. Adcock
Software Mentions: 2
Published: almost 6 years ago

10.1080/15476286.2018.1481697

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum
Cited by: 6
Author(s): Zhen Liao, Jonas Kjellin, Marc P. Hoeppner, Manfred Grabherr, Fredrik Söderbom
Software Mentions: 2
Published: over 8 years ago

10.1098/rsos.171718

Differential gene expression is not required for facultative sex allocation: a transcriptome analysis of brain tissue in the parasitoid wasp Nasonia vitripennis
Cited by: 6
Author(s): Nicola Cook, Rebecca A. Boulton, Jade Green, Urmi Trivedi, Eran Tauber, Bart Pannebakker, Michael G. Ritchie, David M. Shuker
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12917-016-0653-4

Metagenomic analysis of rumen microbial population in dairy heifers fed a high grain diet supplemented with dicarboxylic acids or polyphenols
Cited by: 53
Author(s): Roberta De Nardi, Giorgio Marchesini, Shucong Li, Ehsan Khafipour, Kees Plaizier, Matteo Gianesella, Rebecca Ricci, Igino Andrighetto, Severino Segato
Software Mentions: 2
Published: over 10 years ago

10.1016/j.redox.2019.101397

Effects of diets high in animal or plant protein on oxidative stress in individuals with type 2 diabetes: A randomized clinical trial
Cited by: 20
Author(s): Olga Pivovarova-Ramich, Mariya Markova, Daniela Weber, Stephanie Sucher, Silke Hornemann, Natalia Rudovich, Jens Raila, Daniele Yumi Sunaga-Franze, Sascha Sauer, Sascha Rohn, Andreas F. H. Pfeiffer, Tilman Grune
Software Mentions: 2
Published: almost 7 years ago

10.1016/j.redox.2020.101713

Deletion of NoxO1 limits atherosclerosis development in female mice
Cited by: 11
Author(s): Giulia Buchmann, Christoph Schürmann, Timothy Warwick, Marcel H. Schulz, Manuela Spaeth, Oliver Müller, Katrin Schröder, Hanjoong Jo, Norbert Weißmann, Ralf P. Brandes
Software Mentions: 2
Published: about 6 years ago

10.1016/j.redox.2021.102030

Compensatory expression of NRF2-dependent antioxidant genes is required to overcome the lethal effects of Kv11.1 activation in breast cancer cells and PDOs
Cited by: 5
Author(s): Vitalyi Senyuk, Najmeh Eskandari, Ying Jiang, Rebeca García-Varela, Rachel Sundstrom, Luigi Leanza, Roberta Peruzzo, Mark E. Burkard, Richard D. Minshall, Sandro Gentile
Software Mentions: 2
Published: about 5 years ago

10.26508/lsa.201900495

Conservation of cell-intrinsic immune responses in diverse nonhuman primate species
Cited by: 6
Author(s): Jenna M. Gaska, Lance Parsons, Metodi Balev, Ann Cirincione, Wei Wang, Robert E. Schwartz, Alexander Ploß
Software Mentions: 2
Published: about 7 years ago

10.26508/lsa.201800173

A C/EBPα–Wnt connection in gut homeostasis and carcinogenesis
Cited by: 3
Author(s): Julian Heuberger, Undine Hill, Susann Förster, Karin Zimmermann, Victoria Malchin, Anja A. Kühl, Ulrike Stein, Michael Vieth, Walter Birchmeier, Achim Leutz
Software Mentions: 2
Published: almost 8 years ago

10.3390/ijms22137129

Comparative Transcriptome Analysis Reveals Genetic Mechanisms of Sugarcane Aphid Resistance in Grain Sorghum
Cited by: 9
Author(s): Desalegn D. Serba, Xiaoxi Meng, James C. Schnable, Elfadil M. A. Bashir, J.P. Michaud, P. V. Vara Prasad, Ramasamy Perumal
Software Mentions: 2
Published: over 5 years ago

10.26508/lsa.202000640

EBV renders B cells susceptible to HIV-1 in humanized mice
Cited by: 21
Author(s): Donal McHugh, Renier Myburgh, Nicole Caduff, Michael Spohn, Yik Lim Kok, Christian W. Keller, Anita Murer, Bithi Chatterjee, Julia Rühl, Christine Engelmann, Obinna Chijioke, Isaak Quast, Mohaned Shilaih, Victoria P Strouvelle, Katja Neumann, Thomas Menter, Stephan Dirnhofer, Janice K. P. Lam, Kwai Fung Hui, Simon Bredl, Erika Schlaepfer, Silvia Sorce, Andrea Zbinden, Riccarda Capaul, Jan D. Lünemann, Adriano Aguzzi, Aks Chiang, Werner Kempf, Alexandra Trkola, Karin J. Metzner, Markus G. Manz, Adam Grundhoff, Roberto F. Speck, Christian Münz
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms22136663

Expression Profile of New Marker Genes Involved in Differentiation of Canine Adipose-Derived Stem Cells into Osteoblasts
Cited by: 2
Author(s): Maurycy Jankowski, Mariusz Kaczmarek, Grzegorz Wąsiatycz, Claudia Dompe, Paul Mozdziak, J. M. Jaśkowski, Hanna Piotrowska‐Kempisty, Bartosz Kempisty
Software Mentions: 2
Published: over 5 years ago

10.26508/lsa.201900545

MAPK pathway mutations in head and neck cancer affect immune microenvironments and ErbB3 signaling
Cited by: 25
Author(s): Hoi Lam Ngan, Yuchen Liu, Andrew Yuon Fong, P.W.F. Poon, Chun Yeung, Sharon Suet Man Chan, Amy Hing‐Ling Lau, Wenying Piao, Hui Li, Jessie Sze Wing Tse, Kwok Wai Lo, Siu-Hong Chan, Yu Su, Jason Ying Kuen Chan, Chin Wang Lau, Gordon B. Mills, Jennifer R. Grandis, Vivian Wai Yan Lui
Software Mentions: 2
Published: over 6 years ago

10.1186/s12931-019-1032-z

RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD
Cited by: 37
Author(s): Jarrett Morrow, Robert Chase, Margaret M. Parker, Kimberly Glass, Minseok Seo, Miguel Divo, Caroline A. Owen, Peter J. Castaldi, Dawn L. DeMeo, Edwin K. Silverman, Craig P. Hersh
Software Mentions: 2
Published: over 7 years ago

10.1186/s12931-019-1038-6

AGER expression and alternative splicing in bronchial biopsies of smokers and never smokers
Cited by: 20
Author(s): Alen Faiz, Maarten van den Berge, Cornelis J Vermeulen, Nick H. T. ten Hacken, Victor Guryev, Simon D. Pouwels
Software Mentions: 2
Published: over 7 years ago

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