cran: gplots | Projects | Ecosyste.ms: Papers

10.1016/j.csbj.2021.04.008

Simultaneous profiling of Arabidopsis thaliana and Vibrio vulnificus MO6-24/O transcriptomes by dual RNA-seq analysis
Cited by: 5
Author(s): Yongsoon Park, Jong‐Seok Park, Mi Kyung Lee, Sung‐Hee Jung, Seon‐Kyu Kim, Choong-Min Ryu
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2018.02836

Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System
Cited by: 45
Author(s): Jennifer Bachmann, Tabea Heimbach, Christiane Hassenrück, Gérmán A. Kopprio, Morten Hvitfeldt Iversen, Hans Peter Grossart, Astrid Gärdes
Software Mentions: 3
Published: almost 8 years ago

10.1186/s40001-021-00586-8

NR4A3 and CCL20 clusters dominate the genetic networks in CD146+ blood cells during acute myocardial infarction in humans
Cited by: 3
Author(s): Yanhui Wang, Chen-Xin Li, Jessica M. Stephenson, Sean P. Marrelli, Yanming Kou, Dong Meng, Ting Wu
Software Mentions: 3
Published: almost 5 years ago

10.1016/j.jbc.2021.100285

Decreases in different Dnmt3b activities drive distinct development of hematologic malignancies in mice
Cited by: 4
Author(s): Katarína Lopušná, Paweł Nowialis, Jana Opavska, Ajay Abraham, Alberto Riva, Staci L. Haney, René Opavský
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0066086

Distinct MicroRNAs Expression Profile in Primary Biliary Cirrhosis and Evaluation of miR 505-3p and miR197-3p as Novel Biomarkers
Cited by: 81
Author(s): Masashi Ninomiya, Yasuteru Kondo, Ryo Funayama, Takeshi Nagashima, Takayuki Kogure, Eiji Kakazu, Osamu Kimura, Yoshiyuki Ueno, Keiko Nakayama, Tooru Shimosegawa
Software Mentions: 3
Published: about 13 years ago

10.1002/jcsm.12099

Expression of protocadherin gamma in skeletal muscle tissue is associated with age and muscle weakness
Cited by: 48
Author(s): Roland W. J. Hangelbroek, Parastoo Fazelzadeh, Michael Tieland, Mark V. Boekschoten, Guido Hooiveld, John van Duynhoven, James A. Timmons, Lex B. Verdijk, Lisette C. P. G. M. de Groot, Luc J. C. van Loon, Michael Müller
Software Mentions: 3
Published: over 10 years ago

10.3389/fmicb.2018.01763

Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia
Cited by: 11
Author(s): Yuting Wu, Cheng‐Yu Yang, Pei‐Wen Chiang, Chwan-Lu Tseng, Hsiu‐Hui Chiu, Isaam Saeed, Bayanmunkh Baatar, D. Yu. Rogozin, Saman K. Halgamuge, А. Г. Дегерменджи, Sen‐Lin Tang
Software Mentions: 3
Published: about 8 years ago

10.1186/s12870-015-0555-9

Microspore culture reveals complex meiotic behaviour in a trigenomic Brassica hybrid
Cited by: 20
Author(s): Annaliese S. Mason, Junko Takahira, Chhaya Atri, Birgit Samans, Alice Hayward, Wallace Cowling, Jacqueline Batley, Matthew N. Nelson
Software Mentions: 3
Published: about 11 years ago

10.1186/1471-2105-9-37

Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution
Cited by: 38
Author(s): Rekin’s Janky, Jacques van Helden
Software Mentions: 3
Published: over 18 years ago

10.7150/jca.30336

Prognostic Value of Survival of MicroRNAs Signatures in Non-small Cell Lung Cancer
Cited by: 20
Author(s): Bin Chen, Tianshun Gao, Weiwei Yuan, Weihong Zhao, Tza‐Huei Wang, Jianqing Wu
Software Mentions: 3
Published: over 7 years ago

10.1186/s12866-020-01962-w

Genotyping and plant-derived glycan utilization analysis of Bifidobacterium strains from mother-infant pairs
Cited by: 2
Author(s): Zeyu Kan, Baolong Luo, Jingjing Cai, Yan Zhang, Fengwei Tian, Yuwen Ni
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12870-021-02919-5

Superoxide dismutase (SOD) as a selection criterion for triticale grain yield under drought stress: a comprehensive study on genomics and expression profiling, bioinformatics, heritability, and phenotypic variability
Cited by: 39
Author(s): Armin Saed-Moucheshi, Fatemeh Sohrabi, Elham Fasihfar, Fatemeh Baniasadi, Mehrnaz Riasat, Ali-Akbar Mozafari
Software Mentions: 3
Published: over 5 years ago

10.1093/dnares/dsy044

A unique life-strategy of an endophytic yeast Rhodotorula mucilaginosa JGTA-S1—a comparative genomics viewpoint
Cited by: 24
Author(s): Diya Sen, Karnelia Paul, Chinmay Saha, G. N. Mukherjee, Mayurakshi Nag, Samrat Ghosh, A. K. Das, A. Seal, Sucheta Tripathy
Software Mentions: 3
Published: over 7 years ago

