bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.3390/jcm9010127

Differential Gene Expression in Circulating CD14+ Monocytes Indicates the Prognosis of Critically Ill Patients with Sepsis
Cited by: 15
Author(s): Anke Liepelt, Philipp Hohlstein, Hendrik Gussen, Jia Xue, Anna C. Aschenbrenner, Thomas Ulas, Lukas Buendgens, Klaudia Theresa Warzecha, Matthias Bartneck, Tom Luedde, Christian Trautwein, Joachim L. Schultze, Alexander Koch, Frank Tacke
Software Mentions: 1
Published: almost 7 years ago

10.3390/jcm9051549

Identification of Potential Oral Microbial Biomarkers for the Diagnosis of Periodontitis
Cited by: 23
Author(s): Hee Sam Na, Si Yeong Kim, Hye-Jung Han, Hyun Joo Kim, Ju Youn Lee, Jae Hyung Lee, Jin Chung
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0220907

Altered expression of miRNAs and mRNAs reveals the potential regulatory role of miRNAs in the developmental process of early weaned goats
Cited by: 15
Author(s): Rongrong Liao, Yuhua Lv, Lihui Zhu, Yu Lin
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0201969

Cranberry-derived proanthocyanidins induce a differential transcriptomic response within Candida albicans urinary biofilms
Cited by: 3
Author(s): Anitha Sundararajan, Hallie S. Rane, Thiruvarangan Ramaraj, Johnny A. Sena, Amy B. Howell, Stella M. Bernardo, Faye Schilkey, Samuel A. Lee
Software Mentions: 1
Published: over 8 years ago

10.3390/jcm9061886

Cohen Syndrome Patient iPSC-Derived Neurospheres and Forebrain-Like Glutamatergic Neurons Reveal Reduced Proliferation of Neural Progenitor Cells and Altered Expression of Synapse Genes
Cited by: 8
Author(s): You‐Kyung Lee, Su-Kyeong Hwang, Soo-Kyung Lee, Jung Eun Yang, Jae-Man Kwak, Hyunhyo Seo, Hyunjun Ahn, Yong Seok Lee, Jang Hwan Kim, Chae‐Seok Lim, Bong‐Kiun Kaang, Jae Hyung Lee, Jina Lee, Kyung-Min Lee
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0213770

Investigation of somatic single nucleotide variations in human endogenous retrovirus elements and their potential association with cancer
Cited by: 7
Author(s): Ting-Chia Chang, Santosh Goud, John Torcivia-Rodriguez, Yu Hu, Qing Pan, Robel Kahsay, Jonas Blomberg, Raja Mazumder
Software Mentions: 1
Published: over 7 years ago

10.3390/jcm10030375

Differential microRNA Expression in USP8-Mutated and Wild-Type Corticotroph Pituitary Tumors Reflect the Difference in Protein Ubiquitination Processes
Cited by: 8
Author(s): Mateusz Bujko, Paulina Kober, Joanna Boresowicz, Natalia Rusetska, Natalia Żeber‐Lubecka, Agnieszka Paziewska, Monika Pękul, Grzegorz Zieliński, Andrzej Styk, Jacek Kunicki, Jerzy Ostrowski, Janusz A. Siedlecki, Maria Maksymowicz
Software Mentions: 1
Published: almost 6 years ago

10.3390/jcm10030491

Implication of miR-126 and miR-139-5p in Plasmacytoid Dendritic Cell Dysregulation in Systemic Sclerosis
Cited by: 17
Author(s): Eleni Chouri, Maojie Wang, Maarten R Hillen, Chiara Angiolilli, Sandra Silva-Cardoso, Catharina G K Wichers, Maarten van der Kroef, Cornelis P. J. Bekker, Marta Cossu, Lenny van Bon, Alsya J. Affandi, Tiago Carvalheiro, Aridaman Pandit, Joël A G van Roon, Lorenzo Beretta, Boudewijn M.T. Burgering, Timothy R D J Radstake, Marzia Rossato
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0189608

Microcystin-LR does not induce alterations to transcriptomic or metabolomic profiles of a model heterotrophic bacterium
Cited by: 4
Author(s): Robbie M. Martin, Stephen P. Dearth, Gary R. LeCleir, Shawn R. Campagna, Elizabeth Fozo, Erik R. Zinser, Steven W. Wilhelm
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0248996

Reduction of fibrosis and immune suppressive cells in ErbB2-dependent tumorigenesis by an LXR agonist
Cited by: 3
Author(s): Sheng Gao, Hongyan Yuan, Lü Jin, Suman Ranjit, Julia Panov, Xun Lu, Moshe Levi, Robert I. Glazer
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0254985

Interleukin-22 mitigates acute respiratory distress syndrome (ARDS)
Cited by: 7
Author(s): Sharven Taghavi, Olan Jackson‐Weaver, Sarah Abdullah, Alanna Wanek, Robert Drury, Jacob Packer, Aaron Cotton-Betteridge, Juan Duchesne, Derek Pociask, Jay K. Kolls
Software Mentions: 1
Published: about 5 years ago

10.1017/cts.2021.801

Excess dietary fructose does not alter gut microbiota or permeability in humans: A pilot randomized controlled study
Cited by: 11
Author(s): José O. Alemán, Wendy A. Henderson, Joseph R. Walker, Andrea Ronning, Drew R. Jones, Peter J. Walter, Scott G. Daniel, Kyle Bittinger, Roger Vaughan, Robert B. MacArthur, Kun Chen, Jan L. Breslow, Peter R. Holt
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms22052399

