cran: gplots | Projects | Ecosyste.ms: Papers

10.1042/BSR20191554

Comprehensive analysis of prognostic biomarkers in lung adenocarcinoma based on aberrant lncRNA–miRNA–mRNA networks and Cox regression models
Cited by: 14
Author(s): Yan Yao, Tingting Zhang, Ling‐Yu Qi, Ruijuan Liu, Gongxi Liu, Wei Hua Jia, Qi Song, Changgang Sun
Software Mentions: 2
Published: over 6 years ago

10.3389/fonc.2018.00070

Alterations of the Human Skin N- and O-Glycome in Basal Cell Carcinoma and Squamous Cell Carcinoma
Cited by: 38
Author(s): Uwe Möginger, Sonja Grunewald, René Hennig, Chu-Wei Kuo, Falko Schirmeister, Harald Voth, Erdmann Rapp, Kay‐Hooi Khoo, Peter H. Seeberger, Jan‐Christoph Simon, Daniel Kolarich
Software Mentions: 2
Published: over 8 years ago

10.1038/srep09103

Tissue- and time-dependent transcription in Ixodes ricinus salivary glands and midguts when blood feeding on the vertebrate host
Cited by: 87
Author(s): Michail Kotsyfakis, Alexandra Schwarz, Jan Erhart, José M. C. Ribeiro
Software Mentions: 2
Published: over 11 years ago

10.1038/srep10189

Variation in koala microbiomes within and between individuals: effect of body region and captivity status
Cited by: 72
Author(s): Niccolò Alfano, Alexandre Courtiol, Hanna Vielgrader, Peter Timms, Alfred L. Roca, Alex D. Greenwood
Software Mentions: 2
Published: over 11 years ago

10.14814/phy2.14171

The mitochondrial‐derived peptide MOTS‐c is a regulator of plasma metabolites and enhances insulin sensitivity
Cited by: 33
Author(s): Su-Jeong Kim, Brendan Miller, Hemal H. Mehta, Jialin Xiao, Junxiang Wan, Thalida Em Arpawong, Kelvin Yen, Pinchas Cohen
Software Mentions: 2
Published: about 7 years ago

10.1186/1471-2407-14-46

A comprehensive look at transcription factor gene expression changes in colorectal adenomas
Cited by: 20
Author(s): Janine Vonlanthen, Michał Okoniewski, Mirco Menigatti, Elisa Cattaneo, Daniela Pellegrini-Ochsner, Ritva Haider, Josef Jiricny, Teresa Staiano, Federico Buffoli, Giancarlo Marra
Software Mentions: 2
Published: over 12 years ago

10.1038/srep13098

Characterisation of peripheral blood mononuclear cell microRNA in hepatitis B-related acute-on-chronic liver failure
Cited by: 21
Author(s): Wenchao Ding, Jiaojiao Xin, Liangliang Jiang, Qian Zhou, Tianzhou Wu, Dongyan Shi, Biaoyang Lin, Lanjuan Li, Jun Li
Software Mentions: 2
Published: about 11 years ago

10.1155/2020/3268505

The Role of Overexpressed Apolipoprotein AV in Insulin-Resistant Hepatocytes
Cited by: 0
Author(s): Wang Zhao, Yaqiong Liu, Xiao‐Bo Liao, Shui‐Ping Zhao
Software Mentions: 2
Published: over 6 years ago

10.1186/s12885-017-3109-8

Tumour-associated glial host cells display a stem-like phenotype with a distinct gene expression profile and promote growth of GBM xenografts
Cited by: 12
Author(s): Lina Leiss, Ercan Mutlu, Anne Margrete Øyan, Tao Yan, Oleg Tsinkalovsky, Linda Sleire, Kjell Petersen, Mohummad Aminur Rahman, Mireille Kayitesi Johannessen, Siddharta S. Mitra, Hege Karine Jacobsen, Krishna M. Talasila, Hrvoje Miletić, Inge Jonassen, Xingang Li, Nicolas H.C. Brons, Karl‐Henning Kalland, Jian Wang, Per Øyvind Enger
Software Mentions: 2
Published: over 9 years ago

10.1186/s12885-018-4781-z

Increased insulin-like growth factor 1 production by polyploid adipose stem cells promotes growth of breast cancer cells
Cited by: 14
Author(s): Roberta Fajka‐Boja, Annamária Marton, Ágota Tóth, Péter Blazsó, Vilmos Tubák, Balázs Bálint, István Nagy, Zoltán Hegedűs, Csaba Vízler, Róbert L. Katona
Software Mentions: 2
Published: almost 8 years ago

10.3389/fonc.2020.01421

Analysis of Differentially Expressed Long Non-coding RNAs and the Associated TF-mRNA Network in Tongue Squamous Cell Carcinoma
Cited by: 6
Author(s): Mi Zhang, Zexi Chen, Sihui Zhang, Ling Wu, Yinghui Jie, Ying Liao, Yue Huang, Chen Chen Jiang, Bin Shi
Software Mentions: 2
Published: about 6 years ago