10.3389/fimmu.2019.01177

Differential Pathogenic Th17 Profile in Mesenteric Lymph Nodes of Crohn's Disease and Ulcerative Colitis Patients
Cited by: 34
Author(s): Marwa Bsat, Laurence Chapuy, Manuel Rubio, Ramsès Wassef, Carole Richard, Frank Schwenter, Rasmy Loungnarath, Geneviève Soucy, Heena Mehta, Marika Sarfati
Software Mentions: 3
Published: over 7 years ago

10.3389/fimmu.2018.03106

Expression of the Plasma Cell Transcriptional Regulator Blimp-1 by Dark Zone Germinal Center B Cells During Periods of Proliferation
Cited by: 31
Author(s): Daniel Radtke, Oliver Bannard
Software Mentions: 3
Published: over 7 years ago

10.7150/jca.31287

Comprehensive investigation of key biomarkers and pathways in hepatitis B virus-related hepatocellular carcinoma
Cited by: 9
Author(s): Xiwen Liao, Tingdong Yu, Chengkun Yang, Ketuan Huang, Xiangkun Wang, Chuangye Han, Rui Huang, Xiaoguang Liu, Yu Liu, Guangzhi Zhu, Hao Su, Wei Qin, Deng Jun, Xianmin Zeng, Bowen Han, Quanfa Han, Zheng-Qian Liu, Xin Zhou, Junqi Liu, Yizhen Gong, Zhengtao Liu, Jianlv Huang, Lei Lü, Xinping Ye, Tao Peng
Software Mentions: 3
Published: over 7 years ago

10.3390/cancers11101410

An IKK/NF-κB Activation/p53 Deletion Sequence Drives Liver Carcinogenesis and Tumor Differentiation
Cited by: 3
Author(s): Michael Svinarenko, Sarah‐Fee Katz, Umesh Tharehalli, Medhanie Mulaw, Harald J. Maier, Yoshiaki Sunami, Sarah Fischer, Yuexin Chen, Sabine Heurich, Lena Erkert, Andrea Tannapfel, Thomas Wirth, Reinhold Schirmbeck, Thomas Seufferlein, André Lechel
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-017-00763-y

Identification of a six-lncRNA signature associated with recurrence of ovarian cancer
Cited by: 49
Author(s): Kai Yang, Yan Hou, Ang Li, Zhenzi Li, Wenjie Wang, Hongyu Xie, Zhiwei Rong, Ge Lou, Kang Li
Software Mentions: 3
Published: over 9 years ago

10.1111/jcmm.14664

The non‐coding RNome after splenectomy
Cited by: 12
Author(s): Mihnea P. Dragomir, Ștefan Tudor, Kan Okubo, Masayoshi Shimizu, Meng Chen, Dana Elena Giza, Weixiang He, Cristina Ivan, C Vasilescu
Software Mentions: 3
Published: almost 7 years ago

10.3389/fimmu.2015.00030

Distinct Transcriptomic Features are Associated with Transitional and Mature B-Cell Populations in the Mouse Spleen
Cited by: 35
Author(s): Eden Kleiman, Daria Salyakina, Magali de Heusch, Kristen L. Hoek, Joan M. Llanes, Iris Castro, Jacqueline A. Wright, Emily Clark, Derek M. Dykxhoorn, Enrico Capobianco, Akihiro Takeda, Jean‐Christophe Renauld, Wasif N. Khan
Software Mentions: 3
Published: over 11 years ago

10.1186/s12864-020-07093-w

Ontogeny of hepatic metabolism in mule ducks highlights different gene expression profiles between carbohydrate and lipid metabolic pathways
Cited by: 4
Author(s): William Massimino, Stéphane Davail, Aurélie Secula, Charlotte Andrieux, Marie-Dominique Bernadet, Tracy Pioche, Karine Ricaud, Karine Gontier, Mireille Morisson, Anne Collin, Stéphane Panserat, Marianne Houssier
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2229-13-14

Transcriptional programming during cell wall maturation in the expanding Arabidopsis stem
Cited by: 34
Author(s): Hardy Hall, Brian E. Ellis
Software Mentions: 3
Published: over 13 years ago

10.1186/s12866-018-1326-1

Gut microbiota of preterm infants supplemented with probiotics: sub-study of the ProPrems trial
Cited by: 46
Author(s): Erica L Plummer, Dieter Bulach, Gerald L Murray, Susan E Jacobs, Sepehr N. Tabrizi, Suzanne M. Garland
Software Mentions: 3
Published: almost 8 years ago

10.3390/cancers11081157

A Novel Type of Blood Biomarker: Distinct Changes of Cytokine-Induced STAT Phosphorylation in Blood T Cells Between Colorectal Cancer Patients and Healthy Individuals
Cited by: 14
Author(s): Jae Won Yun, Sejoon Lee, Hye Mi Kim, Sejong Chun, Edgar G. Engleman, Hee Cheol Kim, Eun Suk Kang
Software Mentions: 3
Published: about 7 years ago