Combined Transcriptomic and Metabolomic Analysis Reveals the Role of Phenylpropanoid Biosynthesis Pathway in the Salt Tolerance Process of Sophora alopecuroides
Cited by: 32
Author(s): Youcheng Zhu, Qingyu Wang, Ying Wang, Yang Xu, Jingwen Li, Suoqi Zhao, Doudou Wang, Zuwei Ma, Yanting Fan, Yajing Liu
Software Mentions: 1
Published: over 5 years ago

10.1155/2019/8616373

Comparative Analysis of the Transcriptome of Latent Autoimmune Diabetes in Adult (LADA) Patients from Eastern China
Cited by: 2
Author(s): Yuqiao Ji, Dongmei Jiang, Jian Liu, Xiaolong Chen, Tian Xia, Zhujun Yin, Lei Li, Hao Jin, Hongmei Chen, Mingzhong Sun
Software Mentions: 1
Published: almost 7 years ago

10.1111/jeb.13410

Sexually dimorphic gene expression and transcriptome evolution provide mixed evidence for a fast-Z effect inHeliconius
Cited by: 28
Author(s): Ana Pinharanda, Marjolaine Rousselle, Simon H. Martin, Joe J. Hanly, John W. Davey, Sujai Kumar, Nicolas Galtier, Chris D. Jiggins
Software Mentions: 1
Published: almost 8 years ago

10.3390/ijms22052518

Selenite Inhibits Notch Signaling in Cells and Mice
Cited by: 5
Author(s): Michael R. Powers, Liu Liu, Dane Deemer, Selina Chen, Aaron Scholl, Masafumi Yoshinaga, Zijuan Liu
Software Mentions: 1
Published: over 5 years ago

10.1093/jxb/erw307

The photomorphogenic factors UV-B RECEPTOR 1, ELONGATED HYPOCOTYL 5, and HY5 HOMOLOGUE are part of the UV-B signalling pathway in grapevine and mediate flavonol accumulation in response to the environment
Cited by: 92
Author(s): Rodrigo Loyola, Daniela P Herrera, Abraham Más, D. Wong, Janine Höll, Erika Cavallini, Alessandra Amato, Akifumi Azuma, Tobias Ziegler, Felipe Aquea, Simone D. Castellarin, Jochen Bogs, Giovanni Battista Tornielli, Álvaro Peña‐Neira, Stefan Czemmel, José Antonio Alcalde, José Tomás Matus, Patricio Arce‐Johnson
Software Mentions: 1
Published: about 10 years ago

10.1093/jxb/erw506

Red blotch disease alters grape berry development and metabolism by interfering with the transcriptional and hormonal regulation of ripening
Cited by: 84
Author(s): Bárbara Blanco-Ulate, Helene Hopfer, Rosa Figueroa‐Balderas, Zirou Ye, Rosa M. Rivero, Alfonso Albacete, Francisco Pérez‐Alfocea, Renata Koyama, Michael M. Anderson, Rhonda J. Smith, Susan E. Ebeler, Dario Cantu
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12864-018-4500-9

Transcriptomic changes in Cucurbita pepo fruit after cold storage: differential response between two cultivars contrasting in chilling sensitivity
Cited by: 20
Author(s): Fátima Carvajal, Raquel Rosales, Francisco Palma, Susana Manzano, Joaquı́n Cañizares, Manuel Jamilena, Dolores Garrido
Software Mentions: 1
Published: almost 9 years ago

10.1093/jxb/ery251

An early ABA-induced stomatal closure, Na+ sequestration in leaf vein and K+ retention in mesophyll confer salt tissue tolerance in Cucurbita species
Cited by: 66
Author(s): Mengliang Niu, Jin Xie, Chen Chen, Haishun Cao, Jingyu Sun, Qiusheng Kong, Sergey Shabala, Lana Shabala, Yuan Huang, Zijun Bie
Software Mentions: 1
Published: over 8 years ago

10.1093/jxb/ery244

Rice H2A.Z negatively regulates genes responsive to nutrient starvation but promotes expression of key housekeeping genes
Cited by: 30
Author(s): Sara Zahraeifard, Maryam Foroozani, Aliasghar Sepehri, Dong Ha Oh, Guannan Wang, Venkata Mangu, Bin Chen, Niranjan Baisakh, Maheshi Dassanayake, Aaron P. Smith
Software Mentions: 1
Published: over 8 years ago

10.1093/jxb/ery405

Transcriptome analysis and metabolic profiling reveal the key role of α-linolenic acid in dormancy regulation of European pear
Cited by: 23
Author(s): Gilad Gabay, Adi Faigenboim, Yardena Dahan, Yacov Izhaki, Maxim Itkin, Sergey Malitsky, Yonatan Elkind, Moshe A. Flaishman
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0179571

WetA bridges cellular and chemical development in Aspergillus flavus
Cited by: 34
Author(s): Ming-Yueh Wu, Matthew E. Mead, Sun-Chang Kim, Antonis Rokas, Jae-Hyuk Yu
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0168075

