cran: gplots | Projects | Ecosyste.ms: Papers

10.1002/iid3.246

Flow Plex —A tool for unbiased comprehensive flow cytometry data analysis
Cited by: 0
Author(s): Johannes Nowatzky, Ezra Resnick, Julia Manasson, Cristy Stagnar, Arshed Al-Obeidi, Olivier Manches
Software Mentions: 3
Published: over 7 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/s13099-020-00351-y

Gut microbiome of native Arab Kuwaitis
Cited by: 6
Author(s): Erica L Plummer, Dieter Bulach, Glen P. Carter, M. John Albert
Software Mentions: 3
Published: over 6 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

10.18632/oncotarget.16051

Identification of molecular targets for esophageal carcinoma diagnosis using miRNA-seq and RNA-seq data from The Cancer Genome Atlas: a study of 187 cases
Cited by: 29
Author(s): Jiang‐Hui Zeng, Dandan Xiong, Yu‐Yan Pang, Yu Zhang, Rongjiang Tang, Dan Luo, Gang Chen
Software Mentions: 3
Published: over 9 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

10.3390/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

10.3390/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

10.18632/oncotarget.16252

Niclosamide is a potential therapeutic for familial adenomatosis polyposis by disrupting Axin-GSK3 interaction
Cited by: 26
Author(s): Ahn Sk, Nam Hee Kim, Kyungro Lee, Yong Hoon, Ji Hye Yang, So Young, Eunae Sandra Cho, Yoonmi Lee, Jeong Ho Seok, Hyun Soo Cho, Yongseok Jeon, Young Su Yuk, Suebean Cho, Kyoung Tai No, Hyun Sil Kim, Ho Lee, Jiwon Choi, Jong In Yook
Software Mentions: 3
Published: over 9 years ago

10.1155/2015/878546

Identification of Gene Expression Pattern Related to Breast Cancer Survival Using Integrated TCGA Datasets and Genomic Tools
Cited by: 20
Author(s): Zhenzhen Huang, Huilong Duan, Haomin Li
Software Mentions: 3
Published: over 11 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

10.1371/journal.pone.0213220

miR-7977 inhibits the Hippo-YAP signaling pathway in bone marrow mesenchymal stromal cells
Cited by: 20
Author(s): Masahiro Yoshida, Hyogo Horiguchi, Shohei Kikuchi, Satoshi Iyama, Hiroshi Ikeda, Akinobu Goto, Yutaka Kawano, Kazuyuki Murase, Kohichi Takada, Koji Miyanishi, Junji Kato, Masayoshi Kobune
Software Mentions: 3
Published: over 7 years ago

10.1111/acel.12707

Overexpression of PGC-1α in aging muscle enhances a subset of young-like molecular patterns
Cited by: 50
Author(s): Sofia F. Garcia, Nadee Nissanka, Edson Assunção Mareco, Susana G. Rossi, Susana Peralta, Francisca Díaz, Richard L. Rotundo, Robson Francisco Carvalho, Carlos T. Moraes
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0189334

aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
Cited by: 3
Author(s): Victor Renault, Jörg Tost, Fabien Pichon, Shu‐Fang Wang‐Renault, Éric Letouzé, Sandrine Imbeaud, Jessica Zucman‐Rossi, Jean‐François Deleuze, Alexandre How‐Kit
Software Mentions: 3
Published: over 8 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

10.1155/2020/3075729

Comprehensive Analysis of lncRNAs Related to the Prognosis of Esophageal Cancer Based on ceRNA Network and Cox Regression Model
Cited by: 4
Author(s): Chao Li, Wu Yao, Congcong Zhao, Yang Guo, Jingjing Wei, Yuanmeng Qi, Ruoxuan Huang, Qiuyan Zhao, Changfu Hao
Software Mentions: 3
Published: over 5 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

10.1186/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.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