10.1038/srep17141

Preterm gut microbiota and metabolome following discharge from intensive care
Cited by: 36
Author(s): Christopher J. Stewart, Tom Skeath, Andrew Nelson, Sara Johansson Fernstad, Emma C. L. Marrs, John D. Perry, Stephen Cummings, Janet Berrington, Nicholas D. Embleton
Software Mentions: 3
Published: almost 11 years ago

10.3390/ijms21186817

Genome-Wide Analysis Reveals Dynamic Epigenomic Differences in Soybean Response to Low-Phosphorus Stress
Cited by: 12
Author(s): Shanshan Chu, Xiangqian Zhang, Kaiye Yu, Lingling Lv, Chongyuan Sun, Xiaoqian Liu, Jinyu Zhang, Yongqing Jiao, Dan Zhang
Software Mentions: 3
Published: almost 6 years ago

10.3390/cancers13102499

Expression of Cancer Testis Antigens in Tumor-Adjacent Normal Liver Is Associated with Post-Resection Recurrence of Hepatocellular Carcinoma
Cited by: 3
Author(s): Lisanne Noordam, Zhouhong Ge, Hadiye Özturk, Michail Doukas, Shanta Mancham, Patrick P.C. Boor, Lucia Campos Carrascosa, Guoying Zhou, Thierry van den Bosch, Qiuwei Pan, Jan N.M. IJzermans, Marco J. Bruno, Dave Sprengers, Jaap Kwekkeboom
Software Mentions: 3
Published: over 5 years ago

10.3390/cancers13030550

Extracellular miRNAs as Predictive Biomarkers for Glypican-3-Derived Peptide Vaccine Therapy Response in Ovarian Clear Cell Carcinoma
Cited by: 6
Author(s): Makoto Ukai, Akira Yokoi, Kosuke Yoshida, Shiro Suzuki, Kiyosumi Shibata, Fumitaka Kikkawa, Tetsuya Nakatsura, Hiroaki Kajiyama
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2018.01223

Autophagy Impairment Is Associated With Increased Inflammasome Activation and Reversal Reaction Development in Multibacillary Leprosy
Cited by: 14
Author(s): Mayara Garcia de Mattos Barbosa, Bruno Jorge de Andrade Silva, Tayná Quintella Assis, Rhana Berto da Silva Prata, Helen Ferreira, Priscila Ribeiro Andrade, Jéssica Araújo da Paixão de Oliveira, Gilberto Marcelo Sperandio da Silva, José Augusto da Costa Nery, Euzenir Nunes Sarno, Roberta Olmo Pinheiro
Software Mentions: 3
Published: about 8 years ago

10.3389/fimmu.2017.00723

Unperturbed Cytotoxic Lymphocyte Phenotype and Function in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Patients
Cited by: 15
Author(s): Jakob Theorell, Indrė Bilevičiūtė-Ljungar, Bianca Tesi, Heinrich Schlums, Mette Sophie Johnsgaard, Babak Asadi-Azarbaijani, Elin Bolle Strand, Yenan T. Bryceson
Software Mentions: 3
Published: about 9 years ago

10.3389/fimmu.2019.01098

Functional Phenotypic Diversity of Regulatory T Cells Remaining in Inflamed Skin
Cited by: 18
Author(s): Ryoyo Ikebuchi, Maika Fujimoto, Yasutaka Nakanishi, Hiromi Okuyama, Taiki Moriya, Yutaka Kusumoto, Michio Tomura
Software Mentions: 3
Published: over 7 years ago

10.18632/aging.102736

Anesthesia and surgery induce age-dependent changes in behaviors and microbiota
Cited by: 46
Author(s): Ning Liufu, Ling Liu, Shiqian Shen, Zengliang Jiang, Yuanlin Dong, Yanyan Wang, Deborah J. Culley, Gregory Crosby, Minghui Cao, Yuan Shen, Edward R. Marcantonio, Zhongcong Xie, Yiying Zhang
Software Mentions: 3
Published: over 6 years ago

10.1038/srep44131

Vascular transcriptome profiling identifies Sphingosine kinase 1 as a modulator of angiotensin II-induced vascular dysfunction
Cited by: 36
Author(s): Mateusz Siedliński, Ryszard Nosalski, Piotr Szczepaniak, Agnieszka H. Ludwig-Gałęzowska, T. Mikołajczyk, Magdalena Filip, Grzegorz Osmenda, G. Wilk, Michał Nowak, Paweł Wołkow, Tomasz J. Guzik
Software Mentions: 3
Published: over 9 years ago

10.3390/cancers13020298

Soluble and Exosome-Bound α-Galactosylceramide Mediate Preferential Proliferation of Educated NK Cells with Increased Anti-Tumor Capacity
Cited by: 3
Author(s): Arnika K. Wagner, Ulf Gehrmann, Stefanie Hiltbrunner, Valentina Carannante, Thuy T. Luu, Tanja I. Näslund, Hanna Brauner, Nadir Kadri, Klas Kärre, Susanne Gabrielsson
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms20092265

Effect of Drought Stress and Developmental Stages on Microbial Community Structure and Diversity in Peanut Rhizosphere Soil
Cited by: 58
Author(s): Lei Dai, Guanchu Zhang, Zipeng Yu, Hong Ding, Yang Xu, Zhimeng Zhang
Software Mentions: 3
Published: over 7 years ago

