cran: gplots | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1005835

Type One Protein Phosphatase 1 and Its Regulatory Protein Inhibitor 2 Negatively Regulate ABA Signaling
Cited by: 55
Author(s): Yueh-Ju Hou, Yingfang Zhu, Pengcheng Wang, Yanping Zhao, Shaojun Xie, Giorgia Batelli, Bangshing Wang, Cheng‐Guo Duan, Xingang Wang, Xing Lü, Mingguang Lei, Jun Yan, Xiaohong Zhu, Jian‐Kang Zhu
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pgen.1005423

SLIRP Regulates the Rate of Mitochondrial Protein Synthesis and Protects LRPPRC from Degradation
Cited by: 74
Author(s): Marie Lagouge, Arnaud Mourier, Hyun Ju Lee, Henrik Spåhr, Timothy Wai, Christian Kukat, Eduardo Silva Ramos, Elisa Motori, Jakob D. Busch, Stefan J. Siira, Elisabeth Kremmer, Aleksandra Filipovska, Nils‐Göran Larsson
Software Mentions: 2
Published: over 9 years ago

10.3390/ijms21010239

Cell Wall Proteome of Wheat Grain Endosperm and Outer Layers at Two Key Stages of Early Development
Cited by: 9
Author(s): Mehdi Cherkaoui, Virginie Lollier, Audrey Geairon, Axelle Bouder, Colette Larré, Hélène Rogniaux, Élisabeth Jamet, Fabienne Guillon, Mathilde Francin-Allami
Software Mentions: 2
Published: almost 5 years ago

10.1186/s40168-017-0364-5

Comparing microbiotas in the upper aerodigestive and lower respiratory tracts of lambs
Cited by: 20
Author(s): Laura Glendinning, David Collie, Steven H. Wright, Kenny Rutherford, Gerry McLachlan
Software Mentions: 2
Published: about 7 years ago

10.1186/2049-2618-1-27

Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation
Cited by: 127
Author(s): Katherine E. Price, Thomas H. Hampton, Alex H. Gifford, Emily L. Dolben, Deborah A. Hogan, Hilary G. Morrison, Mitchell L. Sogin, George A. O’Toole
Software Mentions: 2
Published: about 11 years ago

10.1186/1479-5876-10-174

Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury
Cited by: 351
Author(s): Derrick E. Fouts, Rembert Pieper, Sebastian Szpakowski, Hans G. Pohl, Susan M. Knoblach, Moo-Jin Suh, Shih‐Ting Huang, Inger Ljungberg, Bruce M. Sprague, Lucas Sk, Manolito Torralba, Karen E. Nelson, Suzanne L. Groah
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pntd.0003446

Conservation and Immunogenicity of Novel Antigens in Diverse Isolates of Enterotoxigenic Escherichia coli
Cited by: 60
Author(s): Qingwei Luo, Firdausi Qadri, Rita G. Kansal, David A. Rasko, Alaullah Sheikh, James M. Fleckenstein
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pntd.0004180

Changes in the Proteome of Langat-Infected Ixodes scapularis ISE6 Cells: Metabolic Pathways Associated with Flavivirus Infection
Cited by: 40
Author(s): Jeffrey M. Grabowski, Rushika Perera, Ali M. Roumani, Victoria Hedrick, Halina D. Inerowicz, Catherine A. Hill, Richard Kühn
Software Mentions: 2
Published: almost 9 years ago

10.1186/s40168-018-0508-2

The diversity of uncharacterized antibiotic resistance genes can be predicted from known gene variants—but not always
Cited by: 38
Author(s): Johan Bengtsson‐Palme
Software Mentions: 2
Published: over 6 years ago

10.1186/s12967-018-1537-0

Clinicopathologic implication of microRNA-197 in diffuse large B cell lymphoma
Cited by: 16
Author(s): Jeyul Yang, Ji Young Jang, Yoon Kyung Jeon, Jin Ho Paik
Software Mentions: 2
Published: over 6 years ago

10.1186/s40168-017-0271-9

Uncovering the trimethylamine-producing bacteria of the human gut microbiota
Cited by: 300
Author(s): Silke Rath, B. Heidrich, Dietmar H. Pieper, Marius Vital
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0054684

Genome-Wide Association Study on the Development of Cross-Reactive Neutralizing Antibodies in HIV-1 Infected Individuals
Cited by: 21
Author(s): Zelda Euler, Marit J. van Gils, Brigitte Boeser‐Nunnink, Hanneke Schuitemaker, Daniëlle van Manen
Software Mentions: 2
Published: almost 12 years ago

10.1099/mic.0.2006/000562-0

A new environmentally resistant cell type from Dictyostelium
Cited by: 6
Author(s): Ioannis Serafimidis, Gareth Bloomfield, Jason Skelton, Alasdair Ivens, Robert R. Kay
Software Mentions: 2
Published: almost 18 years ago