Two Subclasses of Differentially Expressed TPS1 Genes and Biochemically Active TPS1 Proteins May Contribute to Sugar Signalling in Kiwifruit Actinidia chinensis
Cited by: 3
Author(s): Charlotte Voogd, Lara Brian, Erika Varkonyi‐Gasic
Software Mentions: 1
Published: almost 10 years ago

10.1093/jxb/eraa193

The CLE53–SUNN genetic pathway negatively regulates arbuscular mycorrhiza root colonization in Medicago truncatula
Cited by: 32
Author(s): Magda Karlo, Clarissa Boschiero, Katrine Gram Landerslev, Gonzalo Sancho Blanco, Jiangqi Wen, Kirankumar S. Mysore, Xinbin Dai, Patrick Xuechun Zhao, Thomas C. de Bang
Software Mentions: 1
Published: over 6 years ago

10.1093/jxb/eraa256

The amino acid transporter AAP1 mediates growth and grain yield by regulating neutral amino acid uptake and reallocation in Oryza sativa
Cited by: 57
Author(s): Yuanyuan Ji, Weiting Huang, Bowen Wu, Zhongming Fang, Xuelu Wang
Software Mentions: 1
Published: over 6 years ago

10.1093/jxb/eraa119

EARLY BUD BREAK 1 triggers bud break in peach trees by regulating hormone metabolism, the cell cycle, and cell wall modifications
Cited by: 17
Author(s): Xuehui Zhao, Xiaolun Han, Qingjie Wang, Xuxu Wang, Xiude Chen, Ling Li, Xiling Fu, Dongsheng Gao
Software Mentions: 1
Published: over 6 years ago

10.1093/jxb/eraa451

Functional divergence of diacylglycerol acyltransferases in the unicellular green alga Haematococcus pluvialis
Cited by: 13
Author(s): Haiyan Ma, Xiaoying Wu, Zi-Wang Wei, Liang Zhao, Zhongze Li, Qing Liang, Jie Zheng, Yu Wang, Yanhua Li, Linfei Huang, Qiang Hu, Danxiang Han
Software Mentions: 1
Published: about 6 years ago

10.1093/jxb/eraa574

The WOX family transcriptional regulator SlLAM1 controls compound leaf and floral organ development inSolanum lycopersicum
Cited by: 26
Author(s): Chaoqun Wang, Baolin Zhao, Liangliang He, Shaoli Zhou, Ye Liu, Weiyue Zhao, Shiwei Guo, Ruoruo Wang, Quanzi Bai, Youhan Li, Dongfa Wang, Qing Wu, Yuan‐Fan Yang, Yu Liu, Million Tadege, Jianghua Chen
Software Mentions: 1
Published: almost 6 years ago

10.1093/jxb/eraa601

Host susceptibility factors render ripe tomato fruit vulnerable to fungal disease despite active immune responses
Cited by: 27
Author(s): Christian J. Silva, Casper van den Abeele, Isabel Ortega‐Salazar, Victor Papin, Jaclyn A Adaskaveg, Duoduo Wang, Clare L. Casteel, Graham B. Seymour, Bárbara Blanco-Ulate
Software Mentions: 1
Published: almost 6 years ago

10.1093/jxb/erab102

Penicillium chrysogenum polypeptide extract protects tobacco plants from tobacco mosaic virus infection through modulation of ABA biosynthesis and callose priming
Cited by: 10
Author(s): Yu Liu, Mengting Jiao, Yingjuan Li, Yu Zhong, Xiaoqin Li, Zhuangzhuang Chen, Suiyun Chen, J. G. Wang
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22062803

Overexpression of Salicylic Acid Carboxyl Methyltransferase (CsSAMT1) Enhances Tolerance to Huanglongbing Disease in Wanjincheng Orange (Citrus sinensis (L.) Osbeck)
Cited by: 13
Author(s): Xin Zou, Ke Zhao, Yunuo Liu, Meirong Du, Lin Zheng, Shuai Wang, Le Xu, Aihong Peng, Yongrui He, Long Qin, Shanchun Chen
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.ppat.1005361

A Shift from Cellular to Humoral Responses Contributes to Innate Immune Memory in the Vector Snail Biomphalaria glabrata
Cited by: 94
Author(s): Silvain Pinaud, Julien Portela, David Timothy Duval, Fanny C. Nowacki, Marie-Aude Olive, Jean‐François Allienne, Richard Galinier, Nolwenn M. Dheilly, Sylvie Kieffer‐Jaquinod, Guillaume Mitta, André Thèron, Benjamin Gourbal
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0225267

Genome wide analysis of gene expression changes in skin from patients with type 2 diabetes
Cited by: 17
Author(s): Eri Takematsu, Adrianne Spencer, Jeff Auster, Po-Chih Chen, Annette Graham, Patricia Martin, Aaron Baker
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-019-6391-9

Different transcriptional response between susceptible and resistant common carp (Cyprinus carpio) fish hints on the mechanism of CyHV-3 disease resistance
Cited by: 20
Author(s): Roni Tadmor‐Levi, Adi Doron‐Faigenboim, Evgeniya Marcos‐Hadad, Jules Petit, Gideon Hulata, Maria Forlenza, G.F. Wiegertjes, Lior David
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0167003

Regulation and Maintenance of an Adoptive T-Cell Dependent Memory B Cell Pool
Cited by: 2
Author(s): Marie Anson, Inês F. Amado, Marie-Pierre Mailhé, Emmanuel Donnadieu, Sylvie Garcia, François Huetz, António A. Freitas
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.ppat.1006165

