cran: gplots | Projects | Ecosyste.ms: Papers

10.3389/fonc.2021.641289

Bioinformatics Analysis of a Prognostic miRNA Signature and Potential Key Genes in Pancreatic Cancer
Cited by: 15
Author(s): Shuoling Chen, Chang Gao, Tao Yu, Yueyang Qu, Gary Guishan Xiao, Zunnan Huang
Software Mentions: 3
Published: over 3 years ago

10.3389/fonc.2018.00368

Integrated Analysis of a Competing Endogenous RNA Network Revealing a Prognostic Signature for Cervical Cancer
Cited by: 11
Author(s): Leilei Xia, Han Wang, Shengyun Cai, Xiaoling Su, Jizi Shen, Meng Qi, Yu Chen, Li Li, Jiuqiong Yan, Caihong Zhang, Man Xu
Software Mentions: 3
Published: about 6 years ago

10.3389/fonc.2020.607047

Genome-Wide Identification and Analysis of the Methylation of lncRNAs and Prognostic Implications in the Glioma
Cited by: 4
Author(s): Yijie He, Lidan Wang, Jing Tang, Zhijie Han
Software Mentions: 3
Published: almost 4 years ago

10.3389/fonc.2020.554759

Integrated Analysis of lncRNA–Mediated ceRNA Network in Lung Adenocarcinoma
Cited by: 90
Author(s): Xianxian Wu, Zhilin Sui, Hongdian Zhang, Ying Wang, Zhentao Yu
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2017.02306

Antibiotic-Induced Alterations in Gut Microbiota Are Associated with Changes in Glucose Metabolism in Healthy Mice
Cited by: 89
Author(s): Richard R. Rodrigues, Renee Greer, Xiaoxi Dong, Karen D’Souza, Manoj Gurung, Jia Wu, Andrey Morgun, Natalia Shulzhenko
Software Mentions: 3
Published: about 7 years ago

10.1186/s12859-020-3493-y

Self-analysis of repeat proteins reveals evolutionarily conserved patterns
Cited by: 4
Author(s): M. Merski, Krzysztof Młynarczyk, Jan Ludwiczak, Jakub Skrzeczkowski, Stanisław Dunin-Horkawicz, Maria W. Górna
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2018.00864

Insight Into the Variation of Bacterial Structure in Atrazine-Contaminated Soil Regulating by Potential Phytoremediator: Pennisetum americanum (L.) K. Schum
Cited by: 28
Author(s): Bo Cao, Ying Zhang, Ziyi Wang, Mengyuan Li, Feng Yang, Dagang Jiang, Zhao Jiang
Software Mentions: 3
Published: over 6 years ago

10.3389/fnut.2020.553674

Circulating Branched Chain Amino Acid Concentrations Are Higher in Dairy-Avoiding Females Following an Equal Volume of Sheep Milk Relative to Cow Milk: A Randomized Controlled Trial
Cited by: 9
Author(s): Amber M. Milan, Linda M. Samuelsson, Aahana Shrestha, Pankaja Sharma, Linda Day, David Cameron‐Smith
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2019.02408

Reconstruction of the Functional Ecosystem in the High Light, Low Temperature Union Glacier Region, Antarctica
Cited by: 14
Author(s): Yang Li, Qian‐Qian Cha, Yan-Ru Dang, Xiu-Lan Chen, Min Wang, Andrew McMinn, Giannina Espina, Yuzhong Zhang, Jenny M. Blamey, Qi‐Long Qin
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2020.01139

Comparison of Meconium Microbiome in Dizygotic and Monozygotic Twins Born by Caesarean Section (CS)
Cited by: 8
Author(s): Jing Yang, Su Yao, Kun Cheng, Lili Xu, Lingling Hou, Yuan Wei, Huijun Feng, Xuejian Yu, Xin Zhang, Xiao-Mei Tong, Zailing Li, Yangyu Zhao
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2018.02611