10.18632/aging.202997

Identification of potential autophagy-associated lncRNA in prostate cancer
Cited by: 6
Author(s): Jun Li, Hong Du, Wenqiang Chen, Mingxing Qiu, Peng He, Zhiwei Ma
Software Mentions: 3
Published: over 5 years ago

10.1038/srep42702

Aging and serum exomiR content in women-effects of estrogenic hormone replacement therapy
Cited by: 23
Author(s): Reeta Kangas, Timo Törmäkangas, Vidal Fey, Juha Pursiheimo, Ilkka Miinalainen, Markku Alén, Jaakko Kaprio, Sarianna Sipilä, Anna‐Marja Säämänen, Vuokko Kovanen, Eija K. Laakkonen
Software Mentions: 3
Published: over 9 years ago

10.1038/srep16350

Sample storage conditions significantly influence faecal microbiome profiles
Cited by: 329
Author(s): Jocelyn M. Choo, Lex E. X. Leong, Geraint B. Rogers
Software Mentions: 3
Published: almost 11 years ago

10.3389/fimmu.2021.698900

Association of Gut Microbiota and Metabolites With Disease Progression in Children With Biliary Atresia
Cited by: 12
Author(s): Wei Song, Li‐Ying Sun, Zhaoqiong Zhu, Lin Wei, Wei Qu, Zhi-Gui Zeng, Ying Liu, Haiming Zhang, Wei Guo
Software Mentions: 3
Published: almost 5 years ago

10.1186/s13321-018-0257-z

Adverse drug reactions triggered by the common HLA-B*57:01 variant: virtual screening of DrugBank using 3D molecular docking
Cited by: 5
Author(s): George Van Den Driessche, Denis Fourches
Software Mentions: 3
Published: over 8 years ago

10.1186/s12870-020-02384-6

Identification of polycomb repressive complex 1 and 2 core components in hexaploid bread wheat
Cited by: 13
Author(s): Beáta Strejčková, Radim Čegan, Aleš Pečinka, Zbyněk Milec, Jan Šafář
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12964-019-0332-8

Low levels of pyruvate induced by a positive feedback loop protects cholangiocarcinoma cells from apoptosis
Cited by: 12
Author(s): Mingming Zhang, Yida Pan, Dehua Tang, Robert Dorfman, Lei Xu, Qian Zhou, Lixing Zhou, Yuming Wang, Li Yang, Yuyao Yin, Bo Kong, Helmut Frieß, Shimin Zhao, Jian‐Lin Wu, Lei Wang, Xiaoping Zou
Software Mentions: 3
Published: over 7 years ago

10.1186/s12866-018-1174-z

Environmental factors shaping the diversity of bacterial communities that promote rice production
Cited by: 45
Author(s): Zhaohui Wu, Qingshu Liu, Zhenyu Li, Wanli Cheng, Jun Sun, Zhaohui Guo, Yongmei Li, Jianqun Zhou, Delong Meng, Hongbo Li, Ping Lei, Huaqun Yin
Software Mentions: 3
Published: about 8 years ago

10.1038/srep41502

Conversion from long-term cultivated wheat field to Jerusalem artichoke plantation changed soil fungal communities
Cited by: 8
Author(s): Xingang Zhou, Jianhui Zhang, Danmei Gao, Huan Gao, Meiyu Guo, Li Li, Zhao MengLiang, Fengzhi Wu
Software Mentions: 3
Published: over 9 years ago

10.1038/srep41238

Patient-specific hepatocyte-like cells derived from induced pluripotent stem cells model pazopanib-mediated hepatotoxicity
Cited by: 43
Author(s): Yukti Choudhury, Yi‐Chin Toh, Jiangwa Xing, Yinghua Qu, Jonathan Poh, Huan Li, Hui Shan Tan, Ravindran Kanesvaran, Hanry Yu, Min‐Han Tan
Software Mentions: 3
Published: over 9 years ago

10.1186/s12870-018-1373-7

Comparative root transcriptome of wild Arachis reveals NBS-LRR genes related to nematode resistance
Cited by: 24
Author(s): Ana Paula Zotta Mota, Bruna Vidigal, Étienne Danchin, Roberto Coiti Togawa, Soraya C. M. Leal‐Bertioli, David J. Bertioli, Ana Cláudia Guerra Araújo, Ana Cristina Miranda Brasileiro, P. M. Guimarães
Software Mentions: 3
Published: about 8 years ago

10.1186/s12967-020-02436-3

Presence of a 34-gene signature is a favorable prognostic marker in squamous non-small cell lung carcinoma
Cited by: 8
Author(s): Wendy Theelen, Oscar Krijgsman, Kim Monkhorst, Thomas Kuilman, Dennis Peters, Sten Cornelissen, Maarten A. Ligtenberg, Stefan M. Willems, J. L. G. Blaauwgeers, Carel J. M. van Noesel, Daniel S. Peeper, Michel M. van den Heuvel, Katja Schulze
Software Mentions: 3
Published: about 6 years ago

10.1186/s13072-018-0212-2

CRX directs photoreceptor differentiation by accelerating chromatin remodeling at specific target sites
Cited by: 31
Author(s): Philip A. Ruzycki, Xiaodong Zhang, Shiming Chen
Software Mentions: 3
Published: about 8 years ago

