cran: gplots | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0173106

Stabilization of HIF-1α and HIF-2α, up-regulation of MYCC and accumulation of stabilized p53 constitute hallmarks of CNS-PNET animal model
Cited by: 3
Author(s): Sergey Malchenko, Simone Treiger Sredni, Yingtao Bi, Naira V. Margaryan, Jerusha Boyineni, Indra Mohanam, Tadanori Tomita, Ramana V. Davuluri, Marcelo B. Soares
Software Mentions: 3
Published: over 7 years ago

10.1264/jsme2.ME19077

Distribution of SNSs in Mimivirus Genomes and the Classification of Mimiviruses Isolated from Japan
Cited by: 1
Author(s): Motohiro Akashi, Masaharu Takemura
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-019-5460-4

RNA-sequencing analysis of shell gland shows differences in gene expression profile at two time-points of eggshell formation in laying chickens
Cited by: 22
Author(s): Samiullah Khan, Shu‐Biao Wu, Juliet R. Roberts
Software Mentions: 3
Published: almost 6 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

10.1002/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

10.1099/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

10.1186/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

10.1186/s12870-015-0555-9

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

10.1371/journal.pone.0065793

Plasmidome-Analysis of ESBL-Producing Escherichia coli Using Conventional Typing and High-Throughput Sequencing
Cited by: 41
Author(s): Alma Brolund, Oscar Franzén, Öjar Melefors, Karin Tegmark-Wisell, Linus Sandegren
Software Mentions: 3
Published: over 11 years ago

10.1002/mbo3.494

wblE2 transcription factor in Streptomyces griseus S4‐7 plays an important role in plant protection
Cited by: 7
Author(s): Hyun Ji Cho, Young Chul Kwon, Da-Ran Kim, Gyeongjun Cho, Seong Won Hong, Dong-Won Bae, Youn‐Sig Kwak
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

10.1016/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 5 years ago

10.18632/aging.202997

Identification of potential autophagy-associated lncRNA in prostate cancer
Cited by: 6
Author(s): Jun Li, Hong Du, Wenqiang Chen, Mingxing Qiu, Peng He, Zhiwei Ma
Software Mentions: 3
Published: over 3 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/s13148-020-00895-5

H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts
Cited by: 17
Author(s): Jiayi Pei, Magdaléna Harakaľová, Thomas A. Treibel, R Thomas Lumbers, Bastiaan J. Boukens, Igor R. Efimov, Jip T. van Dinter, Arantxa González, Begoña López, Hamid el Azzouzi, Noortje van den Dungen, Christian G.M. van Dijk, Merle M. Krebber, Hester M. den Ruijter, Gérard Pasterkamp, Dirk J. Duncker, Edward E. S. Nieuwenhuis, Roel de Weger, Manon M. H. Huibers, Aryan Vink, Jason H. Moore, James Moon, Marianne C. Verhaar, Georgios Kararigas, Michal Mokrý, Folkert W. Asselbergs, Caroline Cheng
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0164964

Morphological and Molecular Characterization of Human Dermal Lymphatic Collectors
Cited by: 22
Author(s): Viktoria Hasselhof, Anastasia Sperling, Kerstin Buttler, Philipp Ströbel, Jürgen Becker, Tin Aung, Gunther Felmerer, Jörg Wilting
Software Mentions: 3
Published: about 8 years ago

10.1186/s40168-020-0791-6

It's the fiber, not the fat: significant effects of dietary challenge on the gut microbiome
Cited by: 70
Author(s): Kathleen E. Morrison, Eldin Jašarević, Christopher D. Howard, Tracy L. Bale
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0228982

Cloacal bacterial communities of tree swallows (Tachycineta bicolor): Similarity within a population, but not between pair-bonded social partners
Cited by: 8
Author(s): Jessica Hernandez, Camilo Escallón, Daniel Medina, Ben J. Vernasco, Jenifer B. Walke, Lisa K. Belden
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0135627

Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering
Cited by: 11
Author(s): Alica Chroňáková, Brigitte Schloter-Hai, Viviane Radl, David Endesfelder, Christopher Quince, Dana Elhottová, Miloslav Šimek, Michael Schloter
Software Mentions: 3
Published: over 9 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

10.1186/s40168-016-0199-5

The structure and diversity of human, animal and environmental resistomes
Cited by: 310
Author(s): Chandan Pal, Johan Bengtsson‐Palme, Erik Kristiansson, D. G. Joakim Larsson
Software Mentions: 3
Published: about 8 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

10.1186/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

10.3389/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

10.1186/s12864-018-5207-7

Altered expression of K13 disrupts DNA replication and repair in Plasmodium falciparum
Cited by: 30
Author(s): Justin Gibbons, Katrina A. Button-Simons, Swamy Rakesh Adapa, Suzanne Li, Maxwell Pietsch, Min Zhang, Xiangyun Liao, John Adams, Michael T. Ferdig, Rays H. Y. Jiang
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12870-021-02919-5

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

10.3389/fmicb.2018.02836

Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System
Cited by: 45
Author(s): Jennifer Bachmann, Tabea Heimbach, Christiane Hassenrück, Gérmán A. Kopprio, Morten Hvitfeldt Iversen, Hans Peter Grossart, Astrid Gärdes
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0066086

Distinct MicroRNAs Expression Profile in Primary Biliary Cirrhosis and Evaluation of miR 505-3p and miR197-3p as Novel Biomarkers
Cited by: 81
Author(s): Masashi Ninomiya, Yasuteru Kondo, Ryo Funayama, Takeshi Nagashima, Takayuki Kogure, Eiji Kakazu, Osamu Kimura, Yoshiyuki Ueno, Keiko Nakayama, Tooru Shimosegawa
Software Mentions: 3
Published: over 11 years ago

10.1186/s12864-016-2906-9

An integrative genomics approach for identifying novel functional consequences of PBRM1 truncated mutations in clear cell renal cell carcinoma (ccRCC)
Cited by: 18
Author(s): Yuanyuan Wang, Xingyi Guo, Michael J. Bray, Zhiyong Ding, Zhongming Zhao
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pcbi.1004553

Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response
Cited by: 18
Author(s): Robin van der Lee, Feng Qian, Martijn A. Langereis, Rob ter Horst, Radek Szklarczyk, Mihai G. Netea, Arno C. Andeweg, Frank J. M. van Kuppeveld, Martijn A. Huynen
Software Mentions: 3
Published: about 9 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

10.18632/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

10.1186/1471-2164-14-851

Analysis of banana transcriptome and global gene expression profiles in banana roots in response to infection by race 1 and tropical race 4 of Fusarium oxysporum f. sp. cubense
Cited by: 100
Author(s): Chunqiang Li, Jiaofang Shao, Yejun Wang, Wenbin Li, Dianjing Guo, Bin Yan, Yiji Xia, Ming Peng
Software Mentions: 3
Published: almost 11 years ago

10.18632/aging.101578

High expression of the breast cancer susceptibility gene BRCA1 in long-lived termite kings
Cited by: 9
Author(s): Eisuke Tasaki, Yuki Mitaka, Tomonari Nozaki, Keiko Kobayashi, Kenji Matsuura, Yoshihito Iuchi
Software Mentions: 3
Published: about 6 years ago

10.1007/s10456-021-09777-7

SMAD6 transduces endothelial cell flow responses required for blood vessel homeostasis
Cited by: 18
Author(s): Dana L. Ruter, Ziqing Liu, Kimlynn M. Ngo, X Shaka, Allison Marvin, Danielle B Buglak, Elise Kidder, Victoria L. Bautch
Software Mentions: 3
Published: over 3 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/s13195-020-00641-2

Diverse proteins aggregate in mild cognitive impairment and Alzheimer’s disease brain
Cited by: 20
Author(s): Devin Kepchia, Ling Huang, Richard Dargusch, Robert A. Rissman, Maxim N. Shokhirev, Wolfgang Fischer, David Schubert
Software Mentions: 3
Published: over 4 years ago