10.1371/journal.pone.0239971

Culture-dependent and -independent investigations of bacterial migration into doenjang from its components meju and solar salt
Cited by: 6
Author(s): Jungmin Lee, Seongkook Heo, Yoon-Su Kim, Jong Hoon Lee, Do‐Won Jeong
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0076376

Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis sp. nov., from a Lava Cave in Kīlauea Caldera, Hawai'i
Cited by: 72
Author(s): Jimmy H. Saw, Michael C. Schatz, Mark V. Brown, Dennis D. Kunkel, Jamie S. Foster, H. Shick, Stephanie Christensen, Shaobin Hou, Xuehua Wan, Stuart P. Donachie
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0104560

Ontogeny of Hepatic Energy Metabolism Genes in Mice as Revealed by RNA-Sequencing
Cited by: 15
Author(s): Helen J. Renaud, Yue Cui, Hong Lü, Xiao‐bo Zhong, Curtis D. Klaassen
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0128272

Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils
Cited by: 143
Author(s): Franck Stefani, Terrence H. Bell, Charlotte Marchand, Ivan E. de la Providencia, Abdel El Yassimi, Marc St‐Arnaud, Mohamed Hijri
Software Mentions: 2
Published: over 9 years ago

10.1002/mbo3.230

Characterizing the diversity of active bacteria in soil by comprehensive stable isotope probing of DNA and RNA with H <sub>2</sub> <sup>18</sup> O
Cited by: 19
Author(s): Elizabeth A. Rettedal, Volker S. Brözel
Software Mentions: 2
Published: almost 10 years ago

10.1002/mbo3.330

Bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea
Cited by: 62
Author(s): Qi Ye, Ying Wu, Zhuoyi Zhu, Xiaona Wang, Zhongqiao Li, Jing Zhang
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0184102

Epicuticular chemistry reinforces the new taxonomic classification of the Bactrocera dorsalis species complex (Diptera: Tephritidae, Dacinae)
Cited by: 10
Author(s): Lucie Vaníčková, Radka Nagy, Antonio Pompeiano, Blanka Kalinová
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0096014

Genome-Wide Analysis of the bZIP Transcription Factors in Cucumber
Cited by: 159
Author(s): Mehmet Cengiz Baloğlu, Vahap Eldem, Mortaza Hajyzadeh, Turgay Ünver
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0205292

Elevated cytokine levels in vitreous as biomarkers of disease severity in infectious endophthalmitis
Cited by: 28
Author(s): Dhanshree Deshmukh, Moumita Chakrabarti, Rajagopalaboopathi Jayasudha, Mohammed Ali, Mudit Tyagi, Savitri Sharma, Joveeta Joseph
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0175417

Caste-, sex-, and age-dependent expression of immune-related genes in a Japanese subterranean termite, Reticulitermes speratus
Cited by: 31
Author(s): Yuki Mitaka, Keiko Kobayashi, Kenji Matsuura
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0245534

Gut microbiome dysbiosis and correlation with blood biomarkers in active-tuberculosis in endemic setting
Cited by: 12
Author(s): Aasia Khaliq, Resmi Ravindran, Samia Afzal, Prasant Kumar Jena, Muhammad Akhtar, Atiqa Ambreen, Yu Wan, K. A. Malik, Muhammad Irfan, Imran Khan
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0122304

Redox-Specialized Bacterioplankton Metacommunity in a Temperate Estuary
Cited by: 10
Author(s): Peeter Laas, Jaak Simm, Inga Lips, Urmas Lips, Veljo Kisand, Madis Metsis
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0137762

Using Co-Expression Analysis and Stress-Based Screens to Uncover Arabidopsis Peroxisomal Proteins Involved in Drought Response
Cited by: 27
Author(s): Jiying Li, Jianping Hu
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0131686

Transcriptional Response in Mouse Thyroid Tissue after 211At Administration: Effects of Absorbed Dose, Initial Dose-Rate and Time after Administration
Cited by: 11
Author(s): Nils Rudqvist, Johan Spetz, Emil Schüler, Toshima Z. Parris, Britta Langen, Khalil Helou, Eva Forssell-Aronsson
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0242125

Unmet clinical needs for COVID-19 tests in UK health and social care settings
Cited by: 5
Author(s): Sara Graziadio, Samuel Urwin, Paola Cocco, Massimo Micocci, Amanda Winter, Yaling Yang, David Ashley Price, Mike Messenger, Joy Allen, Bethany Shinkins
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0129318