10.1007/s00359-018-1252-6

Candidate genes for cooperation and aggression in the social wasp Polistes dominula
Cited by: 17
Author(s): Fabio Manfredini, Mark J. F. Brown, Amy L. Toth
Software Mentions: 3
Published: over 8 years ago

10.1038/s41419-018-0671-1

Transcriptome analysis of the adult human Klinefelter testis and cellularity-matched controls reveals disturbed differentiation of Sertoli- and Leydig cells
Cited by: 30
Author(s): Sofia B. Winge, Marlene Danner Dalgaard, Kirstine Belling, James C. Jensen, John Nielsen, Lise Aksglæde, Mikkel Heide Schierup, Søren Brunak, Niels E. Skakkebæk, Anders Juul, Ewa Rajpert‐De Meyts, Kristian Almstrup
Software Mentions: 3
Published: over 8 years ago

10.1038/cddis.2017.426

Common microRNA–mRNA interactions exist among distinct porcine iPSC lines independent of their metastable pluripotent states
Cited by: 8
Author(s): Shiqiang Zhang, Youlong Xie, Hongxia Cao, Huayan Wang
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12859-016-1075-9

A novel procedure on next generation sequencing data analysis using text mining algorithm
Cited by: 10
Author(s): Weizhong Zhao, James J. Chen, Roger Perkins, Yuping Wang, Zhichao Liu, Huixiao Hong, Weida Tong, Wen Zou
Software Mentions: 3
Published: over 10 years ago

10.1038/cddis.2017.487

Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2
Cited by: 20
Author(s): M. Merski, Cátia Moreira, Rui M.V. Abreu, María J. Ramos, Pedro A. Fernandes, L. Miguel Martins, Pedro José Barbosa Pereira, Sandra Macedo-Ribeiro
Software Mentions: 3
Published: almost 9 years ago

10.1038/srep32590

Snapshots of a shrinking partner: Genome reduction in Serratia symbiotica
Cited by: 61
Author(s): Alejandro Manzano-Marı́n, Amparo Latorre
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41419-019-1570-9

BRD9 binds cell type-specific chromatin regions regulating leukemic cell survival via STAT5 inhibition
Cited by: 30
Author(s): Nunzio Del Gaudio, Antonella Di Costanzo, Ning Qing Liu, Lidio Conte, Antimo Migliaccio, Michiel Vermeulen, Joost H.A. Martens, Hendrik G. Stunnenberg, Angela Nebbioso, Lucia Altucci
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-14-578

RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions
Cited by: 41
Author(s): Marc J. Champigny, Wilson W L Sung, Vasile Catana, Rupa Salwan, Peter S. Summers, Susan A. Dudley, Nicholas J. Provart, Robin K. Cameron, G. Brian Golding, Elizabeth A. Weretilnyk
Software Mentions: 3
Published: about 13 years ago

10.1186/1465-9921-11-70

Response of the mouse lung transcriptome to welding fume: effects of stainless and mild steel fumes on lung gene expression in A/J and C57BL/6J mice
Cited by: 25
Author(s): Patti C. Zeidler-Erdely, Michael L. Kashon, Shengqiao Li, James M. Antonini
Software Mentions: 3
Published: about 16 years ago

10.1371/journal.pcbi.1003189

A Self-Directed Method for Cell-Type Identification and Separation of Gene Expression Microarrays
Cited by: 30
Author(s): Neta S. Zuckerman, Yair Noam, Andrea Goldsmith, Peter P. Lee
Software Mentions: 3
Published: about 13 years ago

10.1371/journal.pcbi.1004553

Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response
Cited by: 18
Author(s): Robin van der Lee, Feng Qian, Martijn A. Langereis, Rob ter Horst, Radek Szklarczyk, Mihai G. Netea, Arno C. Andeweg, Frank J. M. van Kuppeveld, Martijn A. Huynen
Software Mentions: 3
Published: almost 11 years ago

10.2196/17186

Communication Behavior Changes Between Patients With Diabetes and Healthcare Providers Over 9 Years: Retrospective Cohort Study
Cited by: 16
Author(s): Arriel Benis, Refael Barkan, Tomer Sela, Nissim Harel
Software Mentions: 3
Published: about 6 years ago

10.1038/ismej.2013.127

Bacterial profiling of White Plague Disease in a comparative coral species framework
Cited by: 115
Author(s): Cornelia Roder, Chatchanit Arif, Till Bayer, Manuel Aranda, Camille Daniels, Ahmed A. Shibl, Suchana Chavanich, Christian R. Voolstra
Software Mentions: 3
Published: about 13 years ago

10.3389/fimmu.2017.01634

Dynamic Changes in Host Gene Expression following In Vitro Viral Mimic Stimulation in Crocodile Cells
Cited by: 1
Author(s): Subir Sarker, Yinan Wang, Brenden Warren-Smith, Karla J. Helbig
Software Mentions: 3
Published: almost 9 years ago