10.1038/srep17551

Transcriptomes reveal the genetic mechanisms underlying ionic regulatory adaptations to salt in the crab-eating frog
Cited by: 14
Author(s): Yong Shao, Lijun Wang, Li Zhong, Mingsheng Hong, Hong‐Man Chen, Robert W. Murphy, Dong‐Dong Wu, Yaping Zhang, Jing Che
Software Mentions: 2
Published: over 10 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: almost 6 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: almost 10 years ago

10.1038/srep19926

Quantitative Analysis of Global Proteome and Lysine Acetylome Reveal the Differential Impacts of VPA and SAHA on HL60 Cells
Cited by: 30
Author(s): Xiaoyu Zhu, Xin Liu, Zhongyi Cheng, Jun Zhu, Lei Xu, Fengsong Wang, Wulin Qi, Jiawei Yan, Ning Liu, Zimin Sun, Huilan Liu, Xiaojun Peng, Yingchan Hao, Zheng Nan, Qiulian Wu
Software Mentions: 2
Published: over 10 years ago

10.7717/peerj.11386

Prokaryotic communities from a lava tube cave in La Palma Island (Spain) are involved in the biogeochemical cycle of major elements
Cited by: 18
Author(s): Jose Luis Gonzalez-Pimentel, Tamara Martin-Pozas, Valme Jurado, Ana Z. Miller, Ana Teresa Caldeira, Octavio Fernandez-Lorenzo, Sergio Sánchez‐Moral, Cesáreo Sáiz‐Jiménez
Software Mentions: 2
Published: over 5 years ago

10.3390/biology10080782

Phylogenomic Analyses of the Genus Pseudomonas Lead to the Rearrangement of Several Species and the Definition of New Genera
Cited by: 105
Author(s): Zaki Saati‐Santamaría, Ezequiel Peral-Aranega, Encarna Velázquez, Raúl Rivas, Paula García‐Fraile
Software Mentions: 2
Published: about 5 years ago

10.3389/fimmu.2019.01965

Systemic Inflammation and the Increased Risk of Inflamm-Aging and Age-Associated Diseases in People Living With HIV on Long Term Suppressive Antiretroviral Therapy
Cited by: 65
Author(s): Hemalatha Babu, Anoop T. Ambikan, Erin E. Gabriel, Sara Svensson Akusjärvi, Alangudi Natarajan Palaniappan, Vijila Sundaraj, Naveen Reddy Mupanni, Maike Sperk, Narayanaiah Cheedarla, Sridhar Ramaswamy, Srikanth Tripathy, Piotr Nowak, Luke Elizabeth Hanna, Ujjwal Neogi
Software Mentions: 2
Published: about 7 years ago

10.1038/srep21764

Succinyl-proteome profiling of a high taxol containing hybrid Taxus species (Taxus × media) revealed involvement of succinylation in multiple metabolic pathways
Cited by: 31
Author(s): Chenjia Shen, Jie Xue, Tao Sun, Hong Guo, Lei Zhang, Yijun Meng, Huizhong Wang
Software Mentions: 2
Published: over 10 years ago

10.3389/fmicb.2019.01474

Comparative Transcriptome Profiling of Gaeumannomyces graminis var. tritici in Wheat Roots in the Absence and Presence of Biocontrol Bacillus velezensis CC09
Cited by: 10
Author(s): Xingxing Kang, Yu Guo, Shuai Leng, Lei Xiao, Lanhua Wang, Yarong Xue, Changhong Liu
Software Mentions: 2
Published: about 7 years ago

10.1038/srep22637

Age-associated metabolic dysregulation in bone marrow-derived macrophages stimulated with lipopolysaccharide
Cited by: 28
Author(s): Fan Fei, Keith M. Lee, Brian E. McCarry, Dawn M. E. Bowdish
Software Mentions: 2
Published: over 10 years ago

10.3390/biology8020021

Transcriptome Analysis of Yamame (Oncorhynchus masou) in Normal Conditions after Heat Stress
Cited by: 1
Author(s): Waraporn Kraitavin, Kazutoshi Yoshitake, Yoji Igarashi, Susumu Mitsuyama, Shigeharu Kinoshita, Daisuke Kambayashi, Shugo Watabe, Shuichi Asakawa
Software Mentions: 2
Published: over 7 years ago

10.18632/oncotarget.27712

Down syndrome iPSC model: endothelial perspective on tumor development
Cited by: 2
Author(s): Mariana Perepitchka, Yekaterina Galat, Igor P. Beletsky, Philip M. Iannaccone, Vasiliy Galat
Software Mentions: 2
Published: almost 6 years ago

10.7717/peerj.7380

Construction and integrated analysis of crosstalking ceRNAs networks in laryngeal squamous cell carcinoma
Cited by: 18
Author(s): Yuehui Liu, Fan Ye
Software Mentions: 2
Published: about 7 years ago

10.3389/fphar.2018.00258

Breathomics for Assessing the Effects of Treatment and Withdrawal With Inhaled Beclomethasone/Formoterol in Patients With COPD
Cited by: 25
Author(s): Paolo Montuschi, Giuseppe Santini, Nadia Mores, Alessia Vignoli, Francesco Montorsi, Rugia Shoreh, Leonardo Tenori, Gina Zini, Leonello Fuso, Chiara Mondino, Corrado Di Natale, A. D’Amico, Claudio Luchinat, Peter J. Barnes, Tim Higenbottam
Software Mentions: 2
Published: over 8 years ago