Genetic Signatures of Dairy Lactobacillus casei Group
Cited by: 15
Author(s): Alessandra Fontana, C. Zacconi, L. Morelli
Software Mentions: 3
Published: about 6 years ago

10.3389/fnmol.2017.00283

RNA-Sequencing Analysis Reveals a Regulatory Role for Transcription Factor Fezf2 in the Mature Motor Cortex
Cited by: 6
Author(s): Alison J Clare, Hollie E. Wicky, Ruth M. Empson, Stephanie M. Hughes
Software Mentions: 3
Published: about 7 years ago

10.1186/s12859-018-2133-2

TIA: algorithms for development of identity-linked SNP islands for analysis by massively parallel DNA sequencing
Cited by: 1
Author(s): Michele Farris, Andrew R. Scott, Pamela A. Texter, Marta Bartlett, Patricia Coleman, David J. Masters
Software Mentions: 3
Published: over 6 years ago

10.3389/fnmol.2016.00062

Effects of Long-Term Environmental Enrichment on Anxiety, Memory, Hippocampal Plasticity and Overall Brain Gene Expression in C57BL6 Mice
Cited by: 71
Author(s): Melanie Hüttenrauch, Gabriela Salinas, Oliver Wirths
Software Mentions: 3
Published: over 8 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: almost 10 years ago

10.1186/s13024-018-0280-6

The Trem2 R47H Alzheimer’s risk variant impairs splicing and reduces Trem2 mRNA and protein in mice but not in humans
Cited by: 83
Author(s): Xianyuan Xiang, Thomas M. Piers, Benedikt Wefers, Kaichuan Zhu, Anna Mallach, Bettina Brunner, Gernot Kleinberger, Wilbur M. Song, Marco Colonna, Jochen Herms, Wolfgang Wurst, Jennifer M. Pocock, Christian Haass
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2180-8-109

Dictyostelium transcriptional responses to Pseudomonas aeruginosa: common and specific effects from PAO1 and PA14 strains
Cited by: 40
Author(s): Sergio Carilla-Latorre, Javier Calvo‐Garrido, Gareth Bloomfield, Jason Skelton, Robert R. Kay, Alasdair Ivens, José Luis Martínez, Ricardo Escalante
Software Mentions: 3
Published: over 16 years ago

10.1186/1471-2164-14-895

Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation
Cited by: 52
Author(s): Adam B. Olson, Heather Kent, Christopher D. Sibley, Margot E. Grinwis, Philip Mabon, Claude Ouellette, Shari Tyson, Morag Graham, Shaun Tyler, Gary Van Domselaar, Michael G. Surette, Cindi R. Corbett
Software Mentions: 3
Published: almost 11 years ago

10.3389/fmicb.2017.00785

Response of Methanogenic Microbial Communities to Desiccation Stress in Flooded and Rain-Fed Paddy Soil from Thailand
Cited by: 31
Author(s): Andreas Reim, Marcela Hernández, Melanie Klose, Amnat Chidthaisong, Monthira Yuttitham, Ralf Conrad
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2020.578600

A Curricular Bioinformatics Approach to Teaching Undergraduates to Analyze Metagenomic Datasets Using R
Cited by: 5
Author(s): Anne Kruchten
Software Mentions: 3
Published: about 4 years ago

10.3389/fmicb.2019.00910

Phylogenomic Rhizobium Species Are Structured by a Continuum of Diversity and Genomic Clusters
Cited by: 20
Author(s): Víctor González, Rosa I. Santamaría, Patricia Bustos, Olga María Pérez-Carrascal, Pablo Vinuesa, Soledad Juárez, Irma Martínez-Flores, Miguel A. Cevallos, Susana Brom, Esperanza Martínez‐Romero, David Romero
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0118201

A Combined Gene Signature of Hypoxia and Notch Pathway in Human Glioblastoma and Its Prognostic Relevance
Cited by: 45
Author(s): Khushboo Irshad, Saroj Kant Mohapatra, Chitrangda Srivastava, Harshit Garg, Seema Mishra, Bhawana Dikshit, Chitra Sarkar, Deepak Gupta, P. Sarat Chandra, Parthaprasad Chattopadhyay, Subrata Sinha, Kunzang Chosdol
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0217431