Transcriptional Profiling in Experimental Visceral Leishmaniasis Reveals a Broad Splenic Inflammatory Environment that Conditions Macrophages toward a Disease-Promoting Phenotype
Cited by: 59
Author(s): Fanlei Kong, Ómar A. Saldarriaga, Heidi Spratt, E. Yaneth Osorio, Bruno L. Travi, Bruce A. Luxon, Peter C. Melby
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.ppat.1006340

Filamentous fungal carbon catabolite repression supports metabolic plasticity and stress responses essential for disease progression
Cited by: 66
Author(s): Sarah R Beattie, Kenneth M. K. Mark, Arsa Thammahong, Laure Nicolas Annick Ries, Sourabh Dhingra, Alayna K. Caffrey-Carr, Chao Cheng, Candice C. Black, Paul Bowyer, Michael Bromley, Joshua J. Obar, Gustavo H. Goldman, Robert A. Cramer
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.ppat.1006471

Cross-modulation of pathogen-specific pathways enhances malnutrition during enteric co-infection with Giardia lamblia and enteroaggregative Escherichia coli
Cited by: 63
Author(s): Luther A. Bartelt, David T. Bolick, Jordi Mayneris‐Perxachs, Glynis L. Kolling, Gregory L. Medlock, Edna I. Zaenker, Jeffery Donowitz, Rose Viguna Thomas-Beckett, Allison R. Rogala, Ian M. Carroll, Steven M. Singer, Jason A. Papin, Jonathan R. Swann, Richard L. Guerrant
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.ppat.1006560

Expression of the RNA-binding protein RBP10 promotes the bloodstream-form differentiation state in Trypanosoma brucei
Cited by: 78
Author(s): Elisha Mugo, Christine Clayton
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.ppat.1006524

Herpesviruses shape tumour microenvironment through exosomal transfer of viral microRNAs
Cited by: 69
Author(s): Ohad Yogev, Stephen Henderson, Matthew J. Hayes, Sara Marelli, Yifat Ofir-Birin, Neta Regev‐Rudzki, Javier Herrero, Tariq Enver
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pgen.1007642

Activating PAX gene family paralogs to complement PAX5 leukemia driver mutations
Cited by: 3
Author(s): Matthew R. Hart, Donovan J. Anderson, Christopher C. Porter, Tobias Neff, Michael Levin, Marshall S. Horwitz
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pgen.1007169

Mutations in THAP1/DYT6 reveal that diverse dystonia genes disrupt similar neuronal pathways and functions
Cited by: 56
Author(s): Zuchra Zakirova, Tomas Fanutza, Justine Bonet, Ben Readhead, Weijia Zhang, Zhengzi Yi, Geneviève Beauvais, Thomas P. Zwaka, Laurie J. Ozelius, Robert D. Blitzer, Pedro Gonzalez‐Alegre, Michelle E. Ehrlich
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.ppat.1006844

RNA-Seq of Kaposi’s sarcoma reveals alterations in glucose and lipid metabolism
Cited by: 40
Author(s): For Yue Tso, Andrew V. Kossenkov, Salum J. Lidenge, Owen Ngalamika, John R. Ngowi, Julius Mwaiselage, Jayamanna Wickramasinghe, Eun Hee Kwon, John T. West, Paul M. Lieberman, Charles Wood
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.ppat.1006802

Regional and subtype-dependent miRNA signatures in sporadic Creutzfeldt-Jakob disease are accompanied by alterations in miRNA silencing machinery and biogenesis
Cited by: 25
Author(s): Franc Llorens, Katrin Thüne, Eulàlia Martı́, Ειrini Kanata, Dimitra Dafou, Daniela Díaz-Lucena, Ana Vivancos, Orr Shomroni, Saima Zafar, Matthias Schmitz, Uwe Michel, Natalia Fernández‐Borges, Olivier Andréoletti, José Antonio del Río, Juana Díez, André Fischer, Stefan Bonn, Theodoros Sklaviadis, Juan María Torres, Isidre Ferrer, Inga Zerr
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.ppat.1006868

Interferon regulatory factor 8 regulates caspase-1 expression to facilitate Epstein-Barr virus reactivation in response to B cell receptor stimulation and chemical induction
Cited by: 40
Author(s): Dongwen Lv, Kun Zhang, Renfeng Li
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.ppat.1006917

SpdC, a novel virulence factor, controls histidine kinase activity in Staphylococcus aureus
Cited by: 38
Author(s): Olivier Poupel, Caroline Proux, Bernd Jabla, Tarek Msadek, Sarah Dubrac
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.ppat.1006940

Pleiotropic roles of Clostridium difficile sin locus
Cited by: 45
Author(s): Brintha P. Girinathan, Jiangtao Ou, Bruno Dupuy, Revathi Govind
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.ppat.1006985

Type I interferon signaling attenuates regulatory T cell function in viral infection and in the tumor microenvironment
Cited by: 64
Author(s): Arunakumar Gangaplara, Craig Martens, Eric Dahlstrom, Amina Metidji, Ameya Gokhale, Deborah D. Glass, Maria Lopez-Ocasio, Rachel Baur, Kishore Kanakabandi, Stephen F. Porcella, Ethan M. Shevach
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.ppat.1007007