10.1186/s40659-020-00299-y

Microarray profiling and functional analysis of differentially expressed plasma exosomal circular RNAs in Graves’ disease
Cited by: 16
Author(s): Ying Sun, Wei Wang, Yuxiao Tang, Daping Wang, Liang Li, Na Min, Guantong Jiang, Qian Li, Shulin Chen, Jin Zhou
Software Mentions: 2
Published: about 6 years ago

10.1038/srep26852

Genome-wide differential expression of genes and small RNAs in testis of two different porcine breeds and at two different ages
Cited by: 24
Author(s): Li Yao, Jialian Li, Fang Cui, Liang Shi, Jinyun Tan, Yan Xiong, Bin Fan, Changchun Li
Software Mentions: 2
Published: over 10 years ago

10.3389/fphar.2021.670785

Co-Treatment With Verapamil and Curcumin Attenuates the Behavioral Alterations Observed in Williams–Beuren Syndrome Mice by Regulation of MAPK Pathway and Microglia Overexpression
Cited by: 5
Author(s): Paula Ortiz‐Romero, Alejandro González-Simón, Gustavo Egea, Luis A. Pérez‐Jurado, Victoria Campuzano
Software Mentions: 2
Published: about 5 years ago

10.1038/srep29313

Proteome-wide analysis of lysine acetylation in the plant pathogen Botrytis cinerea
Cited by: 38
Author(s): Binna Lv, Qiwen Yang, Delong Li, Wenxing Liang, Limin Song
Software Mentions: 2
Published: about 10 years ago

10.3390/ijms15069386

The Transcriptomes of the Crucian Carp Complex (Carassius auratus) Provide Insights into the Distinction between Unisexual Triploids and Sexual Diploids
Cited by: 12
Author(s): Chunyan Li, Jiong-Tang Li, Youyi Kuang, Ruihua Xu, Zixia Zhao, Guangyuan Hou, Hongwei Liang, Xin Sun
Software Mentions: 2
Published: over 12 years ago

10.1038/srep31576

First Comprehensive Proteome Analyses of Lysine Acetylation and Succinylation in Seedling Leaves of Brachypodium distachyon L.
Cited by: 60
Author(s): Shoumin Zhen, Xiong Deng, Jian Wang, Guijie Zhu, Hui Cao, Linlin Yuan, Yueming Yan
Software Mentions: 2
Published: about 10 years ago

10.7717/peerj.10678

TET2 mutations in acute myeloid leukemia: a comprehensive study in patients of Sindh, Pakistan
Cited by: 4
Author(s): Abdul Rehman Shaikh, Ikram Uddin Ujjan, Muhammad Irfan, Arshi Naz, Tahir Shamsi, Muhammad Tariq Masood Khan, Muhammad Shakeel
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2019.01292

Data-Mining Approach on Transcriptomics and Methylomics Placental Analysis Highlights Genes in Fetal Growth Restriction
Cited by: 13
Author(s): Floris Chabrun, Noémie Huetz, Xavier Dieu, Guillaume Rousseau, Guillaume Bouzillé, Juan Manuel Chao de la Barca, Vincent Procaccio, Guy Lenaers, Odile Blanchet, Guillaume Legendre, Delphine Mirebeau‐Prunier, Marc Cuggia, Philippe Guardiola, Pascal Reynier, Géraldine Gascoin
Software Mentions: 2
Published: over 6 years ago

10.1038/srep33102

Pentoxifylline ameliorates non-alcoholic fatty liver disease in hyperglycaemic and dyslipidaemic mice by upregulating fatty acid β-oxidation
Cited by: 23
Author(s): Jia-Hung Ye, Jung Chao, Mau‐Song Chang, Wen-Huang Peng, Hao-Yuan Cheng, Jiunn‐Wang Liao, Li-Heng Pao
Software Mentions: 2
Published: almost 10 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 13 years ago

10.3389/fphys.2019.00261

Arginine Vasotocin and Cortisol Co-regulate Vasotocinergic, Isotocinergic, Stress, and Thyroid Pathways in the Gilthead Sea Bream (Sparus aurata)
Cited by: 11
Author(s): Juan Antonio Martos-Sitcha, Laura Cádiz, Magdalena Gozdowska, Ewa Kulczykowska, Gonzalo Martínez‐Rodríguez, Juan Miguel Mancera
Software Mentions: 2
Published: over 7 years ago

10.3389/fimmu.2021.643441

Comparative Analysis of Global Proteome and Lysine Acetylome Between Naive CD4+ T Cells and CD4+ T Follicular Helper Cells
Cited by: 2
Author(s): Ming Zhao, Sujie Jia, Xiaofei Gao, Hong Qiu, Ruifang Wu, Haijing Wu, Qianjin Lu
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2019.00011

Nasopharyngeal Microbiota in Children With Invasive Pneumococcal Disease: Identification of Bacteria With Potential Disease-Promoting and Protective Effects
Cited by: 28
Author(s): Anny Camelo-Castillo, Desirée Henares, Pedro Brotons, Antonio Galiana, Juan Carlos Rodrı́guez, Álex Mira, Carmen Muñoz-Almagro
Software Mentions: 2
Published: over 7 years ago