10.1155/2019/7376034

Identification of Potential Biomarkers and Survival Analysis for Head and Neck Squamous Cell Carcinoma Using Bioinformatics Strategy: A Study Based on TCGA and GEO Datasets
Cited by: 37
Author(s): Yujie Shen, Jinhui Liu, Liqing Zhang, Shikun Dong, Jiacheng Zhang, Yaqin Liu, Han Zhou, Wei Dong
Software Mentions: 3
Published: about 7 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

10.3390/ijms14048000

Proteins Involved in Distinct Phases of Cold Hardening Process in Frost Resistant Winter Barley (Hordeum vulgare L.) cv Luxor
Cited by: 41
Author(s): Iva Hlaváčková, Pavel Vítámvás, Jiří Šantrůček, Klára Kosová, Sylva Zelenková, Ilja Tom Prášil, Jaroslava Ovesná, Radovan Hynek, Milan Kodı́ček
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pone.0182533

A survey of the mycobiota associated with larvae of the black soldier fly (Hermetia illucens) reared for feed production
Cited by: 73
Author(s): Ilaria Varotto-Boccazzi, M. Ottoboni, Elena Martín, Francesco Comandatore, L. Vallone, Thomas Spranghers, Mia Eeckhout, Valeria Mereghetti, L. Pinotti, Sara Epis
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0176739

Genotypic and phenotypic diversity of Lactobacillus rhamnosus clinical isolates, their comparison with strain GG and their recognition by complement system
Cited by: 21
Author(s): Eija Nissilä, François P. Douillard, Jarmo Ritari, Lars Paulín, Hanna Järvinen, Pia Rasinkangas, Karita Haapasalo, Seppo Meri, Hanna Jarva, Willem M. de Vos
Software Mentions: 3
Published: over 9 years ago

10.1099/mgen.0.000104

Modification of the Streptococcus mutans transcriptome by LrgAB and environmental stressors
Cited by: 16
Author(s): Kelly C. Rice, Matthew E. Turner, O’neshia V. Carney, Tongjun Gu, Sang‐Joon Ahn
Software Mentions: 3
Published: over 9 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/s12864-020-06778-6

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.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

10.1186/s13073-019-0694-y

A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation
Cited by: 41
Author(s): Hannah Demond, Zahra Anvar, Bahia Namavar Jahromi, Ángela Sparago, Ankit Verma, Maryam Davari, Luciano Calzari, Silvia Russo, Mojgan Akbarzadeh‐Jahromi, David Gabriel Monk, Simon Andrews, Andrea Riccio, Gavin Kelsey
Software Mentions: 3
Published: over 6 years ago

10.1093/gbe/evv144

Comparative Genomics of a Bacterivorous Green Alga Reveals Evolutionary Causalities and Consequences of Phago-Mixotrophic Mode of Nutrition
Cited by: 27
Author(s): John A. Burns, Amber Paasch, Apurva Narechania, Eun-Soo Kim
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0010433

The Complete Genome Sequence of Cupriavidus metallidurans Strain CH34, a Master Survivalist in Harsh and Anthropogenic Environments
Cited by: 259
Author(s): Paul Janssen, Rob Van Houdt, Hugo Moors, Pieter Monsieurs, Nicolas Morin, Arlette Michaux, Mohammed Abderrafi Benotmane, Natalie Leys, Tatiana Vallaeys, Alla Lapidus, Sébastien Monchy, Claudine Médigue, Safiyh Taghavi, S. McCorkle, John J. Dunn, Daniël van der Lelie, Max Mergeay
Software Mentions: 3
Published: over 16 years ago

10.1186/s13059-017-1251-x

Dynamic DNA methylation reconfiguration during seed development and germination
Cited by: 187
Author(s): Taiji Kawakatsu, Joseph R. Nery, Rosa Castanon, Joseph R. Ecker
Software Mentions: 3
Published: almost 9 years ago