Complete Genome Sequence of Sporisorium scitamineum and Biotrophic Interaction Transcriptome with Sugarcane
Cited by: 81
Author(s): Lucas Mitsuo Taniguti, Patrícia Dayane Carvalho Schaker, Juliana Benevenuto, Leila Priscila Peters, Gabriela Ferreira Carvalho, Aristides Palhares, Maria Carolina Quecine, Filipe R. S. Nunes, Maria Carolina Pezzo Kmit, Alvan Wai, Georg Hausner, Karen S. Aitken, Paul J. Berkman, James A. Fraser, Paula Moolhuijzen, Luiz Lehmann Coutinho, Silvana Creste, Maria Lúcia Carneiro Vieira, João Paulo Kitajima, Cláudia Barros Monteiro-Vitorello
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0097690

Altered Expression of Circulating MicroRNA in Plasma of Patients with Primary Osteoarthritis and In Silico Analysis of Their Pathways
Cited by: 83
Author(s): Verónica M. Borgonio Cuadra, Norma Celia González-Huerta, Sandra Romero-Córdoba, Alfredo Hidalgo-Miranda, Antonio Miranda‐Duarte
Software Mentions: 2
Published: over 10 years ago

10.1186/s12934-021-01602-6

Superior production of heavy pamamycin derivatives using a bkdR deletion mutant of Streptomyces albus J1074/R2
Cited by: 6
Author(s): Lars Gläser, Martin Kuhl, Julian Stegmüller, Christian Rückert, Maksym Myronovskyi, Jörn Kalinowski, Andriy Luzhetskyy, Christoph Wittmann
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0169670

Species-Specific Responses of Juvenile Rockfish to Elevated pCO2: From Behavior to Genomics
Cited by: 50
Author(s): Scott L. Hamilton, Cheryl A. Logan, Hamilton William Fennie, Susan M. Sogard, James Barry, April D. Makukhov, Lauren R. Tobosa, Kirsten Boyer, C. Lovera, Giacomo Bernardi
Software Mentions: 2
Published: almost 8 years ago

10.15698/mic2021.09.760

Landscapes and bacterial signatures of mucosa-associated intestinal microbiota in Chilean and Spanish patients with inflammatory bowel disease
Cited by: 10
Author(s): Nayaret Chamorro, David A. Montero, Pablo Gallardo, Mauricio J. Farfán, Mauricio Contreras, Marjorie De la Fuente, Karen Dubois, Marcela A. Hermoso, Rodrigo Quera, Marjorie Pizarro-Guajardo, Daniel Paredes-Sabja, Daniel Ginard, Ramon Rosselló‐Móra, Roberto Vidal
Software Mentions: 2
Published: about 3 years ago

10.3390/ijms21124305

Characterization and Analysis of the Full-Length Transcriptomes of Multiple Organs in Pseudotaxus chienii (W.C.Cheng) W.C.Cheng
Cited by: 4
Author(s): Li Liu, Zhen Wang, Yingjuan Su, Ting Wang
Software Mentions: 2
Published: over 4 years ago

10.1111/1751-7915.12342

Use of mulberry–soybean intercropping in salt–alkali soil impacts the diversity of the soil bacterial community
Cited by: 62
Author(s): Xin Li, Meiling Sun, Huihui Zhang, Nan Xu, Sun Guang-yu
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0054732

The Carcinogenic Liver Fluke, Clonorchis sinensis: New Assembly, Reannotation and Analysis of the Genome and Characterization of Tissue Transcriptomes
Cited by: 71
Author(s): Yan Huang, Wenjun Chen, Xiaoyun Wang, Hailiang Liu, Yangyi Chen, Lei Guo, Fang Luo, Jiufeng Sun, Qiang Mao, Pei Liang, Zhizhi Xie, Chenhui Zhou, Yanli Tian, Xiaoli Lv, Lisha Huang, Juanjuan Zhou, Yue Hu, Ran Li, Fan Zhang, Huali Lei, Wenfang Li, Xuchu Hu, Chi Liang, Jin Xu, Xuerong Li, Xinbing Yu
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0190199

Combined oral and topical antimicrobial therapy for male partners of women with bacterial vaginosis: Acceptability, tolerability and impact on the genital microbiota of couples - A pilot study
Cited by: 40
Author(s): Erica L Plummer, Lenka A Vodstrcil, Jennifer Danielewski, Gerald L Murray, Christopher K. Fairley, Suzanne M. Garland, Jane S Hocking, Sepehr N. Tabrizi, Catriona Bradshaw
Software Mentions: 2
Published: almost 7 years ago

10.3390/microarrays4040630

Integrating Colon Cancer Microarray Data: Associating Locus-Specific Methylation Groups to Gene Expression-Based Classifications
Cited by: 3
Author(s): Ana Barat, Heather J. Ruskin, Annette T. Byrne, Jochen H M Prehn
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0063251