10.7554/eLife.47678

Androgen-regulated transcription of ESRP2 drives alternative splicing patterns in prostate cancer
Cited by: 42
Author(s): Jennifer Munkley, Ling Li, Subha Krishnan, Gerald Hysenaj, Emma Scott, Caroline Dalgliesh, Htoo Zarni Oo, Teresa Maia, Kathleen Cheung, Ingrid Ehrmann, Karen E. Livermore, Hanna Zielińska, Oliver Thompson, Bridget Knight, Paul McCullagh, John McGrath, Malcolm Crundwell, Lorna W. Harries, Mads Daugaard, Simon Cockell, Nuno L. Barbosa‐Morais, Sebastian Oltean, David Elliott
Software Mentions: 2
Published: almost 7 years ago

10.1038/srep36695

RNA-seq analyses of the midgut from blood- and serum-fed Ixodes ricinus ticks
Cited by: 67
Author(s): Jan Perner, Jan Provazník, Jana Schrenková, Veronika Urbanová, José M. C. Ribeiro, Petr Kopáček
Software Mentions: 2
Published: almost 10 years ago

10.3389/fimmu.2021.637659

Activation of Toll-Like Receptor 7 Signaling Pathway in Primary Sjögren's Syndrome-Associated Thrombocytopenia
Cited by: 10
Author(s): Shuo Zhang, Jingge Qu, Li Wang, Mengtao Li, Dong Xu, Yan Zhao, Fengchun Zhang, Xiaofeng Zeng
Software Mentions: 2
Published: over 5 years ago

10.1186/1752-0509-5-202

A chemokine gene expression signature derived from meta-analysis predicts the pathogenicity of viral respiratory infections
Cited by: 18
Author(s): Stewart T. Chang, Nicolas Tchitchek, Debashis Ghosh, Arndt Benecke, Michael G. Katze
Software Mentions: 2
Published: over 14 years ago

10.1038/srep37900

Survey of the green picoalga Bathycoccus genomes in the global ocean
Cited by: 51
Author(s): Thomas Vannier, Jade Leconte, Yoann Seeleuthner, Samuel Mondy, Éric Pelletier, Jean‐Marc Aury, Colomban de Vargas, Michael E. Sieracki, Daniele Iudicone, Daniel Vaulot, Patrick Wincker, Olivier Jaillon
Software Mentions: 2
Published: over 9 years ago

10.7717/peerj.3698

Genomic and functional analysis ofRomboutsia ilealisCRIBTreveals adaptation to the small intestine
Cited by: 74
Author(s): J. Gerritsen, Bastian Hornung, Bernadet Renckens, Sacha A. F. T. van Hijum, Vítor A. P. Martins dos Santos, Ger T. Rijkers, Peter J. Schaap, Willem M. de Vos, Hauke Smidt
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12918-015-0159-x

Genome-scale resources for Thermoanaerobacterium saccharolyticum
Cited by: 22
Author(s): Devin H. Currie, Babu Raman, Christopher M. Gowen, Timothy J. Tschaplinski, Miriam Land, Steven D. Brown, Sean F. Covalla, Dawn M. Klingeman, Zamin K. Yang, Nancy L. Engle, C. M. Johnson, Miguel Rodríguez, Aubie Shaw, William R. Kenealy, Lee R. Lynd, Stephen S. Fong, Jonathan R. Mielenz, Brian H. Davison, David A. Hogsett, Christopher D. Herring
Software Mentions: 2
Published: about 11 years ago

10.7717/peerj.6526

TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character ofShewanella putrefaciensstrain Pdp11
Cited by: 3
Author(s): Pedro Seoane, Silvana Tapia‐Paniagua, Rocío Bautista, Elena Alcaide, Consuelo Esteve, Eduardo Martínez‐Manzanares, M.C. Balebona, M. Gonzalo Claros, Miguel A. Moriñigo
Software Mentions: 2
Published: over 7 years ago

10.3389/fpls.2016.01842

Identification and Analysis of NaHCO3 Stress Responsive Genes in Wild Soybean (Glycine soja) Roots by RNA-seq
Cited by: 26
Author(s): Jinlong Zhang, Jiaxue Wang, Wei Jiang, Juge Liu, Songnan Yang, Junyi Gai, Yan Li
Software Mentions: 2
Published: over 9 years ago

10.3390/antibiotics10080886

Impact of Chronic Tetracycline Exposure on Human Intestinal Microbiota in a Continuous Flow Bioreactor Model
Cited by: 7
Author(s): Youngbeom Ahn, Ji Young Jung, Ohgew Kweon, Brian T Veach, Sangeeta Khare, Kuppan Gokulan, Silvia A. Piñeiro, Carl E. Cerniglia
Software Mentions: 2
Published: about 5 years ago

10.1038/srep42062

Proteome and Acetylome Analysis Identifies Novel Pathways and Targets Regulated by Perifosine in Neuroblastoma
Cited by: 13
Author(s): Xiao Gu, Zhongyan Hua, Yuzhu Dong, Yue Zhan, Xiaowen Zhang, Wei Tian, Zhihui Liu, Carol J. Thiele, Zhijie Li
Software Mentions: 2
Published: over 9 years ago