10.1038/srep17737

Lipidomics comparing DCD and DBD liver allografts uncovers lysophospholipids elevated in recipients undergoing early allograft dysfunction
Cited by: 19
Author(s): Jin Xu, Ana María Casas-Ferreira, Yun Ma, Arundhuti Sen, Min Kim, Petroula Proitsi, Maltina Shkodra, Maria Tena, Parthi Srinivasan, Nigel Heaton, Wayel Jassem, Cristina Legido‐Quigley
Software Mentions: 3
Published: over 10 years ago

10.1242/dmm.047803

Mutant non-coding RNA resource in mouse embryonic stem cells
Cited by: 3
Author(s): Jens Hansen, Harald von Melchner, Wolfgang Wurst
Software Mentions: 3
Published: over 5 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

10.15252/embj.201592383

Cytokine‐induced megakaryocytic differentiation is regulated by genome‐wide loss of a <scp>uSTAT</scp> transcriptional program
Cited by: 67
Author(s): Hyun Jung Park, Juan Li, Rebecca Hannah, Simon C. Biddie, Ana Leal-Cervantes, Kristina Kirschner, David Flores Santa Cruz, Veronika Sexl, Berthold Göttgens, Anthony Green
Software Mentions: 3
Published: over 10 years ago

10.15252/emmm.201708274

Identification of potential therapeutic targets in prostate cancer through a cross‐species approach
Cited by: 30
Author(s): Sarah Jurmeister, Antonio Ramos-Montoya, Carmen Sandi, Nelma Pértega‐Gomes, Karan Wadhwa, Alastair Lamb, Mark J. Dunning, Jan Attig, Jason S. Carroll, Lee G.D. Fryer, Sérgio Luís Felisbino, David E. Neal
Software Mentions: 3
Published: over 8 years ago

10.1002/ece3.3542

Precopulatory but not postcopulatory male reproductive traits diverge in response to mating system manipulation inDrosophila melanogaster
Cited by: 15
Author(s): Kristina U. Wensing, Mareike Koppik, Claudia Fricke
Software Mentions: 3
Published: almost 9 years ago

10.12952/journal.elementa.000064

Urban microbial ecology of a freshwater estuary of Lake Michigan
Cited by: 40
Author(s): James S. Fisher, Ryan J. Newton, Deborah K. Dila, Sandra L. McLellan
Software Mentions: 3
Published: over 11 years ago

10.1111/1462-2920.15546

A novel methoxydotrophic metabolism discovered in the hyperthermophilic archaeon Archaeoglobus fulgidus
Cited by: 9
Author(s): Cornelia U. Welte, R.M. de Graaf, Paula Dalcin Martins, Robert S. Jansen, Mike S. M. Jetten, Julia M. Kurth
Software Mentions: 3
Published: over 5 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

10.1186/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

10.1007/s00330-021-07693-4

Reliability of NI-RADS criteria in the interpretation of contrast-enhanced magnetic resonance imaging considering the potential role of diffusion-weighted imaging
Cited by: 5
Author(s): Fabian Henry Jürgen Elsholtz, Christoph Erxleben, Hans-Christian Bauknecht, Patrick Dinkelborg, Kilian Kreutzer, Bernd Hamm, Stefan M. Niehues
Software Mentions: 3
Published: over 5 years ago

10.1111/eva.12762

Patterns of cross‐resistance and collateral sensitivity between clinical antibiotics and natural antimicrobials
Cited by: 15
Author(s): Abigail Colclough, Jukka Corander, Samuel K. Sheppard, Sion C. Bayliss, Michiel Vos
Software Mentions: 3
Published: over 7 years ago

10.3389/fbioe.2020.00047

Metabolic Rearrangements Causing Elevated Proline and Polyhydroxybutyrate Accumulation During the Osmotic Adaptation Response of Bacillus megaterium
Cited by: 14
Author(s): Thibault Godard, Daniela Zühlke, Georg Richter, Melanie M. Wall, Manfred Rohde, Katharina Riedel, Ignacio Poblete‐Castro, Rainer Krull, Rebekka Biedendieck
Software Mentions: 3
Published: over 6 years ago