Gene Expression Changes in the Colon Epithelium Are Similar to Those of Intact Colon during Late Inflammation in Interleukin-10 Gene Deficient Mice
Cited by: 9
Author(s): Anna E Russ, J. S. Peters, Warren C. McNabb, Matthew P. G. Barnett, Rachel C. Anderson, Zaneta Park, Shuotun Zhu, Paul Maclean, Wayne Young, Gordon Reynolds, Nicole C. Roy
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0164735

Variations of Phosphorous Accessibility Causing Changes in Microbiome Functions in the Gastrointestinal Tract of Chickens
Cited by: 34
Author(s): Bruno Tilocca, Maren Witzig, M. Rodehutscord, Jana Seifert
Software Mentions: 2
Published: about 8 years ago

10.1007/s11306-018-1328-x

Weight loss moderately affects the mixed meal challenge response of the plasma metabolome and transcriptome of peripheral blood mononuclear cells in abdominally obese subjects
Cited by: 18
Author(s): Parastoo Fazelzadeh, Roland W. J. Hangelbroek, Peter J. Joris, Casper G. Schalkwijk, Diederik Esser, Lydia A. Afman, Thomas Hankemeier, Doris M. Jacobs, Velitchka V. Mihaleva, Sander Kersten, John van Duynhoven, Mark V. Boekschoten
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0120106

Potential Biomarkers of Fatigue Identified by Plasma Metabolome Analysis in Rats
Cited by: 39
Author(s): Satoshi Kume, Masayuki Yamato, Yasuhisa Tamura, Guanghua Jin, Masayuki Nakano, Yukiharu Miyashige, Akiyo Eguchi, Yasuhiro Ogata, Nobuhito Goda, Kazuhiro Iwaï, Emi Yamano, Yasuyoshi Watanabe, Tomoyoshi Soga, Yosky Kataoka
Software Mentions: 2
Published: over 9 years ago

10.1007/s11306-016-1120-8

Loss of ncm5 and mcm5 wobble uridine side chains results in an altered metabolic profile
Cited by: 11
Author(s): Tony Karlsborn, A. K. M. Firoj Mahmud, Hasan Tükenmez, Andeŕs S. Byström
Software Mentions: 2
Published: about 8 years ago

10.3390/ijms21197199

Transcriptional and Metabolic Profiling of Potato Plants Expressing a Plastid-Targeted Electron Shuttle Reveal Modulation of Genes Associated to Drought Tolerance by Chloroplast Redox Poise
Cited by: 11
Author(s): Juan José Pierella Karlusich, Rocío C. Arce, Fahimeh Shahinnia, Sophia Sonnewald, Uwe Sonnewald, Matías D. Zurbriggen, Mohammad‐Reza Hajirezaei, Néstor Carrillo
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0069790

Identification of Novel Adhesins of M. tuberculosis H37Rv Using Integrated Approach of Multiple Computational Algorithms and Experimental Analysis
Cited by: 26
Author(s): Sanjiv Kumar, Bhanwar Lal Puniya, Shahila Parween, Pradip Nahar, Srinivasan Ramachandran
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0046202

Influence of the Male Ejaculate on Post-Mating Prezygotic Barriers in Field Crickets
Cited by: 22
Author(s): Erica L. Larson, José Á. Andrés, Richard G. Harrison
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0039621

A Daphnane Diterpenoid Isolated from Wikstroemia polyantha Induces an Inflammatory Response and Modulates miRNA Activity
Cited by: 9
Author(s): Anthony Khong, Roberto Forestieri, David E. Williams, Brian O. Patrick, Andrea D. Olmstead, Victoria Svinti, Emily K. Schaeffer, François Jean, Michel Roberge, Raymond J. Andersen, Eric Jan
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0124969

Transcriptional and Phenotypic Characterization of Novel Spx-Regulated Genes in Streptococcus mutans
Cited by: 28
Author(s): Lívia C. C. Galvão, James H. Miller, Jessica K. Kajfasz, Kathy Scott-Anne, Irlan Almeida Freires, Gilson César Nobre Franco, Jacqueline Abranches, Pedro Luiz Rosalen, José A. Lemos
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0208352

Characterization of longitudinal canal tissue in the acorn barnacle Amphibalanus amphitrite
Cited by: 8
Author(s): Chenyue Wang, Janna N. Schultzhaus, Chris R. Taitt, Dagmar H. Leary, Lisa C. Shriver‐Lake, Daniel A. Snellings, Samantha L Sturiale, Stella H. North, Beatriz Orihuela, Daniel Rittschof, Kathryn J. Wahl, Christopher M. Spillmann
Software Mentions: 2
Published: almost 6 years ago