10.3389/fpls.2018.00264

Panax notoginseng Root Cell Death Caused by the Autotoxic Ginsenoside Rg1 Is Due to Over-Accumulation of ROS, as Revealed by Transcriptomic and Cellular Approaches
Cited by: 30
Author(s): Min Yang, Youcong Chuan, Changhong Guo, Jingjing Liao, Yanguo Xu, Xinyue Mei, Yixiang Liu, Huichuan Huang, Xiahong He, Shusheng Zhu
Software Mentions: 2
Published: over 8 years ago

10.1038/srep41234

Paenibacillus polymyxa NSY50 suppresses Fusarium wilt in cucumbers by regulating the rhizospheric microbial community
Cited by: 50
Author(s): Lu Shi, Nanshan Du, Sheng Shu, Jian Sun, Shuzhan Li, Shirong Guo
Software Mentions: 2
Published: over 9 years ago

10.3945/jn.117.248864

Human Milk Microbial Community Structure Is Relatively Stable and Related to Variations in Macronutrient and Micronutrient Intakes in Healthy Lactating Women
Cited by: 100
Author(s): Janet E. Williams, Janae M Carrothers, Kimberly A. Lackey, Nicola F Beatty, Mara A York, Sarah L Brooker, Bahman Shafii, William J. Price, Matthew L. Settles, Mark A. McGuire, Michelle K. McGuire
Software Mentions: 2
Published: almost 9 years ago

10.1038/srep42890

Depth-specific fluctuations of gene expression and protein abundance modulate the photophysiology in the seagrass Posidonia oceanica
Cited by: 47
Author(s): Gabriele Procaccini, Miriam Ruocco, Lázaro Marín-Guirao, Emanuela Dattolo, Christophe Brunet, Daniela D’Esposito, Chiara Lauritano, Silvia Mazzuca, Ilia Anna Serra, Letizia Bernardo, Amalia Piro, Sven Beer, Mats Björk, Martin Gullström, Pimchanok Buapet, Lina M. Rasmusson, Paulo Felisberto, Sylvie Gobert, John W. Runcie, João Silva, Irene Olivé, Monya M. Costa, Isabel Barrote, Rui Santos
Software Mentions: 2
Published: over 9 years ago

10.1186/s12918-018-0639-x

Co-expression of long non-coding RNAs and autism risk genes in the developing human brain
Cited by: 24
Author(s): Steven Cogill, Anand Srivastava, Mary Qu Yang, Liangjiang Wang
Software Mentions: 2
Published: over 7 years ago

10.1038/srep43109

miR-125b-5p enhances chemotherapy sensitivity to cisplatin by down-regulating Bcl2 in gallbladder cancer
Cited by: 62
Author(s): Dong Yang, Ming Zhan, Tao Chen, Wei Chen, Yunhe Zhang, Sunwang Xu, Jinchun Yan, Qihong Huang, Jian Wang
Software Mentions: 2
Published: over 9 years ago

10.3389/fmicb.2017.00202

Three Novel Species with Peptidoglycan Cell Walls form the New Genus Lacunisphaera gen. nov. in the Family Opitutaceae of the Verrucomicrobial Subdivision 4
Cited by: 69
Author(s): Patrick Rast, Ines Glöckner, Christian Boedeker, Olga Jeske, Sandra Wiegand, Richard Reinhardt, Peter Schümann, Manfred Rohde, Stefan Spring, Frank Oliver Glöckner, Christian Jogler, Mareike Jogler
Software Mentions: 2
Published: over 9 years ago

10.7554/eLife.23203

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells
Cited by: 171
Author(s): Sebastian Pott
Software Mentions: 2
Published: about 9 years ago

10.7717/peerj.8176

Systematic evaluation of the gut microbiome of swamp eel (Monopterus albus) by 16S rRNA gene sequencing
Cited by: 6
Author(s): Xuan Chen, Shouguo Fang, Lili Wei, Qiuyan Zhong
Software Mentions: 2
Published: over 6 years ago

10.1038/srep45195

Several microRNAs could predict survival in patients with hepatitis B-related liver cancer
Cited by: 19
Author(s): Zhen Ye, Xinghui Zhao, Chao Wu, Yi Zhao, Jinwen Chen, Ruifang Gao, Chao Zhang, Min Zhao, Changyuan Guo, Yan Fang, Lingfang Du, Long Shen, Wenzhi Shen, Xin Luo, Rong Xiang
Software Mentions: 2
Published: over 9 years ago

10.1038/srep09325

Clustered Distribution of Natural Product Leads of Drugs in the Chemical Space as Influenced by the Privileged Target-Sites
Cited by: 18
Author(s): Tao Lin, Feng Zhu, Qing Chu, Cheng Zhang, Shangying Chen, Peng Zhang, Cunlong Zhang, Chunyan Tan, Chunmei Gao, Zhe Chen, Yuyang Jiang, Yu Zong Chen
Software Mentions: 2
Published: over 11 years ago