10.18632/oncotarget.27306

NOTCH1 signaling in oral squamous cell carcinoma via a TEL2/SERPINE1 axis
Cited by: 6
Author(s): Vasiliki Salameti, Priyanka G. Bhosale, Ashley Ames-Draycott, Kalle Sipilä, Fiona M. Watt
Software Mentions: 3
Published: almost 7 years ago

10.1111/tpj.14417

Poplar carbohydrate‐active enzymes: whole‐genome annotation and functional analyses based on <scp>RNA</scp> expression data
Cited by: 29
Author(s): Vikash Kumar, Matthieu Hainaut, Nicolas Delhomme, Chanaka Mannapperuma, Peter Immerzeel, Nathaniel R. Street, Bernard Henrissat, Ewa J. Mellerowicz
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pgen.1005748

Genome-Wide Transcriptional Regulation Mediated by Biochemically Distinct SWI/SNF Complexes
Cited by: 91
Author(s): Jesse R. Raab, Samuel Resnick, Terry Magnuson
Software Mentions: 3
Published: over 10 years ago

10.14814/phy2.12225

Pattern recognition receptors in the gut: analysis of their expression along the intestinal tract and the crypt/villus axis
Cited by: 44
Author(s): Pascal Gourbeyre, Mustapha Berri, Yannick Lippi, François Meurens, Silvia Vincent‐Naulleau, Joëlle Laffitte, Claire Rogel‐Gaillard, Philippe Pinton, Isabelle P. Oswald
Software Mentions: 3
Published: over 11 years ago

10.3389/fimmu.2016.00361

Tissue-Specific Expression Patterns of MicroRNA during Acute Graft-versus-Host Disease in the Rat
Cited by: 20
Author(s): Dasaradha Jalapothu, Margherita Boieri, Rachel E Crossland, Pranali Shah, Isha A. Butt, Jean Norden, Ralf Dressel, AM Dickinson, Marit Inngjerdingen
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pgen.1007238

EAT1 transcription factor, a non-cell-autonomous regulator of pollen production, activates meiotic small RNA biogenesis in rice anther tapetum
Cited by: 68
Author(s): Seijiro Ono, Hua Liu, Katsutoshi Tsuda, Eigo Fukai, Keisuke Tanaka, Takuji Sasaki, Ken–Ichi Nonomura
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2164-15-773

Maize protein phosphatase gene family: identification and molecular characterization
Cited by: 53
Author(s): Kaifa Wei, Si Pan
Software Mentions: 3
Published: over 12 years ago

10.1002/prp2.386

Rifampin modulation of xeno- and endobiotic conjugating enzyme mRNA expression and associated microRNAs in human hepatocytes
Cited by: 16
Author(s): Brandon T. Gufford, Jason Robarge, Michael T. Eadon, Hongyu Gao, Hai Lin, Yunlong Liu, Zeruesenay Desta, Todd C. Skaar
Software Mentions: 3
Published: over 8 years ago

10.1186/s11658-018-0090-4

Essential genes of the macrophage response to Staphylococcus aureus exposure
Cited by: 6
Author(s): Aixia Sun, Hongwei Zhang, Feng Pang, Guifen Niu, Jianzhong Chen, Fei Chen, Jian Zhang
Software Mentions: 3
Published: over 8 years ago

10.15252/embj.201696056

A novel microglial subset plays a key role in myelinogenesis in developing brain
Cited by: 316
Author(s): Agnieszka Włodarczyk, Inge R. Holtman, Martin Krueger, Nir Yogev, Julia Bruttger, Reza Khorooshi, Anouk Benmamar‐Badel, Jelkje J. de Boer-Bergsma, Nellie Anne Martin, Khalad Karram, Isabella Kramer, Erik Boddeke, Ari Waisman, Bart J. L. Eggen, Trevor Owens
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pgen.1007390

Danger signals activate a putative innate immune system during regeneration in a filamentous fungus
Cited by: 25
Author(s): Elizabeth Medina-Castellanos, José Manuel Villalobos-Escobedo, Meritxell Riquelme, Nick D. Read, Cei Abreu‐Goodger, Alfredo Herrera-Estrella
Software Mentions: 3
Published: over 7 years ago

10.1128/mSystems.00017-20

Isolation and Characterization of the Novel Phage JD032 and Global Transcriptomic Response during JD032 Infection of Clostridioides difficile Ribotype 078
Cited by: 19
Author(s): Tinghua Li, Yan Zhang, Ke Dong, C.J. Kuo, Chong Li, Yaping Zhu, Jinhong Qin, Qingtian Li, Yung‐Fu Chang, Xiaokui Guo, Yongzhang Zhu
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-020-06778-6

Impacts of local population history and ecology on the evolution of a globally dispersed pathogen
Cited by: 18
Author(s): Andreína I. Castillo, Carlos Chacón-Díaz, Neysa Rodríguez-Murillo, Helvécio Della Coletta-Filho, Rodrigo P. P. Almeida
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1006260