Cryptococcus neoformans can form titan-like cells in vitro in response to multiple signals
Cited by: 92
Author(s): Nuria Trevijano-Contador, Haroldo César de Oliveira, Rocío García-Rodas, Suélen Andreia Rossi, Irene L. Llorente, Ángel Zaballos, Guilhem Janbon, Joaquı́n Ariño, Óscar Zaragoza
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.ppat.1007153

The C. difficile clnRAB operon initiates adaptations to the host environment in response to LL-37
Cited by: 21
Author(s): Emily Woods, Adrianne N. Edwards, Kevin O. Childress, Joshua B. Jones, Shonna M. McBride
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.ppat.1007246

Type I IFN signaling blockade by a PASylated antagonist during chronic SIV infection suppresses specific inflammatory pathways but does not alter T cell activation or virus replication
Cited by: 29
Author(s): Krystelle Nganou-Makamdop, James M. Billingsley, Zak A. Yaffe, Gregory O’Connor, Gregory K. Tharp, Amy Ransier, Farida Laboune, Rodrigo Matus‐Nicodemos, Andrea M Lerner, Lavina Gharu, Jennifer Rosenstein, Mandy L. Ford, Martin Schlapschy, Nadine Kuhn, Alexandra Lensch, Jeffrey D. Lifson, Martha Nason, Arne Skerra, Gideon Schreiber, Steven E. Bosinger, Daniel C. Douek
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pgen.1007090

Regulation of transcription elongation in response to osmostress
Cited by: 19
Author(s): Andréa Silva, Santiago Cavero, Victoria Begley, Carme Solé, René Böttcher, Sebastián Chávez, Francesc Posas, Eulàlia de Nadal
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.ppat.1007465

Specificity and functional interplay between influenza virus PA-X and NS1 shutoff activity
Cited by: 34
Author(s): Chutikarn Chaimayo, Megan M Dunagan, Tsuyoshi Hayashi, Netty Santoso, Toru Takimoto
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.ppat.1007491

EspL is essential for virulence and stabilizes EspE, EspF and EspH levels in Mycobacterium tuberculosis
Cited by: 28
Author(s): Claudia Sala, Nina T. Odermatt, Paloma Soler-Arnedo, Muhammet F. Gülen, Sofia von Schultz, Andrej Benjak, Stewart T. Cole
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.ppat.1007164

Plasmodium male gametocyte development and transmission are critically regulated by the two putative deadenylases of the CAF1/CCR4/NOT complex
Cited by: 24
Author(s): Kevin J. Hart, Jenna Oberstaller, Michael P. Walker, Allen M. Minns, Mark Kennedy, Ian Padykula, John Adams, Scott E. Lindner
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.ppat.1007974

Humoral immunity prevents clinical malaria during Plasmodium relapses without eliminating gametocytes
Cited by: 15
Author(s): Chester J. Joyner, Cristiana Ferreira Alves de Brito, Celia L. Saney, Regina Joice Cordy, Maren L. Smith, Stacey A. Lapp, Mónica Cabrera-Mora, Shuya Kyu, Nicolas Lackman, Mustafa V. Nural, Jeremy D. DeBarry, Jessica C. Kissinger, Mark P. Styczynski, F Eun-Hyung Lee, Tracey J. Lamb, Mary R. Galinski
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-020-6648-3

Sexual-biased gene expression of olfactory-related genes in the antennae of Conogethes pinicolalis (Lepidoptera: Crambidae)
Cited by: 7
Author(s): Dapeng Jing, Tiantao Zhang, Shuxiong Bai, Kanglai He, Sivaprasath Prabu, Jing Luan, Zhenying Wang
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.ppat.1008048

Plasmodium kinesin-8X associates with mitotic spindles and is essential for oocyst development during parasite proliferation and transmission
Cited by: 30
Author(s): Mohammad Zeeshan, F. B. Shilliday, Tianyang Liu, Steven Abel, Tobias Mourier, David J. P. Ferguson, Edward Rea, Rebecca R. Stanway, Magali Roques, Desiree Williams, Emilie Daniel, Declan Brady, A. J. Roberts, Anthony A. Holder, Arnab Pain, Karine G. Le Roch, Carolyn A. Moores, Rita Tewari
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.ppat.1008072

Lung transcriptional unresponsiveness and loss of early influenza virus control in infected neonates is prevented by intranasal Lactobacillus rhamnosus GG
Cited by: 37
Author(s): Ogan K. Kumova, Adam J Fike, Jillian L. Thayer, Linda Nguyen, Joshua Chang Mell, Judy Mae Pascasio, Christopher J. Stairiker, Leticia G. León, Peter D. Katsikis, Alison J. Carey
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pgen.1008732

The transcription and export complex THO/TREX contributes to transcription termination in plants
Cited by: 10
Author(s): Ghazanfar Abbas Khan, Jules Deforges, Rodrigo S. Reis, Yi-Fang Hsieh, Jonatan Montpetit, Wojciech Antosz, Luca Santuari, Christian S. Hardtke, Klaus D. Grasser, Yves Poirier
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1009543

Multi-omics approach identifies germline regulatory variants associated with hematopoietic malignancies in retriever dog breeds
Cited by: 9
Author(s): Judith Evans, Heidi G. Parker, Gerard R. Rutteman, Jocelyn Plassais, Guy C. M. Grinwis, Alex C. Harris, Susan E. Lana, Elaine A. Ostrander
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1009821

RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics
Cited by: 14
Author(s): Donghui Choe, Richard Szubin, Saugat Poudel, Anand V. Sastry, Yoseb Song, Yong Jae Lee, Suhyung Cho, Jaehyung Kim, Byung-Kwan Cho
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pcbi.1008596

Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types
Cited by: 13
Author(s): Ke Chen, Amitesh Anand, Connor A. Olson, Troy E. Sandberg, Ye Gao, Nathan Mih, Jaehyung Kim
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.ppat.1008270

New 2-Ethylthio-4-methylaminoquinazoline derivatives inhibiting two subunits of cytochrome bc1 in Mycobacterium tuberculosis
Cited by: 36
Author(s): Andréanne Lupien, Caroline S. Foo, Svetlana Savina, Anthony Vocat, Jérémie Piton, Natalia Monakhova, Andrej Benjak, Dirk A. Lamprecht, Adrie J. C. Steyn, Kévin Pethe, Vadim Makarov, Stewart T. Cole
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12284-021-00512-w

Characterization and Evaluation of Transgenic Rice Pyramided with the Pi Genes Pib, Pi25 and Pi54
Cited by: 8
Author(s): Peng Ma, Lin X, Xingjia Xiang, Haiyan Ren, Xiaoqin Fan, Kegui Chen
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pcbi.1005287

m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks
Cited by: 35
Author(s): Song-Yao Zhang, Shaowu Zhang, Lian Liu, Jia Meng, Yufei Huang
Software Mentions: 1
Published: almost 10 years ago

10.1016/j.xpro.2021.100447

Application of high-throughput 5′P sequencing for the study of co-translational mRNA decay
Cited by: 4
Author(s): Yujie Zhang, Vicent Pelechano
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22073688

Dose-Dependent Physiological and Transcriptomic Responses of Lettuce (Lactuca sativa L.) to Copper Oxide Nanoparticles—Insights into the Phytotoxicity Mechanisms
Cited by: 25
Author(s): Tiantian Xiong, Shasha Zhang, Zhuangzhuang Kang, Ting Zhang, Shaoshan Li
Software Mentions: 1
Published: over 5 years ago

10.1016/j.xpro.2021.100716

Protocol to generate and characterize biofouling transformants of a model marine diatom
Cited by: 0
Author(s): Weiqi Fu, Bushra Dohai, Diana Charles El Assal, Sarah Daakour, Amnah Alzahmi, David R. Nelson, Ashish Jaiswal, Alexandra Mystikou, Mehar Sultana, James Weston, Kourosh Salehi‐Ashtiani
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pcbi.1007562

Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection
Cited by: 10
Author(s): Jinyuan Yan, Henri Estanbouli, Chen Liao, Wook Kim, Jonathan M. Monk, Rayees Rahman, Mini Kamboj, Bernhard Ø. Palsson, Wang Qiu, João B. Xavier
Software Mentions: 1
Published: almost 7 years ago

10.1093/schbul/sby017.541

F10. DIFFERENTIAL EXPRESSION OF MICRORNAS IN CEREBROSPINAL FLUID AND PLASMA SAMPLES IN SCHIZOPHRENIA
Cited by: 5
Author(s): Juan Gallego, Eric Alsop, Todd Lencz, Kendall Van Keuren‐Jensen, Anil K. Malhotra
Software Mentions: 1
Published: over 8 years ago

10.1126/sciadv.aau7314

Improving the metabolic fidelity of cancer models with a physiological cell culture medium
Cited by: 226
Author(s): Johan Vande Voorde, Tobias Ackermann, Nadja Pfetzer, David Sumpton, Gillian Mackay, Gabriela Kalna, Colin Nixon, Karen Blyth, Eyal Gottlieb, Saverio Tardito
Software Mentions: 1
Published: almost 8 years ago

10.3390/ijms22073581

Variation in Parasitoid Virulence of Tetrastichus brontispae during the Targeting of Two Host Beetles
Cited by: 1
Author(s): Hua-Jian Zhang, Ya‐Ping Lin, Hongyu Li, Wang Rui, Lang Fu, Qing-Chen Jia, Youming Hou
Software Mentions: 1
Published: over 5 years ago

10.1126/sciadv.abb3713

GADL1 is a multifunctional decarboxylase with tissue-specific roles in β-alanine and carnosine production
Cited by: 23
Author(s): Elaheh Mahootchi, Selina Cannon Homaei, Rune Kleppe, Ingeborg Winge, Tor‐Arne Hegvik, Ricardo Pérez, Christian Totland, Floriana Mogavero, Anne Baumann, Jeffrey Glennon, Hrvoje Miletić, Petri Kursula, Jan Haavik
Software Mentions: 1
Published: over 6 years ago

10.1126/sciadv.aba0353

Metabolic multistability and hysteresis in a model aerobe-anaerobe microbiome community
Cited by: 23
Author(s): Tahmineh Khazaei, Rory L. Williams, Said R. Bogatyrev, John C. Doyle, Christopher S. Henry, Rustem F. Ismagilov
Software Mentions: 1
Published: over 6 years ago