10.3389/fpls.2016.01958

Global Scale Transcriptional Profiling of Two Contrasting Barley Genotypes Exposed to Moderate Drought Conditions: Contribution of Leaves and Crowns to Water Shortage Coping Strategies
Cited by: 12
Author(s): Pavel Svoboda, Anna Janská, Vojtěch Spiwok, Ilja Tom Prášil, Klára Kosová, Pavel Vítámvás, Jaroslava Ovesná
Software Mentions: 2
Published: over 9 years ago

10.1186/1756-0500-7-761

Expression level of a flavonoid 3′-hydroxylase gene determines pathogen-induced color variation in sorghum
Cited by: 20
Author(s): Hiroshi Mizuno, Takayuki Yazawa, Shigemitsu Kasuga, Yuji Sawada, Jun Ogata, Tsuyu Ando, Hajime Kanamori, Jun‐ichi Yonemaru, Jianzhong Wu, Masami Yokota Hirai, Takashi Matsumoto, Hiroyuki Kawahigashi
Software Mentions: 2
Published: almost 12 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: almost 14 years ago

10.1186/1756-0500-7-440

Evolutionary and sequence-based relationships in bacterial AdoMet-dependent non-coding RNA methyltransferases
Cited by: 13
Author(s): Jeanneth Mosquera-Rendón, Sonia Cárdenas-Brito, Juan D Pineda, Mauricio Corredor, Alfonso Benı́tez-Páez
Software Mentions: 2
Published: about 12 years ago

10.1186/s13104-015-1017-z

BMX: a tool for computing bacterial phyletic composition from orthologous maps
Cited by: 8
Author(s): Benard W. Kulohoma
Software Mentions: 2
Published: over 11 years ago

10.3390/ani10030534

A Novel Therapeutic Reagent, KA-1002 for Alleviating Lysophosphatidic Acid-Mediated Inflammation Related Gene Expression in Swine Macrophages
Cited by: 0
Author(s): Hyeon-Jeong Hwang, Tamina Park, Miok Kim, Hee-Su Shin, Woo-Yeon Hwang, Yong Ki Min, Sukgil Song, Daeui Park, Chang Hoon Lee
Software Mentions: 2
Published: over 6 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: over 13 years ago

10.1038/s41598-017-02128-x

Quantitative Succinyl-Proteome Profiling of Camellia sinensis cv. ‘Anji Baicha’ During Periodic Albinism
Cited by: 35
Author(s): Yan-Xia Xu, Chenjia Shen, Jianqiang Ma, Wei Chen, Juan Mao, Yanyan Zhou, Liang Chen
Software Mentions: 2
Published: over 9 years ago

10.7717/peerj.8101

Co-expression analysis and ceRNA network reveal eight novel potential lncRNA biomarkers in hepatocellular carcinoma
Cited by: 6
Author(s): Renchao Zou, Zhitian Shi, Shufeng Xiao, Ke Yang, Haoran Tang, Taihu Wu, Zhitang Guo, Ni Fan, Sanqi An, Lin Wang
Software Mentions: 2
Published: over 6 years ago

10.1186/s12870-021-02969-9

The physiological and molecular mechanisms of N transfer in Eucalyptus and Dalbergia odorifera intercropping systems using root proteomics
Cited by: 6
Author(s): Xianyu Yao, Lusheng Liao, Yongzhen Huang, Ge Fan, Mei Yang, Shaoming Ye
Software Mentions: 2
Published: over 5 years ago

10.3389/fpls.2017.00914

Comparative Transcriptome Analysis Reveals Critical Function of Sucrose Metabolism Related-Enzymes in Starch Accumulation in the Storage Root of Sweet Potato
Cited by: 48
Author(s): Kai Zhang, Zhengdan Wu, Daobin Tang, Kai Luo, Huixiang Lu, Yingying Liu, Jie Dong, Xin Wang, Changwen Lv, Jichun Wang, Kun Lü
Software Mentions: 2
Published: about 9 years ago

10.1038/s41598-017-03198-7

Transmission of Induced Chromosomal Aberrations through Successive Mitotic Divisions in Human Lymphocytes after In Vitro and In Vivo Radiation
Cited by: 25
Author(s): Akram Kaddour, Bruno Colicchio, Diane Buron, Elie Maalouf, Eric Laplagne, Claire Borie, Michelle Ricoul, Aude Lenain, William M. Hempel, Luc Morat, Mustafa Al Jawhari, Corina Cuceu, Leonhard Heidingsfelder, Éric Jeandidier, Georges Deschênes, Alain Dieterlen, Michèle El May, T. Girinsky, Annelise Bennaceur-Griscelli, Patrice Carde, Laure Sabatier, Radhia M’Kacher
Software Mentions: 2
Published: about 9 years ago

10.1186/s12870-016-0880-7

A fast and simple LC-MS-based characterization of the flavonoid biosynthesis pathway for few seed(ling)s
Cited by: 11
Author(s): Benjamin Jaegle, M. Kalle Uroic, Xu Holtkotte, Christina Lucas, Andreas Ole Termath, Hans‐Günther Schmalz, Marcel Bucher, Ute Hoecker, Martin Hülskamp, Andrea Schrader
Software Mentions: 2
Published: almost 10 years ago