Comparison of bacterial community structure and potential functions in hypoxic and non-hypoxic zones of the Changjiang Estuary
Cited by: 27
Author(s): Dongmei Wu, Qiu-Ping Dai, Xuezhu Liu, Yingping Fan, Jianxin Wang
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-021-07655-6

Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines
Cited by: 9
Author(s): Virginia Mwape, Fredrick M. Mobegi, Roshan Regmi, Toby E. Newman, Lars G. Kamphuis, Mark Derbyshire
Software Mentions: 3
Published: over 3 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 7 years ago

10.1186/1471-2180-11-126

Protein expression dynamics during Escherichia Coli glucose-lactose diauxie
Cited by: 19
Author(s): Ekaterina Mostovenko, André M. Deelder, Magnus Palmblad
Software Mentions: 3
Published: almost 14 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 8 years ago

10.3389/fmicb.2020.555795

Environmental Parameters and Substrate Type Drive Microeukaryotic Community Structure During Short-Term Experimental Colonization in Subtropical Eutrophic Freshwaters
Cited by: 7
Author(s): Changyu Zhu, David Bass, Yutao Wang, Zhuo Shen, Weibo Song, Zhenzhen Yi
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0118424

Non-Viral Generation of Marmoset Monkey iPS Cells by a Six-Factor-in-One-Vector Approach
Cited by: 38
Author(s): Katharina Debowski, Rita Warthemann, Jana Lentes, Gabriela Salinas-Riester, Ralf Dressel, Daniel Langenstroth, Jörg Gromoll, Erika Sasaki, Rüdiger Behr
Software Mentions: 3
Published: over 9 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: about 4 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 7 years ago

10.3389/fmicb.2020.00737

Phenotypic and Genetic Characterization of the Cheese Ripening Yeast Geotrichum candidum
Cited by: 19
Author(s): Vincent Perkins, Stéphanie Vignola, Marie-Hélène Lessard, Pier-Luc Plante, Jacques Corbeil, Éric Dugat-Bony, Michel Frenette, Steve Labrie
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2020.01296

BALOs Improved Gut Microbiota Health in Postlarval Shrimp (Litopenaeus vannamei) After Being Subjected to Salinity Reduction Treatment
Cited by: 13
Author(s): Qingqing Cao, Farhana Najnine, Hongcao Han, Bing Wu, Jin Cai
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2018.01913

Broad Bean (Vicia faba L.) Induces Intestinal Inflammation in Grass Carp (Ctenopharyngodon idellus C. et V) by Increasing Relative Abundances of Intestinal Gram-Negative and Flagellated Bacteria
Cited by: 12
Author(s): Zhifei Li, Ermeng Yu, Guangjun Wang, Deguang Yu, Kai Zhang, Wangbao Gong, Jun Xie
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2014.00487

Aerobic methanotrophic communities at the Red Sea brine-seawater interface
Cited by: 28
Author(s): Rehab Z. Abdallah, Mustafa Adel, Amged Ouf, Ahmed A. Sayed, Mohamed A. Ghazy, Intikhab Álam, Magbubah Essack, Feras F. Lafi, Vladimir B. Bajic, Hamza A. El-Dorry, Rania Siam
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0131292

An Insight into the Sialome of the Lone Star Tick, Amblyomma americanum, with a Glimpse on Its Time Dependent Gene Expression
Cited by: 95
Author(s): Shahid Karim, José M. C. Ribeiro
Software Mentions: 3
Published: over 9 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: about 4 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: over 3 years ago

10.1038/s41598-020-66728-w

GlioM&M: Web-based tool for studying circulating and infiltrating monocytes and macrophages in glioma
Cited by: 9
Author(s): Erik R. Abels, Sybren L. N. Maas, Eric C. Tai, David T. Ting, Marike L. D. Broekman, Xandra O. Breakefield, Joseph El Khoury
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-65369-3