10.3390/microorganisms8081196

Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci
Cited by: 13
Author(s): Bruno Cavadas, Rui Camacho, Joana Ferreira, Rui M. Ferreira, Céu Figueiredo, Alvis Brāzma, Nuno A. Fonseca, Luı́sa Pereira
Software Mentions: 3
Published: over 4 years ago

10.3390/cells9051149

Large-Scale Profiling of Signaling Pathways Reveals a Distinct Demarcation between Normal and Extended Liver Resection
Cited by: 3
Author(s): Pieter Borger, Anton Buzdin, Maksim Sorokin, Ekaterina Kachaylo, Bostjan Humar, Rolf Graf, Pierre-Alien Clavien
Software Mentions: 3
Published: over 4 years ago

10.3390/cancers11101410

An IKK/NF-κB Activation/p53 Deletion Sequence Drives Liver Carcinogenesis and Tumor Differentiation
Cited by: 3
Author(s): Michael Svinarenko, Sarah‐Fee Katz, Umesh Tharehalli, Medhanie Mulaw, Harald J. Maier, Yoshiaki Sunami, Sarah Fischer, Yuexin Chen, Sabine Heurich, Lena Erkert, Andrea Tannapfel, Thomas Wirth, Reinhold Schirmbeck, Thomas Seufferlein, André Lechel
Software Mentions: 3
Published: about 5 years ago

10.1242/bio.014308

Genome-wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells
Cited by: 40
Author(s): Catriona Manville, Kayleigh A. Smith, Zbysław Sońdka, Holly Ashlene Rance, Simon Cockell, Ian G. Cowell, Ka Cheong Lee, Nicholas J. Morris, Kay Padget, Graham Jackson, Caroline A. Austin
Software Mentions: 3
Published: about 9 years ago

10.1186/s12864-021-07426-3

Transcriptome analysis of the transdifferentiation of canine BMSCs into insulin producing cells
Cited by: 2
Author(s): Jinglu Wang, Pengxiu Dai, Tong Zou, Yangou Lv, Wen Zhao, Xinke Zhang, Yihua Zhang
Software Mentions: 3
Published: over 3 years ago

10.1186/s12870-020-02384-6

Identification of polycomb repressive complex 1 and 2 core components in hexaploid bread wheat
Cited by: 13
Author(s): Beáta Strejčková, Radim Čegan, Aleš Pečinka, Zbyněk Milec, Jan Šafář
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pcbi.1003189

A Self-Directed Method for Cell-Type Identification and Separation of Gene Expression Microarrays
Cited by: 30
Author(s): Neta S. Zuckerman, Yair Noam, Andrea Goldsmith, Peter P. Lee
Software Mentions: 3
Published: over 11 years ago

10.3390/microorganisms8010007

Comparative Pangenomics of the Mammalian Gut Commensal Bifidobacterium longum
Cited by: 20
Author(s): Korin Albert, Asha Rani, David A. Sela
Software Mentions: 3
Published: almost 5 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

10.3390/cancers11081157

A Novel Type of Blood Biomarker: Distinct Changes of Cytokine-Induced STAT Phosphorylation in Blood T Cells Between Colorectal Cancer Patients and Healthy Individuals
Cited by: 14
Author(s): Jae Won Yun, Sejoon Lee, Hye Mi Kim, Sejong Chun, Edgar G. Engleman, Hee Cheol Kim, Eun Suk Kang
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-018-4510-7

Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster
Cited by: 30
Author(s): Michael P. Meers, Karen Adelman, Robert J. Duronio, Brian D. Strahl, Daniel J. McKay, A. Gregory Matera
Software Mentions: 3
Published: almost 7 years ago

10.3390/microorganisms9061117

Reassessment of the Columnea latent viroid (CLVd) Taxonomic Classification
Cited by: 1
Author(s): Parichate Tangkanchanapas, Annelies Haegeman, Monica Höfte, Kris De Jonghe
Software Mentions: 3
Published: over 3 years ago