10.3389/fcimb.2019.00403

Mapping Alterations Induced by Long-Term Axenic Cultivation of Leishmania amazonensis Promastigotes With a Multiplatform Metabolomic Fingerprint Approach
Cited by: 1
Author(s): Frederico Crepaldi, Juliano Simões de Toledo, Anderson Oliveira do Carmo, Leopoldo Ferreira Marques Machado, Daniela Diniz Viana de Brito, Ângela Vieira Serufo, Ana Paula Martins Almeida, Laser Antônio Machado Oliveira, Tiago Queiroga Nery Ricotta, Douglas de Souza Moreira, Silvane Maria Fonseca Murta, Ariane Barros Diniz, Gustavo B. Menezes, Ángeles López‐Gonzálvez, Coral Barbas, Ana Paula Fernandes
Software Mentions: 3
Published: over 6 years ago

10.3389/fcimb.2021.662404

Proteomic Analysis of Copper Toxicity in Human Fungal Pathogen Cryptococcus neoformans
Cited by: 4
Author(s): Tianshu Sun, Yanjian Li, Yingxing Li, Hailong Li, Yiyi Gong, Jianhuang Wu, Ya-Ting Ning, Chen Ding, Yingchun Xu
Software Mentions: 3
Published: about 5 years ago

10.3389/fcimb.2020.00129

Pathobionts in the Vaginal Microbiota: Individual Participant Data Meta-Analysis of Three Sequencing Studies
Cited by: 26
Author(s): Janneke van de Wijgert, Marijn C. Verwijs, A. Christina Gill, Hanneke Borgdorff, Charlotte van der Veer, Philippe Mayaud
Software Mentions: 3
Published: over 6 years ago

10.3389/fcimb.2018.00160

Group A Streptococcus M1T1 Intracellular Infection of Primary Tonsil Epithelial Cells Dampens Levels of Secreted IL-8 Through the Action of SpyCEP
Cited by: 20
Author(s): Amelia T. Soderholm, Timothy C. Barnett, Othmar Korn, Tania Rivera-Hernandez, Lisa M. Seymour, Benjamin L. Schulz, Victor Nizet, Christine A. Wells, Matthew J. Sweet, Mark J. Walker
Software Mentions: 3
Published: over 8 years ago

10.3389/fgene.2018.00749

The Gene Toolkit Implicated in Functional Sex in Sparidae Hermaphrodites: Inferences From Comparative Transcriptomics
Cited by: 13
Author(s): Alexandros Tsakogiannis, Tereza Manousaki, Jacques Lagnel, Nikolaos Papanikolaou, Nikos Papandroulakis, Constantinos C. Mylonas, Costas S. Tsigenopoulos
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2021.689801

A Prognostic Autophagy-Related Gene Pair Signature and Small-Molecule Drugs for Hepatocellular Carcinoma
Cited by: 2
Author(s): Ze-bing Song, GuoPei Zhang, Yang Yu, shaoqiang li
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2020.503256

Construction and Analysis of a ceRNA Network in Cardiac Fibroblast During Fibrosis Based on in vivo and in vitro Data
Cited by: 7
Author(s): Qingyuan Gao, Haifeng Zhang, Zhi-Teng Chen, Yuewei Li, Shaohua Wang, Zheng Wen, Yong Xie, Jing-Ting Mai, Jingfeng Wang, Yangxin Chen
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2020.00850

Genome-Wide Transcriptional Regulation of the Long Non-coding RNA Steroid Receptor RNA Activator in Human Erythroblasts
Cited by: 5
Author(s): Waritta Sawaengdee, Kairong Cui, Keji Zhao, Suradej Hongeng, Suthat Fucharoen, Patompon Wongtrakoongate
Software Mentions: 3
Published: about 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

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

10.3389/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

10.1038/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

10.1038/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

10.1038/srep18178

Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq
Cited by: 138
Author(s): Luís R. Saraiva, Ximena Ibarra-Soria, Mona Khan, Masayo Omura, Antonio Scialdone, Peter Mombaerts, John C. Marioni, Darren W. Logan
Software Mentions: 3
Published: over 10 years ago