Measuring Cancer Hallmark Mediation of the TET1 Glioma Survival Effect with Linked Neural-Network Based Mediation Experiments
Cited by: 2
Author(s): Thomas Luechtefeld, Nole Lin, Channing J. Paller, Katherine J. Kuhns, John Laterra, Joseph Bressler
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-62776-4

Apoptosis characterization in mononuclear blood leukocytes of HIV patients during dengue acute disease
Cited by: 2
Author(s): Amanda Torrentes-Carvalho, Juan Camilo Sánchez‐Arcila, Tamiris Azamor, Luciana Santos Barbosa, Eugênio D. Hottz, Mariana Gandini, Fernando A. Bozza, Rivaldo Venâncio da Cunha, Luciana Wernersbach Pinto, Paulo Vieira Damasco, Elzinandes Leal de Azeredo
Software Mentions: 3
Published: over 4 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: over 6 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 11 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: about 6 years ago

10.1038/s41598-020-61688-7

Prognostic implications of EGFR protein expression in sporadic colorectal tumors: Correlation with copy number status, mRNA levels and miRNA regulation
Cited by: 15
Author(s): Sofía Del Carmen, Luis A. Corchete, Ruth Gervás, A Barrio Rodriguez, María José García, José A. Sánchez Alcázar, José María Sánchez García, Óscar Bengoechea, Luís Muñoz-Bellvis, José María Sayagués, Mónica Viñarás Abad
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2021.655903

Lead Drives Complex Dynamics of a Conjugative Plasmid in a Bacterial Community
Cited by: 3
Author(s): Valentine Cyriaque, Jonas Stenløkke Madsen, Laurence Fiévez, Baptiste Leroy, Lars Hansen, Fabrice Bureau, Søren J. Sørensen, Ruddy Wattiez
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0171078

Metabolite profiling of the carnivorous pitcher plants Darlingtonia and Sarracenia
Cited by: 16
Author(s): Hannu Hotti, Peddinti Gopalacharyulu, Tuulikki Seppänen‐Laakso, Heiko Rischer
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0110664

Soil Temperature Determines the Reaction of Olive Cultivars to Verticillium dahliae Pathotypes
Cited by: 29
Author(s): Rocío Calderón, Carlos Lucena, J. L. Trapero-Casas, Pablo J. Zarco‐Tejada, Juan A Navas‐Cortés
Software Mentions: 3
Published: about 10 years ago

10.1038/s41598-020-61420-5

Eosinophil accumulation in postnatal lung is specific to the primary septation phase of development
Cited by: 17
Author(s): Lucas F. Loffredo, Mackenzie E. Coden, Brian M. Jeong, Matthew T. Walker, Kishore R. Anekalla, Ton C. Doan, Raul I. Rodriguez, M.J. Browning, Ki-Won Nam, James J. Lee, Hiam Abdala‐Valencia, Sergejs Berdnikovs
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0130198

Chronic Insulin Exposure Induces ER Stress and Lipid Body Accumulation in Mast Cells at the Expense of Their Secretory Degranulation Response
Cited by: 10
Author(s): William E. Greineisen, Kristina Maaetoft-Udsen, Mark Speck, Januaria M. Balajadia, Lori M. N. Shimoda, Carl Sung, Helen Turner
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2019.02687

Effect of Diet on the Enteric Microbiome of the Wood-Eating Catfish Panaque nigrolineatus
Cited by: 9
Author(s): Ryan McDonald, Joy E. M. Watts, Harold J. Schreier
Software Mentions: 3
Published: almost 5 years ago

10.3389/fmicb.2017.00238

Fungal ITS1 Deep-Sequencing Strategies to Reconstruct the Composition of a 26-Species Community and Evaluation of the Gut Mycobiota of Healthy Japanese Individuals
Cited by: 55
Author(s): Daisuke Motooka, Kosuke Fujimoto, Reiko Tanaka, Takashi Yaguchi, Kazuyoshi Gotoh, Yukihide Maeda, Yoshikazu Furuta, Takashi Kurakawa, Naohisa Goto, Teruo Yasunaga, Masashi Narazaki, Atsushi Kumanogoh, Toshihiro Horii, Tetsuya Iida, Kiyoshi Takeda, Shota Nakamura
Software Mentions: 3
Published: almost 8 years ago