10.1186/s12937-018-0381-7

Role of whole grains versus fruits and vegetables in reducing subclinical inflammation and promoting gastrointestinal health in individuals affected by overweight and obesity: a randomized controlled trial
Cited by: 67
Author(s): Julianne C. Kopf, Mallory J. Suhr, Jennifer Clarke, Seong‐il Eyun, Jean-Jack M. Riethoven, Amanda E. Ramer‐Tait, Devin J. Rose
Software Mentions: 1
Published: over 8 years ago

10.1126/sciadv.abg5283

Human tumor microenvironment chip evaluates the consequences of platelet extravasation and combinatorial antitumor-antiplatelet therapy in ovarian cancer
Cited by: 35
Author(s): Biswajit Saha, Tanmay Mathur, James J. Tronolone, Mithil Chokshi, Giriraj Lokhande, Amirali Selahi, Akhilesh K. Gaharwar, Vahid Afshar-Kharghan, Anil K. Sood, Gang Bao, Abhishek Jain
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22084157

Effects of Environmental Conditions on Nephron Number: Modeling Maternal Disease and Epigenetic Regulation in Renal Development
Cited by: 2
Author(s): Lars Fuhrmann, Saskia Lindner, Alexander‐Thomas Hauser, Clemens Höse, Oliver Kretz, Clemens D. Cohen, Maja T. Lindenmeyer, Wolfgang Sippl, Manfred Jung, Tobias B. Huber, Nicola Wanner
Software Mentions: 1
Published: over 5 years ago

10.1126/sciadv.abc8145

NSG-Pro mouse model for uncovering resistance mechanisms and unique vulnerabilities in human luminal breast cancers
Cited by: 9
Author(s): Yunguang Sun, Ning Yang, Fransiscus E. Utama, Sameer S. Udhane, Junling Zhang, Amy R. Peck, Alicia F Yanac, Katherine E. Duffey, John F. Langenheim, Vindhya Udhane, Guanjun Xia, Jess F. Peterson, Julie M. Jorns, Marja T. Nevalainen, Romain Rouet, Peter Schofield, Daniel Christ, Christopher J. Ormandy, Anne Rosenberg, Inna Chervoneva, Shirng‐Wern Tsaih, Michael J. Flister, Serge Y. Fuchs, Kay Uwe Wagner, Hallgeir Rui
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pbio.2006134

KDM5 histone demethylases repress immune response via suppression of STING
Cited by: 89
Author(s): Lizhen Wu, Jian Cao, Wesley L. Cai, Sabine M. Lang, J.R. Horton, Daniel J. Jansen, Zongzhi Z. Liu, Jocelyn F. Chen, Meiling Zhang, Bryan T. Mott, Katherine Pohida, Ganesha Rai, Stephen C. Kales, Mark J. Henderson, Xin Hu, Ajit Jadhav, David J. Maloney, Anton Simeonov, Shu Zhu, Akiko Iwasaki, Matthew D. Hall, Xiaodong Cheng, Gerald S. Shadel, Qin Yan
Software Mentions: 1
Published: over 8 years ago

10.1038/sdata.2016.101

ROCK signalling induced gene expression changes in mouse pancreatic ductal adenocarcinoma cells
Cited by: 7
Author(s): Nicola Rath, Gabriela Kalna, William Clark, Michael F. Olson
Software Mentions: 1
Published: about 10 years ago

10.1038/sdata.2017.172

Transcriptomic profiling of human breast and melanoma cells selected by migration through narrow constraints
Cited by: 6
Author(s): Dominika A. Rudzka, William Clark, Ann Hedley, Gabriela Kalna, Michael F. Olson
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pbio.2004328

The Plasmodium falciparum transcriptome in severe malaria reveals altered expression of genes involved in important processes including surface antigen–encoding var genes
Cited by: 56
Author(s): Gerry Tonkin‐Hill, Leily Trianty, Rintis Noviyanti, Hanh Thi Ngoc Nguyen, Boni F. Sebayang, Daniel A. Lampah, Jutta Marfurt, Simon A. Cobbold, Janavi S. Rambhatla, Malcolm J. McConville, Stephen J. Rogerson, Graham V. Brown, Karen P. Day, Ric N. Price, Nicholas M. Anstey, Anthony T. Papenfuss, Michael Duffy
Software Mentions: 1
Published: over 8 years ago

10.1038/sdata.2018.123

Transcriptional profiling of stellate ganglia from normotensive and spontaneously hypertensive rat strains
Cited by: 9
Author(s): Harvey Davis, Emma N. Bardsley, David J. Paterson
Software Mentions: 1
Published: over 8 years ago

10.1038/sdata.2018.170

Transcriptomic analyses of murine ventricular cardiomyocytes
Cited by: 14
Author(s): Morgan Yoann Edwin Chevalier, Sarah H. Vermij, Kurt Wyler, Ludovic Gillet, Irene Keller, Hugues Abriel
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pbio.2000949

Pancreas lineage allocation and specification are regulated by sphingosine-1-phosphate signalling
Cited by: 24
Author(s): Ioannis Serafimidis, Eva Rodriguez-Aznar, Mathias Lesche, Kazuaki Yoshioka, Yoh Takuwa, Andreas Dahl, Duojia Pan, Anthony Gavalas
Software Mentions: 1
Published: over 9 years ago

10.1038/s41597-019-0101-y

Transcriptome profiles of three Muscat table grape cultivars to dissect the mechanism of terpene biosynthesis
Cited by: 5
Author(s): Lina Sun, Baoqing Zhu, Xuanyin Zhang, Guojun Zhang, Ailing Yan, Huiling Wang, Xiaoyue Wang, Huini Xu
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms22105058