10.3390/cancers13102499

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

10.3390/cancers13030550

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

10.1186/s12864-017-3663-0

Transcriptome analysis of the two unrelated fungal β-lactam producers Acremonium chrysogenum and Penicillium chrysogenum: Velvet-regulated genes are major targets during conventional strain improvement programs
Cited by: 22
Author(s): Dominik Terfehr, Tim A. Dahlmann, Ulrich Kück
Software Mentions: 3
Published: over 7 years ago

10.1186/s12870-018-1373-7

Comparative root transcriptome of wild Arachis reveals NBS-LRR genes related to nematode resistance
Cited by: 24
Author(s): Ana Paula Zotta Mota, Bruna Vidigal, Étienne Danchin, Roberto Coiti Togawa, Soraya C. M. Leal‐Bertioli, David J. Bertioli, Ana Cláudia Guerra Araújo, Ana Cristina Miranda Brasileiro, P. M. Guimarães
Software Mentions: 3
Published: over 6 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: almost 7 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

10.3390/cancers13020298

Soluble and Exosome-Bound α-Galactosylceramide Mediate Preferential Proliferation of Educated NK Cells with Increased Anti-Tumor Capacity
Cited by: 3
Author(s): Arnika K. Wagner, Ulf Gehrmann, Stefanie Hiltbrunner, Valentina Carannante, Thuy T. Luu, Tanja I. Näslund, Hanna Brauner, Nadir Kadri, Klas Kärre, Susanne Gabrielsson
Software Mentions: 3
Published: almost 4 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: almost 7 years ago

10.1007/s00253-019-09701-6

Uncovering carbohydrate metabolism through a genotype-phenotype association study of 56 lactic acid bacteria genomes
Cited by: 52
Author(s): G. Buron-Moles, Anna Chailyan, Igor Dolejš, Jochen Förster, Marta Hanna Mikš
Software Mentions: 3
Published: over 5 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: over 7 years ago

10.18632/aging.101871

Anesthesia and surgery induce cognitive dysfunction in elderly male mice: the role of gut microbiota
Cited by: 46
Author(s): Gaofeng Zhan, Hua Duan, Niannian Huang, Yue Wang, Shan Li, Zhiqiang Zhou, Ning Yang, Ruiwei Jiang, Bin Zhu, Ling Yang, Yu Fan, Hui Xu, Chun Yang, Ailin Luo
Software Mentions: 3
Published: over 5 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 7 years ago

10.1186/1471-2164-14-540

Solanum torvum responses to the root-knot nematode Meloidogyne incognita
Cited by: 38
Author(s): Paolo Bagnaresi, T. Sala, Tiziana Irdani, Cristina Scotto, Antonella Lamontanara, Massimiliano Beretta, Giuseppe Leonardo Rotino, S. Sestili, Luigi Cattivelli, E. Sabatini
Software Mentions: 3
Published: over 11 years ago

10.3389/fmicb.2018.01635

New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes
Cited by: 49
Author(s): Marie E. Kroeger, Tom O. Delmont, A. Murat Eren, Kyle Meyer, Jiarong Guo, Kiran Yasmin Khan, Jorge L. Mazza Rodrigues, Brendan J. M. Bohannan, Susannah G. Tringe, Clóvis Daniel Borges, James M. Tiedje, Siu Mui Tsai, Klaus Nüsslein
Software Mentions: 3
Published: over 6 years ago

10.1186/s12964-019-0332-8

Low levels of pyruvate induced by a positive feedback loop protects cholangiocarcinoma cells from apoptosis
Cited by: 12
Author(s): Mingming Zhang, Yida Pan, Dehua Tang, Robert Dorfman, Lei Xu, Qian Zhou, Lixing Zhou, Yuming Wang, Li Yang, Yuyao Yin, Bo Kong, Helmut Frieß, Shimin Zhao, Jian‐Lin Wu, Lei Wang, Xiaoping Zou
Software Mentions: 3
Published: over 5 years ago