10.1038/srep24180

Population Dynamics of Bulking and Foaming Bacteria in a Full-scale Wastewater Treatment Plant over Five Years
Cited by: 21
Author(s): Xiaotao Jiang, Feng Guo, Tong Zhang
Software Mentions: 3
Published: over 10 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/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

10.1038/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/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/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

10.1038/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

10.1038/s41598-017-07862-w

E-Liquid Autofluorescence can be used as a Marker of Vaping Deposition and Third-Hand Vape Exposure
Cited by: 15
Author(s): Eric S. Davis, Maria F. Sassano, Henry P. Goodell, Robert Tarran
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-017-08134-3

Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs
Cited by: 46
Author(s): Anna García-Elías, Leonor Alloza, Eulàlia Puigdecanet, Lara Nonell, Marta Tajes, João Curado, Cristina Enjuanes, Óscar Díaz, Jordi Bruguera, Julio Martí‐Almor, Josep Comín‐Colet, Begoña Benito
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-017-08615-5

Genome-scale analysis identifies NEK2, DLGAP5 and ECT2 as promising diagnostic and prognostic biomarkers in human lung cancer
Cited by: 52
Author(s): Yuan-Xiang Shi, Ji‐Ye Yin, Yao Shen, Wei Zhang, Hong‐Hao Zhou, Zhao‐Qian Liu
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-017-09431-7

Biogeography shaped the metabolome of the genus Espeletia: a phytochemical perspective on an Andean adaptive radiation
Cited by: 25
Author(s): Guillermo F. Padilla-González, Mauricio Diazgranados, Fernando Batista Da Costa
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-017-11304-y

Dynamic Changes in the Splenic Transcriptome of Chickens during the Early Infection and Progress of Marek’s Disease
Cited by: 5
Author(s): Di Lu, Maikun Teng, Huawei Li, Huizhen Li, Shenglin Ma, Pengwei Zhao, Xiujie Li, Ruiguang Deng, Gaiping Zhang, Jun Luo
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-017-12087-y

Gene expression meta-analysis in diffuse low-grade glioma and the corresponding histological subtypes
Cited by: 20
Author(s): Siqi Wang, Feng Jin, Wenliang Fan, Fang Liu, Yutong Zou, Xuehan Hu, Haibo Xu, Ping Han
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-017-13844-9

Genome-wide discovery of long intergenic noncoding RNAs and their epigenetic signatures in the rat
Cited by: 3
Author(s): Aimin Li, Zhongyin Zhou, Xinhong Hei, Newton O. Otecko, Junying Zhang, Yajun Liu, Huanfu Zhou, Zhiqiang Zhao, Lei Wang
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-017-16193-9

PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens
Cited by: 66
Author(s): Philipp N. Spahn, Tyler Bath, Ryan J. Weiss, Jihoon Kim, Jeffrey D. Esko, Nathan E. Lewis, Olivier Harismendy
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-017-18132-0

IFNγ induces PD-L1 overexpression by JAK2/STAT1/IRF-1 signaling in EBV-positive gastric carcinoma
Cited by: 85
Author(s): Ji Wook Moon, Su Kang Kong, Byung Soo Kim, Hyun Ji Kim, Hyangsoon Lim, Kyeonga Noh, Younghye Kim, Jung Woo Choi, Ju Han Lee, Young Sik Kim
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-25434-4

Identification and application of exogenous dsRNA confers plant protection against Sclerotinia sclerotiorum and Botrytis cinerea
Cited by: 135
Author(s): Austein McLoughlin, Nick Wytinck, P.L. Walker, Ian J. Girard, K. Y. Rashid, Teresa de Kievit, W. G. Dilantha Fernando, Steve Whyard, Mark F. Belmonte
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-26375-8