10.1007/s11306-019-1599-x

Metabolomics: a search for biomarkers of visceral fat and liver fat content
Cited by: 19
Author(s): Sebastiaan C. Boone, Dennis O. Mook‐Kanamori, Frits R. Rosendaal, Martin den Heijer, Hildo J. Lamb, Albert de Roos, Saskia le Cessie, Ko Willems van Dijk, Renée de Mutsert
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0089680

A Selected Core Microbiome Drives the Early Stages of Three Popular Italian Cheese Manufactures
Cited by: 1,029
Author(s): Francesca De Filippis, Antonietta La Storia, Giuseppina Stellato, Monica Gatti
Software Mentions: 2
Published: almost 11 years ago

10.3390/ijms21218210

Comparative Ubiquitome Analysis under Heat Stress Reveals Diverse Functions of Ubiquitination in Saccharina japonica
Cited by: 7
Author(s): Pengyan Zhang, Fuli Liu, Siqing Chen, Zhourui Liang, Wenjun Wang, Xiuyun Sun
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0240612

Study of the differentially abundant proteins among Leishmania amazonensis, L. braziliensis, and L. infantum
Cited by: 1
Author(s): Bruna Soares de Souza Lima, Barbara Beiral Esteves, Luiz Carlos Fialho-Júnior, Tiago Antônio de Oliveira Mendes, Simone da Fonseca Pires, Alexander Chapeourouge, Jonás Perales, Hélida Monteiro de Andrade
Software Mentions: 2
Published: about 4 years ago

10.1007/s11306-019-1564-8

A large-scale analysis of targeted metabolomics data from heterogeneous biological samples provides insights into metabolite dynamics
Cited by: 47
Author(s): Ho‐Joon Lee, Daniel M. Kremer, Peter Sajjakulnukit, Li Zhang, Costas A. Lyssiotis
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0179652

Contrasting bacterial communities in two indigenous Chionochloa (Poaceae) grassland soils in New Zealand
Cited by: 14
Author(s): Jocelyn Chua Griffith, William G. Lee, David A. Orlovich, Tina C. Summerfield
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0111581

MiRNA Expression May Account for Chronic but Not for Acute Regulation of mRNA Expression in Human Thyroid Tumor Models
Cited by: 9
Author(s): Sébastien Floor, Aline Hébrant, Jaime Miguel Gomes Pita, Manuel Saiselet, Christophe Trésallet, Frédérick Libert, Guy Andry, Jacques Emile Dumont, Wilma Van Staveren, Carine Maenhaut
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0097338

Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses
Cited by: 18
Author(s): Ari J. S. Ferreira, Rania Siam, João Carlos Setúbal, Ahmed Moustafa, Ahmed A. Sayed, Felipe S. Chambergo, Adam Dawe, Mohamed A. Ghazy, Hazem Sharaf, Amged Ouf, Intikhab Álam, Alyaa M. Abdel-Haleem, Heikki Lehväslaiho, Eman Ramadan, André Antunes, Ulrich Stingl, John Archer, Boris R. Janković, Mitchell L. Sogin, Vladimir B. Bajic, Hamza A. El-Dorry
Software Mentions: 2
Published: over 10 years ago

10.1111/acel.12472

Mitochondrial‐targeted catalase is good for the old mouse proteome, but not for the young: ‘reverse’ antagonistic pleiotropy?
Cited by: 31
Author(s): Nathan Basisty, Dao Fu Dai, Arni Gagnidze, Lemuel Gitari, Jeanne Fredrickson, Yvonne Maina, Richard P. Beyer, Mary J. Emond, Edward J. Hsieh, Michael J. MacCoss, George M. Martin, Peter S. Rabinovitch
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0160574

Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers
Cited by: 15
Author(s): Michelle Davison, Todd J. Treangen, Sergey Koren, Mihai Pop, Devaki Bhaya
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0231049

Zika virus infection differentially affects genome-wide transcription in neuronal cells and myeloid dendritic cells
Cited by: 7
Author(s): Tamina Park, Myung-Gyun Kang, Seung‐Hwa Baek, Chang Hoon Lee, Daeui Park
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0086569

Ion Channel Gene Expression in Lung Adenocarcinoma: Potential Role in Prognosis and Diagnosis
Cited by: 31
Author(s): Jae Hong Ko, Wanjun Gu, Inja Lim, Hyoweon Bang, Eun A. Ko, Tong Zhou
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0203953

Biodiversity of cyanobacteria and other aquatic microorganisms across a freshwater to brackish water gradient determined by shotgun metagenomic sequencing analysis in the San Francisco Estuary, USA
Cited by: 18
Author(s): Tomofumi Kurobe, Peggy W. Lehman, Bruce G. Hammock, Melissa B. Bolotaolo, Sarah Lesmeister, Swee J. Teh
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0049130