Analysis of Circulating miRNA Profile in Plasma Samples of Glioblastoma Patients
Cited by: 3
Author(s): Dóra Géczi, Bálint Nagy, Melinda Szilágyi, András Penyige, Álmos Klekner, Adrienn Jenei, József Virga, Zsuzsanna Birkó
Software Mentions: 1
Published: over 5 years ago

10.1038/s41597-019-0210-7

Transcriptomic profiling of cotton Gossypium hirsutum challenged with low-temperature gradients stress
Cited by: 13
Author(s): Zhibo Li, Zeng XiaoYan, Jianwei Xu, Ruihai Zhao, Wei Yinong
Software Mentions: 1
Published: about 7 years ago

10.3390/nu13082609

The Role of Reduced Methionine in Mediating the Metabolic Responses to Protein Restriction Using Different Sources of Protein
Cited by: 6
Author(s): Fei Han, Kirsten P. Stone, Sujoy Ghosh, Laura A. Forney, Thomas W. Gettys
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pbio.1002558

Disruption of an Evolutionarily Novel Synaptic Expression Pattern in Autism
Cited by: 70
Author(s): Xiling Liu, Dingding Han, Mehmet Somel, Xi Jiang, Hai Hu, Patricia Guijarro, Ning Zhang, Amanda Mitchell, Tobias B. Halene, John J. Ely, Chet C. Sherwood, Patrick R. Hof, Zilong Qiu, Svante Pääbo, Schahram Akbarian, Philipp Khaitovich
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pbio.3000640

MKS-NPHP module proteins control ciliary shedding at the transition zone
Cited by: 25
Author(s): Delphine Gogendeau, Michel Lemullois, P. Le Borgne, Manon Castelli, Anne Aubusson-Fleury, Olivier Arnaiz, Jean Cohen, Christine Vesque, Sylvie Schneider‐Maunoury, Khaled Bouhouche, France Koll, Anne‐Marie Tassin
Software Mentions: 1
Published: over 6 years ago

10.1038/srep11126

Co-existence of intact stemness and priming of neural differentiation programs in mES cells lacking Trim71
Cited by: 38
Author(s): Sibylle Mitschka, Thomas Ulas, Tobias Goller, Karin Schneider, Angela Egert, Jérôme Mertens, Oliver Brüstle, Hubert Schorle, Marc Beyer, Kathrin Klee, Jia Xue, Patrick Günther, Kevin Baßler, Joachim L. Schultze, Waldemar Kolanus
Software Mentions: 1
Published: over 11 years ago

10.1038/srep13443

CADBURE: A generic tool to evaluate the performance of spliced aligners on RNA-Seq data
Cited by: 7
Author(s): Praveen Kumar, Thanh Hoang, Michael L. Robinson, Panagiotis A. Tsonis, Chun Liang
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pbio.3000287

Placental chemokine compartmentalisation: A novel mammalian molecular control mechanism
Cited by: 16
Author(s): Kit Ming Lee, G. L. Wilson, Marieke Pingen, Ayumi Fukuoka, Christopher A.H. Hansell, Robin Bartolini, Laura Medina-Ruiz, Gerard J. Graham
Software Mentions: 1
Published: over 7 years ago

10.1038/srep14976

A high-throughput RNA-seq approach to profile transcriptional responses
Cited by: 23
Author(s): Gregory A Moyerbrailean, Gordon O Davis, Chris T. Harvey, Donovan Watza, Xiaoquan Wen, Roger Piqué-Regi, Francesca Luca
Software Mentions: 1
Published: about 11 years ago

10.3390/ijms22116020

Role of Long Noncoding RNAs ZlMSTRG.11348 and UeMSTRG.02678 in Temperature-Dependent Culm Swelling in Zizania latifolia
Cited by: 0
Author(s): Zhenghong Wang, Yan Ning, Xi Luo, Sai-Sai Guo, Shu-Qin Xue, Jiang-Qiong Liu, Shenshen Zhang, Lianfang Zheng, Jingze Zhang, Danlu Guo
Software Mentions: 1
Published: over 5 years ago

10.1038/srep20316

Dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention
Cited by: 21
Author(s): Samantha N. McNulty, Christina Strübe, Bruce A. Rosa, John Martin, Rahul Tyagi, Young Jun Choi, Qi Wang, Kymberlie H. Pepin, Xu Zhang, Philip Ozersky, Richard K. Wilson, Paul W. Sternberg, Robin B. Gasser, Makedonka Mitreva
Software Mentions: 1
Published: almost 11 years ago

10.1038/srep21962

Improved lipids, diastolic pressure and kidney function are potential contributors to familial longevity: a study on 60 Chinese centenarian families
Cited by: 13
Author(s): Yonghan He, Shao-Yan Pu, Fu-Hui Xiao, Xiao‐Qiong Chen, Dongjing Yan, Yaowen Liu, Rong Lin, Xiaoping Liao, Qin Yu, Libin Yang, Xiaoxi Yang, Ming-Xia Ge, Ying Liu, Jianjun Jiang, Wei Cai, Qing‐Peng Kong
Software Mentions: 1
Published: over 10 years ago

Projects: bioconductor: DESeq2

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Papers Mentioning DESeq2 9,583