Novel Genetic Variants for Cartilage Thickness and Hip Osteoarthritis
Cited by: 73
Author(s): Martha C. Castaño-Betancourt, Dan S. Evans, Yolande F M Ramos, Cindy G. Boer, Sarah Metrustry, Youfang Liu, Wouter den Hollander, Jeroen van Rooij, Virginia B. Kraus, Michelle S. Yau, Braxton D. Mitchell, Kenneth Muir, Albert Hofman, Michael Doherty, Sally Doherty, Weiya Zhang, Robert Kraaij, Fernando Rivadeneira, Elizabeth Barrett‐Connor, Rose A. Maciewicz, N K Arden, Rob G H H Nelissen, Margreet Kloppenburg, Joanne M. Jordan, Michael C. Nevitt, P. Eline Slagboom, Deborah Hart, Floris P. J. G. Lafeber, Unnur Styrkársdóttir, Eleftheria Zeggini, Εvangelos Εvangelou, Tim D. Spector, André G. Uitterlinden, Nancy E Lane, Ingrid Meulenbelt, Ana M. Valdes, Joyce B. J. van Meurs
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pgen.1006405

Signaling through Lrg1, Rho1 and Pkc1 Governs Candida albicans Morphogenesis in Response to Diverse Cues
Cited by: 30
Author(s): Jinglin Lucy Xie, Nora Grahl, Trevor J.L. Sless, Michelle Leach, Sang Hu Kim, Deborah A. Hogan, Nicole Robbins, Leah E. Cowen
Software Mentions: 3
Published: almost 10 years ago

10.7717/peerj.9701

A prognostic long non-coding RNA-associated competing endogenous RNA network in head and neck squamous cell carcinoma
Cited by: 13
Author(s): Chengyao Zhang, Wei Cao, Jiawu Wang, Jiannan Liu, Jialiang Li, Hao Wu, Siyi Li, Chenping Zhang
Software Mentions: 3
Published: almost 6 years ago

10.7717/peerj.5705

Variations in the reproductive strategies of three populations of <i>Phrynocephalus helioscopus</i> in China
Cited by: 3
Author(s): Tao Liang, Zhengxin Lu, Wenfeng He, Xiao Li-rong, Lei Shi
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12866-021-02284-1

Comparison of three amplicon sequencing approaches to determine staphylococcal populations on human skin
Cited by: 3
Author(s): Charlotte Marie Ahle, Kristian Stødkilde, Anja Poehlein, Wolfgang R. Streit, Jennifer Hüpeden, Holger Brüggemann
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1008212

Longevity is determined by ETS transcription factors in multiple tissues and diverse species
Cited by: 21
Author(s): A. Dobson, Richard Boulton-McDonald, Lara Houchou, Tatiana Svermova, Zhijian Ren, Jeremie Subrini, Mireya Vazquez-Prada, Mimoza Hoti, María Rodríguez López, Rita Ibrahim, Afroditi Gregoriou, Alexis Gkantiragas, Jürg Bähler, Marina Ezcurra, Nazif Alic
Software Mentions: 3
Published: about 7 years ago

10.7717/peerj.11574

Shifts in gut and vaginal microbiomes are associated with cancer recurrence time in women with ovarian cancer
Cited by: 11
Author(s): David P. Jacobson, Kathleen Moore, Camille C. Gunderson, M. Rowland, Rita M. Austin, Tanvi P. Honap, Jiawu Xu, Christina Warinner, Krithivasan Sankaranarayanan, Cecil M. Lewis
Software Mentions: 3
Published: about 5 years ago

10.1093/jxb/ert234

Nitrogen metabolism of two contrasting poplar species during acclimation to limiting nitrogen availability
Cited by: 172
Author(s): Jie Luo, Hong Li, Tong‐Xian Liu, Andrea Polle, Changhui Peng, Zhibin Luo
Software Mentions: 3
Published: about 13 years ago

10.1016/j.celrep.2019.11.034

Compromised Metabolic Reprogramming Is an Early Indicator of CD8+ T Cell Dysfunction during Chronic Mycobacterium tuberculosis Infection
Cited by: 48
Author(s): Sarah Russell, Dirk A. Lamprecht, Tawanda Mandizvo, Terrence T. Jones, Vanessa Naidoo, Kelvin W Addicott, Chivonne Moodley, Bongani Ngcobo, David K. Crossman, Gordon Wells, Adrie J. C. Steyn
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pntd.0008684

Expanded genome-wide comparisons give novel insights into population structure and genetic heterogeneity of Leishmania tropica complex
Cited by: 12
Author(s): Tamara Salloum, Rim Moussa, Ryan Rahy, Jospin Al Deek, Ibrahim Khalifeh, Rana El Hajj, Neil Hall, Robert P. Hirt, Sima Tokajian
Software Mentions: 3
Published: almost 6 years ago

10.1093/jxb/erv532

Proteomic profiling of maize opaque endosperm mutants reveals selective accumulation of lysine-enriched proteins
Cited by: 27
Author(s): Kyla J. Morton, Shangang Jia, Chi Zhang, David R. Holding
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pntd.0003372

An Updated Insight into the Sialotranscriptome of Triatoma infestans: Developmental Stage and Geographic Variations
Cited by: 35
Author(s): Alexandra Schwarz, Nora Medrano-Mercado, Günter A. Schaub, Cláudio J. Struchiner, M. D. Bargues, Michael Z. Levy, José M. C. Ribeiro
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pntd.0007397