10.18632/aging.203451

Intravascular emboli relates to immunosuppressive tumor microenvironment and predicts prognosis in stage III colorectal cancer
Cited by: 1
Author(s): Xiangping Song, Di Xie, Fengbo Tan, Yuan Zhou, Yuqiang Li, Zhongyi Zhou, Qian Pei, Haiping Pei
Software Mentions: 3
Published: about 3 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: about 11 years ago

10.3389/fimmu.2021.698900

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

10.1002/mbo3.312

Evaluation of <scp>DNA</scp> extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions
Cited by: 52
Author(s): Katharina Burbach, Jana Seifert, Dietmar H. Pieper, Amélia Camarinha‐Silva
Software Mentions: 3
Published: about 9 years ago

10.1186/s12864-018-5241-5

The impact of genome evolution on the allotetraploid Nicotiana rustica – an intriguing story of enhanced alkaloid production
Cited by: 22
Author(s): Nicolas Sierro, James N. D. Battey, Lucien Bovet, Verena Liedschulte, Sonia Ouadi, JH Thomas, Hervé Broye, Hélène Laparra, Aline Vuarnoz, Gerhard K. Lang, Simon Goepfert, Manuel C. Peitsch, Nikolai V. Ivanov
Software Mentions: 3
Published: almost 6 years ago

10.1111/tpj.14417

Poplar carbohydrate‐active enzymes: whole‐genome annotation and functional analyses based on <scp>RNA</scp> expression data
Cited by: 29
Author(s): Vikash Kumar, Matthieu Hainaut, Nicolas Delhomme, Chanaka Mannapperuma, Peter Immerzeel, Nathaniel R. Street, Bernard Henrissat, Ewa J. Mellerowicz
Software Mentions: 3
Published: over 5 years ago

10.1186/s13071-020-04035-z

Dafachronic acid and temperature regulate canonical dauer pathways during Nippostrongylus brasiliensis infectious larvae activation
Cited by: 10
Author(s): Katherine Omueti Ayoade, Faith R. Carranza, Woong Hee Cho, Zhu Wang, Steven A. Kliewer, David J. Mangelsdorf, Jonathan D. C. Stoltzfus
Software Mentions: 3
Published: over 4 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 6 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: about 7 years ago

10.18632/aging.102736

Anesthesia and surgery induce age-dependent changes in behaviors and microbiota
Cited by: 46
Author(s): Ning Liufu, Ling Liu, Shiqian Shen, Zengliang Jiang, Yuanlin Dong, Yanyan Wang, Deborah J. Culley, Gregory Crosby, Minghui Cao, Yuan Shen, Edward R. Marcantonio, Zhongcong Xie, Yiying Zhang
Software Mentions: 3
Published: almost 5 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: about 7 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

10.1038/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 5 years ago

10.3389/fmicb.2020.615661

A Model System for Feralizing Laboratory Mice in Large Farmyard-Like Pens
Cited by: 10
Author(s): Henriette Arnesen, Linn Emilie Knutsen, Bente Wabakken Hognestad, G. Johansen, Mats Bemark, Oliver Pabst, Anne K. Storset, Preben Boysen
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2015.01537

Microbial Community Structure in the Rhizosphere of Rice Plants
Cited by: 118
Author(s): Björn Breidenbach, Judith Pump, Marc G. Dumont
Software Mentions: 3
Published: almost 9 years ago

10.1007/s00784-021-03860-5

Gingival phenotype assessment methods and classifications revisited: a preclinical study
Cited by: 7
Author(s): Kai R. Fischer, Jasmin Büchel, Tiziano Testori, Giulio Rasperini, Thomas Attin, Patrick R. Schmidlin
Software Mentions: 3
Published: over 3 years ago