Fertilization shapes a well-organized community of bacterial decomposers for accelerated paddy straw degradation
Cited by: 42
Author(s): Yushan Zhan, Wenjing Liu, Yuanyuan Bao, Jianwei Zhang, Evangelos Petropoulos, Zhongpei Li, Xiangui Lin, Youzhi Feng
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-26648-2

New universal ITS2 primers for high-resolution herbivory analyses using DNA metabarcoding in both tropical and temperate zones
Cited by: 57
Author(s): Rosemary J. Moorhouse‐Gann, Jenny C. Dunn, Natasha de Vere, Martine Goder, Nik C. Cole, Helen Hipperson, William Oliver Christian Symondson
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-27705-6

Need for focus on microbial species following ice melt and changing freshwater regimes in a Janus Arctic Gateway
Cited by: 17
Author(s): Nathalie Joli, Michel Gosselin, Mathieu Ardyna, Marcel Babin, Deo Florence L. Onda, Jean‐Éric Tremblay, Connie Lovejoy
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-28862-4

Gut Sphingolipid Composition as a Prelude to Necrotizing Enterocolitis
Cited by: 19
Author(s): Brigida Rusconi, Xuntian Jiang, Rohini Sidhu, Daniel S. Ory, Barbara B. Warner, Phillip I. Tarr
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-021-87479-2

Soil CO2 emission and soil attributes associated with the microbiota of a sugarcane area in southern Brazil
Cited by: 3
Author(s): Mara Regina Moitinho, Daniel De Bortoli Teixeira, Elton da Silva Bicalho, Alan Rodrigo Panosso, Antônio Sérgio Ferraudo, Gener Tadeu Pereira, Siu Mui Tsai, Beatriz Maria Ferrari Borges, Newton La Scala
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-96331-6

Genetic homogeneity, lack of larvae recruitment, and clonality in absence of females across western Mediterranean populations of the starfish Coscinasterias tenuispina
Cited by: 1
Author(s): Rocío Pérez‐Portela, Álex García-Cisneros, Marta Campos-Canet, Creu Palacín
Software Mentions: 3
Published: about 5 years ago

10.3390/s20123362

The Role of Dactylis Glomerata and Diesel Oil in the Formation of Microbiome and Soil Enzyme Activity
Cited by: 13
Author(s): Agata Borowik, Jadwiga Wyszkowska, M. Kucharski, J. Kucharski
Software Mentions: 3
Published: about 6 years ago

10.1186/s13287-019-1209-x

Human iPSC-derived MSCs (iMSCs) from aged individuals acquire a rejuvenation signature
Cited by: 76
Author(s): Lucas‐Sebastian Spitzhorn, Matthias Megges, Wasco Wruck, Shaifur Rahman, Jörg Otte, Özer Degistirici, Roland Meisel, Rüdiger V. Sorg, Richard O.C. Oreffo, James Adjaye
Software Mentions: 3
Published: over 7 years ago

10.1007/s00122-021-03781-7

Identification of eight QTL controlling multiple yield components in a German multi-parental wheat population, including Rht24, WAPO-A1, WAPO-B1 and genetic loci on chromosomes 5A and 6A
Cited by: 16
Author(s): Beatrice Corsi, Lia Obinu, Camila Martini Zanella, Saverio Cutrupi, Rob Day, Manuel Geyer, Morten Lillemo, Min Lin, Lorenzo Mazza, Lawrence Percival‐Alwyn, Melanie Stadlmeier, Volker Mohler, L. Hartl, James Cockram
Software Mentions: 3
Published: over 5 years ago

10.7150/thno.44693

A lab-on-a-disc platform enables serial monitoring of individual CTCs associated with tumor progression during EGFR-targeted therapy for patients with NSCLC
Cited by: 16
Author(s): Minji Lim, Juhee Park, Alarice Lowe, Hyoung-oh Jeong, Semin Lee, Hee Chul Park, Kyusang Lee, Gwang Ha Kim, Mi‐Hyun Kim, Yoon‐Kyoung Cho
Software Mentions: 3
Published: over 6 years ago