10.3389/fmicb.2020.586050

The Aromatic Plant Clary Sage Shaped Bacterial Communities in the Roots and in the Trace Element-Contaminated Soil More Than Mycorrhizal Inoculation – A Two-Year Monitoring Field Trial
Cited by: 13
Author(s): Robin Raveau, Joël Fontaine, Mohamed Hijri, Anissa Lounès-Hadj Sahraoui
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2018.02512

Microbial Community Dynamics in Mother’s Milk and Infant’s Mouth and Gut in Moderately Preterm Infants
Cited by: 51
Author(s): Elena Biagi, Arianna Aceti, Sara Quercia, Isadora Beghetti, Simone Rampelli, Silvia Turroni, Matteo Soverini, Angelo Vittorio Zambrini, Giacomo Faldella, Marco Candela, Luigi Corvaglia, Patrizia Brigidi
Software Mentions: 3
Published: about 6 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: almost 17 years ago

10.3389/fmicb.2015.00569

RNA-Seq analysis of isolate- and growth phase-specific differences in the global transcriptomes of enteropathogenic Escherichia coli prototype isolates
Cited by: 27
Author(s): Tracy H. Hazen, Sean C. Daugherty, Amol C. Shetty, Anup Mahurkar, Owen White, James B. Kaper, David A. Rasko
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0213823

Natural and human-impacted diversity of bryophytes along an elevational gradient on an oceanic island (La Palma, Canarias)
Cited by: 4
Author(s): Raquel Hernández‐Hernández, Jürgen Kluge, Claudine Ah‐Peng, Juana María González‐Mancebo
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-59988-z

A salivary metabolite signature that reflects gingival host-microbe interactions: instability predicts gingivitis susceptibility
Cited by: 0
Author(s): Marcela M. Fernandez-Gutierrez, Sultan Imangaliyev, Andrei Prodan, Bruno G. Loos, Bart J. F. Keijser, Michiel Kleerebezem
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12859-017-1575-2

ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface
Cited by: 16
Author(s): Anke Fähnrich, Moritz Krebbel, Normann Decker, Martin Leucker, Felix D. Lange, Kathrin Kalies, Steffen Möller
Software Mentions: 3
Published: over 7 years ago

10.1155/2014/857245

Intestinal Parasites Coinfection Does Not Alter Plasma Cytokines Profile Elicited in Acute Malaria in Subjects from Endemic Area of Brazil
Cited by: 13
Author(s): Juan Camilo Sánchez‐Arcila, Daiana de Souza Perce-da-Silva, Mariana Pinheiro Alves Vasconcelos, Rodrigo Nunes Rodrigues-da-Silva, Virgínia Araújo Pereira, Cesarino Junior Lima Aprígio, Cleoni Alves Mendes de Lima, Bruna de Paula Fonseca e Fonseca, Dalma Maria Banic, Josué da Costa Lima-Junior, Joseli Oliveira-Ferreira
Software Mentions: 3
Published: almost 11 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 6 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 5 years ago

10.1371/journal.pone.0119741

Multivariate and Phylogenetic Analyses Assessing the Response of Bacterial Mat Communities from an Ancient Oligotrophic Aquatic Ecosystem to Different Scenarios of Long-Term Environmental Disturbance
Cited by: 12
Author(s): Silvia Pajares, Valeria Souza, Luis E. Eguiarte
Software Mentions: 3
Published: over 9 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: about 4 years ago

10.1371/journal.pone.0200818

Heterogeneity of circulating CD8 T-cells specific to islet, neo-antigen and virus in patients with type 1 diabetes mellitus
Cited by: 26
Author(s): Sandra Laban, Jessica S. Suwandi, Vincent van Unen, J. Pool, Joris Wesselius, Thomas Höllt, Nicola Pezzotti, Anna Vilanova, Boudewijn P. F. Lelieveldt, Bart O. Roep
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0210542