10.1186/s12862-019-1522-0

RADseq population genomics confirms divergence across closely related species in blue coral (Heliopora coerulea)
Cited by: 11
Author(s): Akira Iguchi, Yuki Yoshioka, Zac H. Forsman, Ingrid S. Knapp, Robert J. Toonen, Yuki Hongo, Satoshi Nagai, Nina Yasuda
Software Mentions: 3
Published: about 5 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 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: over 3 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: over 6 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

10.1155/2020/8831331

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 4 years ago

10.1074/jbc.M114.634816

Early Growth Response Genes 2 and 3 Regulate the Expression of Bcl6 and Differentiation of T Follicular Helper Cells
Cited by: 26
Author(s): Ane Ogbe, Tizong Miao, Alistair L. J. Symonds, Becky Omodho, Randeep Singh, Punamdip Bhullar, Suling Li, Ping Wang
Software Mentions: 3
Published: over 9 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 6 years ago

10.1016/j.jbc.2021.100285

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

10.1002/jcsm.12099

Expression of protocadherin gamma in skeletal muscle tissue is associated with age and muscle weakness
Cited by: 48
Author(s): Roland W. J. Hangelbroek, Parastoo Fazelzadeh, Michael Tieland, Mark V. Boekschoten, Guido Hooiveld, John van Duynhoven, James A. Timmons, Lex B. Verdijk, Lisette C. P. G. M. de Groot, Luc J. C. van Loon, Michael Müller
Software Mentions: 3
Published: almost 9 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 6 years ago

10.7150/jca.30336

Prognostic Value of Survival of MicroRNAs Signatures in Non-small Cell Lung Cancer
Cited by: 20
Author(s): Bin Chen, Tianshun Gao, Weiwei Yuan, Weihong Zhao, Tza‐Huei Wang, Jianqing Wu
Software Mentions: 3
Published: almost 6 years ago

10.7150/jca.31287

Comprehensive investigation of key biomarkers and pathways in hepatitis B virus-related hepatocellular carcinoma
Cited by: 9
Author(s): Xiwen Liao, Tingdong Yu, Chengkun Yang, Ketuan Huang, Xiangkun Wang, Chuangye Han, Rui Huang, Xiaoguang Liu, Yu Liu, Guangzhi Zhu, Hao Su, Wei Qin, Deng Jun, Xianmin Zeng, Bowen Han, Quanfa Han, Zheng-Qian Liu, Xin Zhou, Junqi Liu, Yizhen Gong, Zhengtao Liu, Jianlv Huang, Lei Lü, Xinping Ye, Tao Peng
Software Mentions: 3
Published: almost 6 years ago

10.18632/oncotarget.20739

Biomarkers identified for prostate cancer patients through genome-scale screening
Cited by: 10
Author(s): Lei‐Yun Wang, Jiajia Cui, Tao Zhu, Wei Shao, Yi Zhao, Qianqian Wang, Yupeng Zhang, Ji-Chu Wu, Le Zhang
Software Mentions: 3
Published: about 7 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: almost 7 years ago

10.1111/jcmm.14664

The non‐coding RNome after splenectomy
Cited by: 12
Author(s): Mihnea P. Dragomir, Ștefan Tudor, Kan Okubo, Masayoshi Shimizu, Meng Chen, Dana Elena Giza, Weixiang He, Cristina Ivan, C Vasilescu
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1007238

EAT1 transcription factor, a non-cell-autonomous regulator of pollen production, activates meiotic small RNA biogenesis in rice anther tapetum
Cited by: 68
Author(s): Seijiro Ono, Hua Liu, Katsutoshi Tsuda, Eigo Fukai, Keisuke Tanaka, Takuji Sasaki, Ken–Ichi Nonomura
Software Mentions: 3
Published: almost 7 years ago

10.1186/s13321-018-0257-z

Adverse drug reactions triggered by the common HLA-B*57:01 variant: virtual screening of DrugBank using 3D molecular docking
Cited by: 5
Author(s): George Van Den Driessche, Denis Fourches
Software Mentions: 3
Published: almost 7 years ago

Projects: cran: gplots

Papers Mentioning gplots 2,122