Genome-Wide Expression Analysis in Down Syndrome: Insight into Immunodeficiency
Cited by: 12
Author(s): Chong Li, Lan Jin, Yun Bai, Qimin Chen, Lei Fu, Minjun Yang, Huasheng Xiao, Guoping Zhao, Shengyue Wang
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0060321

Biological Characteristics and Genetic Heterogeneity between Carcinoma-Associated Fibroblasts and Their Paired Normal Fibroblasts in Human Breast Cancer
Cited by: 67
Author(s): Qiongle Peng, Liuyang Zhao, Yixuan Hou, Yan Sun, Liyang Wang, Haojun Luo, Huimin Peng, Manran Liu
Software Mentions: 2
Published: over 11 years ago

10.3390/ijms21249380

Structural Diversity and Highly Specific Host-Pathogen Transcriptional Regulation of Defensin Genes Is Revealed in Tomato
Cited by: 5
Author(s): Nikolaos Nikoloudakis, Polyxeni Pappi, Emmanouil A. Markakis, Spyridoula N. Charova, Dimitrios Fanourakis, Konstantinos Paschalidis, Costas Delis, Emmanuel A. Tzortzakakis, Georgios Tsaniklidis
Software Mentions: 2
Published: almost 4 years ago

10.3390/metabo11070427

Primary Metabolite Profile Changes in Coffea spp. Promoted by Single and Combined Exposure to Drought and Elevated CO2 Concentration
Cited by: 12
Author(s): Ana Margarida Rodrigues, Tiago F. Jorge, Sonia Osorio, Delphine M. Pott, Fernando C. Lidon, Fábio M. DaMatta, Isabel Marques, Ana I. Ribeiro‐Barros, José C. Ramalho, Carla António
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0039786

Characterization of miRNAs in Response to Short-Term Waterlogging in Three Inbred Lines of Zea mays
Cited by: 74
Author(s): Zhijie Liu, Sunita Kumari, Lifang Zhang, Yanyan Zheng, Doreen Ware
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0148726

Transcriptome Analysis of Chemically-Induced Sensory Neuron Ablation in Zebrafish
Cited by: 5
Author(s): Jane A. Cox, Bo Zhang, Holly M. Pope, Mark M. Voigt
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0180385

Autoimmunity and allergy control in adults submitted to complete thymectomy early in infancy
Cited by: 13
Author(s): Susana L. Silva, Adriana S. Albuquerque, Andreia J. Amaral, Quan Zhen Li, Catarina Mota, Rémi Cheynier, Rui M. M. Victorino, Maria Conceição Pereira-Santos, Ana E. Sousa
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0029596

Trypanosoma cruzi Gene Expression in Response to Gamma Radiation
Cited by: 14
Author(s): Priscila Grynberg, Danielle Gomes Passos‐Silva, Marina Moraes Mourão, Roberto Hirata, Andréa Mara Macedo, Carlos Renato Machado, Daniella Castanheira Bartholomeu, Glória Regina Franco
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0093258

RNA Sequence Reveals Mouse Retinal Transcriptome Changes Early after Axonal Injury
Cited by: 65
Author(s): Masayuki Yasuda, Yuji Tanaka, Morin Ryu, S. Tsuda, Toru Nakazawa
Software Mentions: 2
Published: over 10 years ago

10.1080/10872981.2019.1635844

Information within residency monthly evaluation forms at two institutions
Cited by: 0
Author(s): Christopher J. Cooper, Paulette Wehner, Cindy Dailey, Nanette O'Connor, James Kleshinski, Joseph I. Shapiro
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms22031495

Comparative Analysis Identifies Similarities between the Human and Murine Microglial Sensomes
Cited by: 18
Author(s): Erik R. Abels, Lisa Nieland, Suzanne E. Hickman, Marike L D Broekman, Joseph El Khoury, Sybren L. N. Maas
Software Mentions: 2
Published: almost 4 years ago

10.1111/liv.14692

The biological process of lysine‐tRNA charging is therapeutically targetable in liver cancer
Cited by: 8
Author(s): Ruyi Zhang, Lisanne Noordam, Xumin Ou, Bo Ma, Yunlong Li, Priyadip Das, Shaojun Shi, Jiaye Liu, Ling Wang, Pengfei Li, Monique M A Verstegen, D. Srinivasa Reddy, Luc J. W. van der Laan, Maikel P. Peppelenbosch, Jaap Kwekkeboom, Ron Smits
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0181427

Habitat and indigenous gut microbes contribute to the plasticity of gut microbiome in oriental river prawn during rapid environmental change
Cited by: 51
Author(s): Cheng-Yu Chen, Po‐Cheng Chen, Francis Cheng-Hsuan Weng, Grace Tzun-Wen Shaw, Daryi Wang
Software Mentions: 2
Published: over 7 years ago