10.3389/fpls.2015.00739

Global analysis of lysine acetylation in strawberry leaves
Cited by: 60
Author(s): Xianping Fang, Wenyue Chen, Yun Zhao, Songlin Ruan, Heng-Mu Zhang, Chengqi Yan, Liang Jin, Lingling Cao, Jun Zhu, Huiqin Ma, Zhongyi Cheng
Software Mentions: 2
Published: almost 11 years ago

10.1038/s41598-017-04228-0

Multiple origins and a narrow genepool characterise the African tea germplasm: concordant patterns revealed by nuclear and plastid DNA markers
Cited by: 19
Author(s): Moses C. Wambulwa, M. K. Meegahakumbura, S. M. Kamunya, Alice Muchugi, Michael Möller, Jie Liu, Jianchu Xu, Li D, Lian‐Ming Gao
Software Mentions: 2
Published: about 9 years ago

10.1186/s12864-020-06999-9

Mining and evolution analysis of lateral organ boundaries domain (LBD) genes in Chinese white pear (Pyrus bretschneideri)
Cited by: 14
Author(s): Bobo Song, Zikai Tang, Xiaolong Li, Jiaming Li, Mingyue Zhang, Kunkun Zhao, Hainan Liu, Shaoling Zhang, Jun Wu
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12870-014-0281-8

Non-specific lipid transfer proteins in maize
Cited by: 68
Author(s): Kaifa Wei, Xiaojun Zhong
Software Mentions: 2
Published: almost 12 years ago

10.1038/s41598-017-06231-x

CREB Regulates Distinct Adaptive Transcriptional Programs in Astrocytes and Neurons
Cited by: 33
Author(s): Luis Pardo, Luis M. Valor, Abel Eraso-Pichot, Ángel Barco, Arantxa Golbano, Giles E. Hardingham, Roser Masgrau, Elena Galea
Software Mentions: 2
Published: about 9 years ago

10.7717/peerj.1597

Comparative morphology of the mouthparts of the megadiverse South African monkey beetles (Scarabaeidae: Hopliini): feeding adaptations and guild structure
Cited by: 20
Author(s): Florian Karolyi, Teresa Hansal, Harald W. Krenn, Jonathan F. Colville
Software Mentions: 2
Published: over 10 years ago

10.7717/peerj.9054

Intra-lake response of Arcellinida (testate lobose amoebae) to gold mining-derived arsenic contamination in northern Canada: Implications for environmental monitoring
Cited by: 5
Author(s): Nawaf A. Nasser, R. Timothy Patterson, Jennifer M. Galloway, Hendrik Falck
Software Mentions: 2
Published: over 6 years ago

10.3390/nu11122839

Hormonal Therapy Resistance and Breast Cancer: Involvement of Adipocytes and Leptin
Cited by: 21
Author(s): Laëtitia Delort, Laurianne Bougaret, Juliette Cholet, Marion Vermerie, Hermine Billard, Caroline Decombat, Céline Bourgne, Marc Berger, Charles Dumontet, Florence Caldefie‐Chezet
Software Mentions: 2
Published: almost 7 years ago

10.7717/peerj.10053

Silicon flow from root to shoot in pepper: a comprehensive in silico analysis reveals a potential linkage between gene expression and hormone signaling that stimulates plant growth and metabolism
Cited by: 9
Author(s): Fernando Carlos Gómez-Meriño, Libia Iris Trejo-Téllez, Atonaltzin García-Jiménez, Hugo Fernando Escobar-Sepúlveda, Sara Monzerrat Ramírez-Olvera
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12870-018-1529-5

Comparative functional genomics analysis of bHLH gene family in rice, maize and wheat
Cited by: 56
Author(s): Kaifa Wei, Huiqin Chen
Software Mentions: 2
Published: almost 8 years ago

10.7554/eLife.42989

Haplotypes spanning centromeric regions reveal persistence of large blocks of archaic DNA
Cited by: 46
Author(s): Sasha A. Langley, Karen H. Miga, Gary H. Karpen, Charles H. Langley
Software Mentions: 2
Published: about 7 years ago

10.3389/fgene.2021.690990

Identification and Validation of Potential Candidate Genes of Colorectal Cancer in Response to Fusobacterium nucleatum Infection
Cited by: 0
Author(s): Jiangguo Zhang, Zhimo Wang, Hong Liu, Guojun Li
Software Mentions: 2
Published: almost 5 years ago

10.3389/fpls.2021.716955

The Haplotype-Based Analysis of Aegilops tauschii Introgression Into Hard Red Winter Wheat and Its Impact on Productivity Traits
Cited by: 6
Author(s): Moses Nyine, Elina Adhikari, Marshall Clinesmith, Robert M. Aiken, Bliss Betzen, Wei Wang, Dwight Davidson, Zitong Yu, Yuanwen Guo, Fei He, Alina Akhunova, Katherine Jordan, Allan K. Fritz, Eduard Akhunov
Software Mentions: 2
Published: about 5 years ago

10.1186/s12870-017-1068-5

Ambient temperature and genotype differentially affect developmental and phenotypic plasticity in Arabidopsis thaliana
Cited by: 64
Author(s): Carla Ibáñez, Yvonne Poeschl, Tom Peterson, Julia Bellstädt, Kathrin Denk, Andreas Gogol-Döring, Marcel Quint, Carolin Delker
Software Mentions: 2
Published: about 9 years ago