Endophytic bacterial communities in peels and pulp of five root vegetables
Cited by: 20
Author(s): Viia Kõiv, Krõõt Arbo, Ülo Maiväli, Veljo Kisand, Märt Roosaare, Maido Remm, Tanel Tenson
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0135494

Characterization of the Intestinal Lactobacilli Community following Galactooligosaccharides and Polydextrose Supplementation in the Neonatal Piglet
Cited by: 19
Author(s): Jennifer L. Hoeflinger, Dimitri Kashtanov, Stephen B. Cox, Scot E. Dowd, Zeina E. Jouni, Sharon M. Donovan, Michael J. Miller
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-019-51673-0

Comparative analysis of obesity-related cardiometabolic and renal biomarkers in human plasma and serum
Cited by: 15
Author(s): Meenu Rohini Rajan, Matúš Soták, Fredrik Barrenäs, Tong Shen, Kamil Borkowski, Nicholas J. Ashton, Christina Biörserud, Tomas Lindahl, Sofia Ramström, Michael Schöll, Per Lindahl, Oliver Fiehn, John W. Newman, Rosie Perkins, Ville Wallenius, Stephan Lange, Emma Börgeson
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-50272-3

Patterns of Anatomic Injury in Critically Injured Combat Casualties: A Network Analysis
Cited by: 20
Author(s): Jud C. Janak, Edward L. Mazuchowski, Russ S Kotwal, Zsolt T. Stockinger, Jeffrey T. Howard, Frank K. Butler, Jonathan A. Sosnov, Jennifer M Gurney, Stacy Shackelford
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0174514

Oxygen tension regulates the miRNA profile and bioactivity of exosomes released from extravillous trophoblast cells – Liquid biopsies for monitoring complications of pregnancy
Cited by: 89
Author(s): Grace Truong, Dominic Guanzon, Vyjayanthi Kinhal, Omar Elfeky, Andrew Lai, Sherri Longo, Zarin Nuzhat, Carlos Palma, Katherin Scholz-Romero, Ramkumar Menon, Ben Willem J. Mol, Gregory E. Rice, Carlos Salomón
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0124599

Sex, Body Mass Index, and Dietary Fiber Intake Influence the Human Gut Microbiome
Cited by: 303
Author(s): Christine Dominianni, Rashmi Sinha, James J. Goedert, Zhiheng Pei, Liying Yang, Richard B. Hayes, Jiyoung Ahn
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 7 years ago

10.1002/1878-0261.12753

Identification of BLNK and BTK as mediators of rituximab‐induced programmed cell death by CRISPR screens in GCB‐subtype diffuse large B‐cell lymphoma
Cited by: 15
Author(s): Emil Aagaard Thomsen, Anne Bruun Rovsing, Mads Valdemar Anderson, Hanne Due, Jinrong Huang, Yonglun Luo, Karen Dybkær, Jacob Giehm Mikkelsen
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0161967

CYR61 and TAZ Upregulation and Focal Epithelial to Mesenchymal Transition May Be Early Predictors of Barrett’s Esophagus Malignant Progression
Cited by: 6
Author(s): Joana Cardoso, Marta Mesquita, António Dias Pereira, Mónica Bettencourt-Dias, Paula Chaves, José B. Pereira-Leal
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-019-50227-8

Proinflammatory profile of neonatal monocytes induced by microbial ligands is downmodulated by histamine
Cited by: 4
Author(s): Anna Cláudia Calvielli Castelo Branco, Newton Lindolfo Pereira, Fábio Seiti Yamada Yoshikawa, Luanda Mara da Silva Oliveira, Franciane Mouradian Emidio Teixeira, Lucas Ferrari de Oliveira, Anna Julia Pietrobon, Marina Passos Torrealba, Jozely Francisca Mello Lima, Alberto José da Silva Duarte, Maria Notomi Sato
Software Mentions: 3
Published: about 5 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: about 4 years ago