10.26508/lsa.201900554

TRAIL-induced variation of cell signaling states provides nonheritable resistance to apoptosis
Cited by: 10
Author(s): Reema Baskar, Harris G. Fienberg, Zumana Khair, Patrícia Favaro, Samuel C. Kimmey, Douglas R. Green, Garry P. Nolan, Sylvia K. Plevritis, Sean C. Bendall
Software Mentions: 2
Published: about 5 years ago

10.26508/lsa.201800197

A role for MED14 and UVH6 in heterochromatin transcription upon destabilization of silencing
Cited by: 13
Author(s): Pierre Bourguet, Stève de Bossoreille, Leticia López-González, Marie-Noëlle Pouch-Pélissier, Ángeles Gómez-Zambrano, Anthony Devert, Thierry Pélissier, Romain Pogorelcnik, Isabelle Vaillant, Olivier Mathieu
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0239998

Distinctiveness of genes contributing to growth of Pseudomonas syringae in diverse host plant species
Cited by: 10
Author(s): Tyler C. Helmann, Adam M. Deutschbauer, Steven E. Lindow
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0025584

An Integrated Transcriptomic and Meta-Analysis of Hepatoma Cells Reveals Factors That Influence Susceptibility to HCV Infection
Cited by: 19
Author(s): Jamie MacPherson, Ben S. Sidders, Stefan Wieland, Jin Zhong, Paul Targett-Adams, Volker Lohmann, Perdita Backes, Oona E Delpuech-Adams, Francis V. Chisari, Marilyn Lewis, Tanya Parkinson, David L. Robertson
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0051075

Bacterial Indicator of Agricultural Management for Soil under No-Till Crop Production
Cited by: 75
Author(s): Eva Lucía Margarita Figuerola, Leandro D. Guerrero, Silvina Mariana Rosa, Leandro Simonetti, Matías Ezequiel Duval, Juán Alberto Galantini, José Camilo Bedano, Luis Gabriel Wall, Leonardo Erijman
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0103115

Microbial Diversity in Hummock and Hollow Soils of Three Wetlands on the Qinghai-Tibetan Plateau Revealed by 16S rRNA Pyrosequencing
Cited by: 54
Author(s): Yangfan Deng, Xiaoyong Cui, Marcela Hernández, Marc G. Dumont
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0227243

Transcriptome-wide identification of novel circular RNAs in soybean in response to low-phosphorus stress
Cited by: 21
Author(s): Lingling Lv, Kaiye Yu, Haiyan Lü, Xiangqian Zhang, Xiaoqian Liu, Chongyuan Sun, Huanqing Xu, Jinyu Zhang, Xiaohong He, Dan Zhang
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0128872

Multi-Pathway Cellular Analysis on Crude Natural Drugs/Herbs from Japanese Kampo Formulations
Cited by: 1
Author(s): Shizuka Eshima, Satoru Yokoyama, Takashi Abe, Yoshihiro Hayakawa, Ikuo Saiki
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0088584

Effect of Diet on Expression of Genes Involved in Lipid Metabolism, Oxidative Stress, and Inflammation in Mouse Liver–Insights into Mechanisms of Hepatic Steatosis
Cited by: 73
Author(s): Helen J. Renaud, Julia Yue Cui, Hong Lü, Curtis D. Klaassen
Software Mentions: 2
Published: almost 11 years ago

10.3390/ijms22052452

A Systems Biology Approach to Investigating the Interaction between Serotonin Synthesis by Tryptophan Hydroxylase and the Metabolic Homeostasis
Cited by: 11
Author(s): Suhyeon Park, Yumin Kim, Jibeom Lee, Jeong Yun Lee, Hail Kim, Sunjae Lee, Chang‐Myung Oh
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms22062936

Overexpression of AtBBD1, Arabidopsis Bifunctional Nuclease, Confers Drought Tolerance by Enhancing the Expression of Regulatory Genes in ABA-Mediated Drought Stress Signaling
Cited by: 10
Author(s): Amdadul Huque, Wonmi So, Minsoo Noh, Min Kyoung You, Jeong Sheop Shin
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0197911

Deconvolution of expression microarray data reveals 131I-induced responses otherwise undetected in thyroid tissue
Cited by: 5
Author(s): Britta Langen, Nils Rudqvist, Johan Spetz, Khalil Helou, Eva Forssell-Aronsson
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0190960

A systematic approach to analyze the social determinants of cardiovascular disease
Cited by: 23
Author(s): Mireya Martínez-García, Magaly Salinas-Ortega, Iván Estrada-Arriaga, Enrique Hernández‐Lemus, Rodrigo García-Herrera, Maité Vallejo
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0174411