10.1128/mSphere.00017-18

Air-Dried Brown Seaweed, Ascophyllum nodosum , 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

10.1128/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

10.1128/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

10.1038/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

10.7150/ijms.63402

Bioinformatics analysis identified shared differentially expressed genes as potential biomarkers for Hashimoto's thyroiditis-related papillary thyroid cancer
Cited by: 8
Author(s): Chang Liu, Yu Pan, Qinyu Li, Yifan Zhang
Software Mentions: 3
Published: over 5 years ago

10.1155/2018/2837328

Illumina MiSeq Sequencing for Preliminary Analysis of Microbiome Causing Primary Endodontic Infections in Egypt
Cited by: 15
Author(s): Sally Ali Tawfik, Marwa Azab, Ali Abdellah Abdelrahman Ahmed, Dalia Mukhtar Fayyad
Software Mentions: 3
Published: over 8 years ago

10.1155/2020/8831331

Differential Expression and PAH Degradation: What Burkholderia vietnamiensis G4 Can Tell Us?
Cited by: 7
Author(s): Guilherme Pinto Cauduro, Ana Lusia Leal, Tiago Falcón Lopes, Marcela Marmitt, Victor Hugo Valiati
Software Mentions: 3
Published: about 6 years ago

10.1186/s40594-021-00306-y

Am I getting through? Surveying students on what messages they recall from the first day of STEM classes
Cited by: 6
Author(s): Clara L. Meaders, Lillian G. Senn, Brian A. Couch, A. Kelly Lane, Marilyne Stains, MacKenzie R. Stetzer, Erin Vinson, Michelle K. Smith
Software Mentions: 3
Published: about 5 years ago

10.1093/infdis/jiu615

Gene Expression and Cytokine Profile Correlate With Mycobacterial Growth in a Human BCG Challenge Model
Cited by: 29
Author(s): Magali Matsumiya, Iman Satti, Agnieszka Chomka, Stephanie A. Harris, Lisa Stockdale, Joel N. Meyer, Helen A. Fletcher, Helen McShane
Software Mentions: 3
Published: almost 12 years ago

10.7554/eLife.68466

LIN37-DREAM prevents DNA end resection and homologous recombination at DNA double-strand breaks in quiescent cells
Cited by: 10
Author(s): Bo-Ruei Chen, Yinan Wang, Anthony Tubbs, Dali Zong, Faith C Fowler, Nicholas Zolnerowich, Wei Wu, Amelia Bennett, Chun-Chin Chen, Wendy Feng, André Nussenzweig, Jessica K. Tyler, Barry P. Sleckman
Software Mentions: 3
Published: almost 5 years ago

10.7554/eLife.11469

An experimentally validated network of nine haematopoietic transcription factors reveals mechanisms of cell state stability
Cited by: 55
Author(s): Judith Schütte, Huange Wang, Stella Antoniou, Andrew Jarratt, Nicola K. Wilson, Joey Riepsaame, Fernando J. Calero-Nieto, Victoria Moignard, Silvia Basilico, Sarah Kinston, Rebecca Hannah, Mun Chiang Chan, Sylvia Nürnberg, Willem H. Ouwehand, Nicola Bonzanni, Marella Ftr de Bruijn, Berthold Göttgens
Software Mentions: 3
Published: over 10 years ago

10.7554/eLife.47866

Elevating acetyl-CoA levels reduces aspects of brain aging
Cited by: 72
Author(s): António Currais, Ling Huang, Joshua Goldberg, Michael Petrascheck, Gamze Ates, António Pinto-Duarte, Maxim N. Shokhirev, David Schubert, Pamela Maher
Software Mentions: 3
Published: almost 7 years ago

10.7554/eLife.50765

Midkine is a dual regulator of wound epidermis development and inflammation during the initiation of limb regeneration
Cited by: 27
Author(s): Stephanie Tsai, Clara Baselga-Garriga, Douglas A. Melton
Software Mentions: 3
Published: over 6 years ago

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