10.1038/s41598-019-49421-5

Staphylococcal enterotoxins modulate the effector CD4+ T cell response by reshaping the gene expression profile in adults with atopic dermatitis
Cited by: 11
Author(s): Raquel Leão Orfali, Fábio Seiti Yamada Yoshikawa, Luanda Mara da Silva Oliveira, Newton Lindolfo Pereira, Jozely Francisca Mello Lima, Yasmim Álefe Leuzzi Ramos, Alberto José da Silva Duarte, Maria Notomi Sato, Valéria Aoki
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-49031-1

Novel computational model of gastrula morphogenesis to identify spatial discriminator genes by self-organizing map (SOM) clustering
Cited by: 10
Author(s): Takahide Mori, Haruka Takaoka, Junko Yamane, Cantas Alev, Wataru Fujibuchi
Software Mentions: 3
Published: about 5 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: almost 6 years ago

10.1371/journal.pone.0233896

Phenotypic responses of foxtail millet (Setaria italica) genotypes to phosphate supply under greenhouse and natural field conditions
Cited by: 12
Author(s): S. Antony Ceasar, Muthusamy Ramakrishnan, K. K. Vinod, G. Victor Roch, Hari D. Upadhyaya, Alison Baker, S. Ignacimuthu
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0228550

Phenotypic diversity of Methylobacterium associated with rice landraces in North-East India
Cited by: 5
Author(s): Pratibha Sanjenbam, Radhika Buddidathi, Radhika Venkatesan, P. V. Shivaprasad, Deepa Agashe
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-47757-6

The Genomic Landscape of Centromeres in Cancers
Cited by: 17
Author(s): Anjan K. Saha, Mohamad Mourad, Mark H. Kaplan, Ilana Chefetz, Sami N. Malek, Ronald J. Buckanovich, David M. Markovitz, Rafael Contreras-Galindo
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-45764-1

Varroa destructor parasitism has a greater effect on proteome changes than the deformed wing virus and activates TGF-β signaling pathways
Cited by: 20
Author(s): Tomáš Erban, B. Sopko, Klara Kadlikova, Pavel Talacko, Karel Harant
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0146125

Caste-Specific and Sex-Specific Expression of Chemoreceptor Genes in a Termite
Cited by: 35
Author(s): Yuki Mitaka, Keiko Kobayashi, Alexander S. Mikheyev, Mandy M. Y. Tin, Yutaka Watanabe, Kenji Matsuura
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 5 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: about 6 years ago

10.18632/aging.101102

Molecular pathway activation features of pediatric acute myeloid leukemia (AML) and acute lymphoblast leukemia (ALL) cells
Cited by: 15
Author(s): Ivan Petrov, Maria Suntsova, Olga Mutorova, Maxim Sorokin, Andrew Garazha, Elena Tarasovna Ilnitskaya, Pavel Spirin, Sergey Larin, Olga Kovalchuk, Vladimir Prassolov, Alex Zhavoronkov, Alexander Roumiantsev, Anton Buzdin
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0169805

Novel Analysis of Immune Cells from Nasal Microbiopsy Demonstrates Reliable, Reproducible Data for Immune Populations, and Superior Cytokine Detection Compared to Nasal Wash
Cited by: 47
Author(s): Simon P. Jochems, Katherine Piddock, Jamie Rylance, Hugh Adler, Beatriz F. Carniel, Andrea Collins, Jenna F. Gritzfeld, Carole A. Hancock, Helen Hill, Jesús Reiné, Alexandra L. Seddon, Carla Solórzano, Syba Sunny, A Zachary Trimble, A. Wright, Seher Zaidi, Stephen B. Gordon, Daniela M. Ferreira
Software Mentions: 3
Published: almost 8 years ago