10.3390/ijms18040894

Altered Adipogenesis in Zebrafish Larvae Following High Fat Diet and Chemical Exposure Is Visualised by Stimulated Raman Scattering Microscopy
Cited by: 40
Author(s): Marjo J. den Broeder, Miriam J. B. Moester, Jorke H. Kamstra, P.H. Cenijn, Valentina Davidoiu, Leonie M. Kamminga, Freek Ariese, Johannes F. de Boer, Juliette Legler
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-017-11781-1

Sources of Variation in the Gut Microbial Community of Lycaeides melissa Caterpillars
Cited by: 28
Author(s): Samridhi Chaturvedi, Alexandre Rêgo, Lauren K. Lucas, Zachariah Gompert
Software Mentions: 2
Published: almost 9 years ago

10.18632/oncotarget.9858

Breast cancer subtype dictates DNA methylation and ALDH1A3-mediated expression of tumor suppressor RARRES1
Cited by: 23
Author(s): Krysta M. Coyle, John P. Murphy, Dejan Vidovic, Ahmad Vaghar-Kashani, Cheryl A. Dean, Mohammad Sultan, Derek R. Clements, Melissa Wallace, Margaret Lois Thomas, Amos Hundert, Carman A. Giacomantonio, Lucy Helyer, Shashi Gujar, Patrick W.K. Lee, Ian C.G. Weaver, Paola Marcato
Software Mentions: 2
Published: about 10 years ago

10.18632/oncotarget.9859

UCN-01 enhances cytotoxicity of irinotecan in colorectal cancer stem-like cells by impairing DNA damage response
Cited by: 16
Author(s): Michele Signore, Mariachiara Buccarelli, Emanuela Pilozzi, Gabriele De Luca, Marianna Cappellari, Maurizio Fanciulli, Frauke Goeman, Elisa Melucci, Mauro Biffoni, Lucia Ricci‐Vitiani
Software Mentions: 2
Published: about 10 years ago

10.3390/pathogens6040045

The Use of Hyperimmune Chicken Reference Sera Is Not Appropriate for the Validation of Influenza Pseudotype Neutralization Assays
Cited by: 0
Author(s): Francesca Ferrara, Eleonora Molesti, Simon D. Scott, Giovanni Cattoli, Nigel Temperton
Software Mentions: 2
Published: almost 9 years ago

10.3390/ijms18102155

Predicting Amyloidogenic Proteins in the Proteomes of Plants
Cited by: 29
Author(s): Kirill S. Antonets, Anton A. Nizhnikov
Software Mentions: 2
Published: almost 9 years ago

10.1186/s13071-019-3405-z

Interpreting mosquito feeding patterns in Australia through an ecological lens: an analysis of blood meal studies
Cited by: 18
Author(s): Eloise Stephenson, Amanda K. Murphy, Cassie C. Jansen, Alison J. Peel, Hamish McCallum
Software Mentions: 2
Published: over 7 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: about 12 years ago

10.3389/fmicb.2017.02132

Ecogenomics and Taxonomy of Cyanobacteria Phylum
Cited by: 82
Author(s): Juline M. Walter, Felipe H. Coutinho, Bas E. Dutilh, Jean Swings, Fabiano L. Thompson, Cristiane C. Thompson
Software Mentions: 2
Published: almost 9 years ago

10.1186/s13071-016-1642-y

CAP protein superfamily members in Toxocara canis
Cited by: 6
Author(s): Andreas J. Stroehlein, Neil D. Young, Ross S. Hall, Pasi K. Korhonen, Andreas Hofmann, Paul W. Sternberg, Abdul Jabbar, Robin B. Gasser
Software Mentions: 2
Published: about 10 years ago

10.1186/s13071-018-3007-1

Hints on T cell responses in a fish-parasite model: Enteromyxum leei induces differential expression of T cell signature molecules depending on the organ and the infection status
Cited by: 24
Author(s): M. Carla Piazzon, Itziar Estensoro, Josep Àlvar Calduch-Giner, R. del Pozo, Amparo Picard‐Sánchez, Jaume Pérez‐Sánchez, Ariadna Sitjà‐Bobadilla
Software Mentions: 2
Published: about 8 years ago

10.1186/s12866-020-1698-x

Genome-resolved metagenomics analysis provides insights into the ecological role of Thaumarchaeota in the Amazon River and its plume
Cited by: 14
Author(s): Otávio Henrique Bezerra Pinto, Thais F. Silva, Carla Simone Vizzotto, Renata Henrique Santana, Fabyano Álvares Cardoso Lopes, Bruno Santana da Silva, Fabiano L. Thompson
Software Mentions: 2
Published: over 6 years ago

10.18632/oncotarget.12211

Methylation of RAD51B, XRCC3 and other homologous recombination genes is associated with expression of immune checkpoints and an inflammatory signature in squamous cell carcinoma of the head and neck, lung and cervix
Cited by: 27
Author(s): Damian Rieke, Sebastian Ochsenreither, Konrad Klinghammer, Tanguy Y. Seiwert, Frederick Klauschen, Ingeborg Tinhofer, Ulrich Keilholz
Software Mentions: 2
Published: almost 10 years ago

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