The rhizospheric microbial community structure and diversity of deciduous and evergreen forests in Taihu Lake area, China
Cited by: 39
Author(s): Zhiwen Wei, Xiaolong Hu, Xunhang Li, Yanzhou Zhang, Leichun Jiang, Jing Li, Guan Zhang, Yujie Cai, Xiangru Liao
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0245855

Transcriptomic analysis reveals key transcription factors associated to drought tolerance in a wild papaya (Carica papaya) genotype
Cited by: 9
Author(s): Humberto Estrella‐Maldonado, Amaranta Girón Ramírez, Gabriela Fuentes Ortíz, Santy Peraza-Echeverría, Octavio Martínez-de la Vega, Elsa Góngora-Castillo, Jorge M. Santamaría
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12935-020-1128-z

Establishment and characterization of patient-derived cancer models of malignant peripheral nerve sheath tumors
Cited by: 10
Author(s): Rieko Oyama, Fusako Kito, Mami Takahashi, Emi Hattori, Rei Noguchi, Yoko Takai, Marimu Sakumoto, Zhiwei Qiao, Shunichi Toki, Michio Sugawara, Yoshikazu Tanzawa, Eisuke Kobayashi, Fumihiko Nakatani, Shintaro Iwata, Akihiko Yoshida, Akira Kawai, Tadashi Kondo
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0160577

Diurnal Variations of Human Circulating Cell-Free Micro-RNA
Cited by: 42
Author(s): Niels H. H. Heegaard, Anting Liu Carlsen, Berit Lilje, Kim Lee Ng, Birte Svensson, Henrik L. Jørgensen, Henriette P Sennels, Jan Fahrenkrug
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0171797

Transcriptional response to 131I exposure of rat thyroid gland
Cited by: 10
Author(s): Nils Rudqvist, Johan Spetz, Emil Schüler, Toshima Z. Parris, Britta Langen, Khalil Helou, Eva Forssell-Aronsson
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0065347

Impact of Oil on Bacterial Community Structure in Bioturbated Sediments
Cited by: 61
Author(s): Magalie Stauffert, Cristiana Cravo‐Laureau, Ronan Jézéquel, Sandra Barantal, Philippe Cuny, Franck Gilbert, Christine Cagnon, Cécile Militon, David Amouroux, Fatima Mahdaoui, Brice Bouyssière, Georges Stora, François-Xavier Merlin, Robert Duran
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0135565

Temporal Gene Expression of the Cyanobacterium Arthrospira in Response to Gamma Rays
Cited by: 10
Author(s): Hanène Badri, Pieter Monsieurs, Ilse Coninx, Robin Nauts, Ruddy Wattiez, Natalie Leys
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0233729

Plant life at the dry limit—Spatial patterns of floristic diversity and composition around the hyperarid core of the Atacama Desert
Cited by: 15
Author(s): Jonathan Ruhm, Tim Böhnert, Maximilian Weigend, Félix F. Merklinger, Alexandra Stoll, Dietmar Quandt, Federico Luebert
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0186440

Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium
Cited by: 13
Author(s): Roberto Orellana, Gina Chaput, Lye Meng Markillie, Hugh D. Mitchell, Matt Gaffrey, Galya Orr, Kristen M. DeAngelis
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0096333

Profiling of Olfactory Receptor Gene Expression in Whole Human Olfactory Mucosa
Cited by: 103
Author(s): Christophe Verbeurgt, Françoise Wilkin, Maxime Tarabichi, Françoise Grégoire, Jacques Emile Dumont, Pierre Chatelain
Software Mentions: 2
Published: over 10 years ago

10.1093/brain/awz291

Mutations in PCYT2 disrupt etherlipid biosynthesis and cause a complex hereditary spastic paraplegia
Cited by: 73
Author(s): Frédéric M. Vaz, John H McDermott, Mariëlle Alders, Saskia B. Wortmann, Stefan Kölker, Mia L. Pras‐Raves, Martin A. T. Vervaart, Henk van Lenthe, Angela C. M. Luyf, Hyung L. Elfrink, Kay Metcalfe, Sara Cuvertino, Peter E. Clayton, Rebecca Yarwood, Martin Lowe, Simon C. Lovell, R. Curtis Rogers, Deciphering Developmental Disorders Study, Antoine H. C. van Kampen, J. P. N. Ruiter, Ronald J. A. Wanders, Sacha Ferdinandusse, Michel van Weeghel, Marc Engelen, Siddharth Banka
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0074599

Specific Extracellular Matrix Remodeling Signature of Colon Hepatic Metastases
Cited by: 42
Author(s): Maguy Del Rio, Caroline Mollévi, Nadia Vezzio-Vié, Fréderic Bibeau, Marc Ychou, Pierre Martineau
Software Mentions: 2
Published: about 11 years ago

Projects: cran: gplots

Papers Mentioning gplots 2,122