10.26508/lsa.201800205

Innate extracellular vesicles from melanoma patients suppress β-catenin in tumor cells by miRNA-34a
Cited by: 22
Author(s): Jung-Hyun Lee, Jochen Dindorf, Martin Eberhardt, Xin Lai, Christian Ostalecki, Nina Koliha, Stefani Gross, Katja Blume, Heiko Bruns, Stefan Wild, Gerold Schuler, Julio Vera, Andreas S. Baur
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-42691-z

Ancestral Stress Alters Lifetime Mental Health Trajectories and Cortical Neuromorphology via Epigenetic Regulation
Cited by: 20
Author(s): Mirela Ambeskovic, Olena Mykolaivna Babenko, Yaroslav Ilnytskyy, Igor Kovalchuk, Bryan Kolb, Gerlinde A. S. Metz
Software Mentions: 3
Published: over 5 years ago

10.1099/mgen.0.000154

Comparative transcriptomics of Aspergillus fumigatus strains upon exposure to human airway epithelial cells
Cited by: 16
Author(s): Tonya Watkins, Hong Liu, Matthew Chung, Tracy H. Hazen, Julie C. Dunning Hotopp, Scott G. Filler, Vincent M. Bruno
Software Mentions: 3
Published: almost 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: over 3 years ago

10.18632/oncotarget.24598

Tracking cellular and molecular changes in a species-specific manner during experimental tumor progression <i>in vivo</i>
Cited by: 9
Author(s): Émilie Indersie, Katarzyna B. Hooks, Caroline Capdevielle, Monique Fabrè, Nathalie Dugot‐Senant, Angélique Desplat, Sébastien Lepreux, Aksam Merched, Christophe Grosset, Martin Hagedorn
Software Mentions: 3
Published: over 6 years ago

10.1186/s12885-019-5403-0

Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers
Cited by: 80
Author(s): Bernardo P. de Almeida, Joana Apolónio, Alexandra Binnie, Pedro Castelo‐Branco
Software Mentions: 3
Published: over 5 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: almost 9 years ago

10.1186/s12985-014-0236-6

Differential regulation of cytotoxicity pathway discriminating between HIV, HCV mono- and co-infection identified by transcriptome profiling of PBMCs
Cited by: 4
Author(s): Jing Qin Wu, Monica Miranda Saksena, Vincent Soriano, Eugenia Vispo, Nitin K. Saksena
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0148771

Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis
Cited by: 41
Author(s): Venkata Suresh Bonthala, Katie Mayes, Joanna Moreton, Martin Blythe, Victoria Wright, Sean May, Festo Massawe, Sean Mayes, Jamie Twycross
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0149998

Analysis of Lung Microbiota in Bronchoalveolar Lavage, Protected Brush and Sputum Samples from Subjects with Mild-To-Moderate Cystic Fibrosis Lung Disease
Cited by: 106
Author(s): Deborah A. Hogan, Sven D. Willger, Emily L. Dolben, Thomas H. Hampton, Bruce A. Stanton, Hilary G. Morrison, Mitchell L. Sogin, Julianna M. Czum, Alix Ashare
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0162807

Genetic Determinism of Sensitivity to Corynespora cassiicola Exudates in Rubber Tree (Hevea brasiliensis)
Cited by: 16
Author(s): Dinh Minh Tran, André Clément-Demange, Marine Déon, Dominique García, Vincent Le Guen, Anne Clément‐Vidal, Mouman Soumahoro, Aurélien Masson, Philippe Label, Mau Tuy Le, Valérie Pujade-Renaud
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-36561-3

Uncovering secondary metabolite evolution and biosynthesis using gene cluster networks and genetic dereplication
Cited by: 30
Author(s): Sebastian Theobald, Tammi Camilla Vesth, Jakob Kræmmer Haar Rendsvig, Kristian Fog Nielsen, Robert Riley, Lucas M. Abreu, Asaf Salamov, Jens Christian Frisvad, Thomas Ostenfeld Larsen, Mikael Rørdam Andersen, Jakob Blæsbjerg Hoof
Software Mentions: 3
Published: almost 6 years ago

Projects: cran: gplots

Papers Mentioning gplots 2,122