Interplay between proinflammatory cytokines, miRNA, and tissue lesions in Anisakis-infected Sprague-Dawley rats
Cited by: 21
Author(s): Jerko Hrabar, Željka Trumbić, Ivana Bočina, Ivana Bušelić, Anamarija Vrbatović, Ivona Mladineo
Software Mentions: 3
Published: over 7 years ago

10.1128/mSystems.00075-16

Zonal Soil Type Determines Soil Microbial Responses to Maize Cropping and Fertilization
Cited by: 27
Author(s): Mengxin Zhao, Bo Sun, Linwei Wu, Qun Gao, Wang Feng, Chongqing Wen, Mengmeng Wang, Yuting Liang, Lauren Hale, Jizhong Zhou, Yunfeng Yang
Software Mentions: 3
Published: about 10 years ago

10.1186/s12864-016-3203-3

Functional variants of human papillomavirus type 16 demonstrate host genome integration and transcriptional alterations corresponding to their unique cancer epidemiology
Cited by: 33
Author(s): Robert Jackson, Bruce A. Rosa, Sonia Lameiras, Sean Cuninghame, Josee Bernard, Wely B. Floriano, Paul F. Lambert, Alain Nicolas, Ingeborg Zehbe
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12864-016-3237-6

Analysis of the association between codon optimality and mRNA stability in Schizosaccharomyces pombe
Cited by: 64
Author(s): Yuriko Harigaya, Roy Parker
Software Mentions: 3
Published: almost 10 years ago

10.1016/j.celrep.2019.02.077

Oxidative Stress Triggers Selective tRNA Retrograde Transport in Human Cells during the Integrated Stress Response
Cited by: 32
Author(s): Hagen Schwenzer, Frank Jühling, Alexander L. Chu, Laura J. Pallett, Thomas F. Baumert, Mala K. Maini, Ariberto Fassati
Software Mentions: 3
Published: over 7 years ago

10.7717/peerj.1602

Characterisation of the human uterine microbiome in non-pregnant women through deep sequencing of the V1-2 region of the 16S rRNA gene
Cited by: 195
Author(s): Hans Verstraelen, Ramiro Vílchez-Vargas, Fabian Desimpel, Ruy Jáuregui, Nele Vankeirsbilck, Steven Weyers, Rita Verhelst, Petra De Sutter, Dietmar H. Pieper, Tom Van de Wiele
Software Mentions: 3
Published: over 10 years ago

10.7717/peerj.175

Data reuse and the open data citation advantage
Cited by: 358
Author(s): Heather Piwowar
Software Mentions: 3
Published: almost 13 years ago

10.1128/mSphere.00017-18

Air-Dried Brown Seaweed, <i>Ascophyllum nodosum</i> , Alters the Rumen Microbiome in a Manner That Changes Rumen Fermentation Profiles and Lowers the Prevalence of Foodborne Pathogens
Cited by: 30
Author(s): Mi Zhou, Martin Hünerberg, Yanhong Chen, Tim Reuter, Tim A. McAllister, F. D. Evans, Alan T. Critchley, Le Luo Guan
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pntd.0005461

Modulation of the immune response by Fonsecaea pedrosoi morphotypes in the course of experimental chromoblastomycosis and their role on inflammatory response chronicity
Cited by: 26
Author(s): Isaque Medeiros Siqueira, Raffael Júnio Araújo de Castro, Luiza Chaves de Miranda Leonhardt, Márcio Sousa Jerônimo, A.J.M. Soares, Tainá Raiol, Christiane Nishibe, Nalvo F. Almeida, Aldo Henrique Tavares, Christian Hoffmann, Anamélia Lorenzetti Bocca
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pntd.0006410

Sialome diversity of ticks revealed by RNAseq of single tick salivary glands
Cited by: 61
Author(s): Jan Perner, Sára Kropáčková, Petr Kopáček, José M. C. Ribeiro
Software Mentions: 3
Published: over 8 years ago

10.1093/jxb/erx391

Sugar metabolism reprogramming in a non-climacteric bud mutant of a climacteric plum fruit during development on the tree
Cited by: 36
Author(s): Macarena Farcuh, Bosheng Li, Rosa M. Rivero, Lyudmila Shlizerman, Avi Sadka, Eduardo Blumwald
Software Mentions: 3
Published: almost 9 years ago

10.1016/j.celrep.2020.108154

Protein Stability Buffers the Cost of Translation Attenuation following eIF2α Phosphorylation
Cited by: 15
Author(s): Kim Schneider, Geoffrey M. Nelson, J. P. Watson, Jörg Morf, Maximillian M. Dalglish, Laura M. Luh, Annika Weber, Anne Bertolotti
Software Mentions: 3
Published: almost 6 years ago

10.3389/fimmu.2018.02990

CD8+XCR1neg Dendritic Cells Express High Levels of Toll-Like Receptor 5 and a Unique Complement of Endocytic Receptors
Cited by: 9
Author(s): Ben Wylie, James F. Read, Anthony Buzzai, Teagan Wagner, Niamh M. Troy, Genevieve Syn, Shane R. Stone, Bree Foley, Anthony Bosco, Mark N Cruickshank, Jason Waithman
Software Mentions: 3
Published: over 7 years ago

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