bioconductor: KEGGREST | Projects

10.3390/metabo9100200

The metaRbolomics Toolbox in Bioconductor and beyond
Cited by: 61
Author(s): Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy A. Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Michael Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski, Michael A. Stravs, Etienne Thévenot, Hendrik Treutler, Ralf Weber, Egon Willighagen, Michael Witting, Steffen Neumann
Software Mentions: 92
Published: about 5 years ago

10.1128/MRA.00129-19

omu, a Metabolomics Count Data Analysis Tool for Intuitive Figures and Convenient Metadata Collection
Cited by: 12
Author(s): Connor R. Tiffany, Andreas J. Bäumler
Software Mentions: 16
Published: over 5 years ago

10.3390/cells10061292

Effect of Differences in the Microbiome of Cyp17a1-Deficient Mice on Atherosclerotic Background
Cited by: 1
Author(s): Axel Künstner, Rédouane Aherrahrou, Misa Hirose, Petra Bruse, Saleh M. Ibrahim, Hauke Busch, Jeanette Erdmann, Zouhair Aherrahrou
Software Mentions: 15
Published: over 3 years ago

10.1186/s12859-016-0884-1

Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis
Cited by: 62
Author(s): Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer
Software Mentions: 14
Published: almost 9 years ago

10.1371/journal.pcbi.1007859

Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease
Cited by: 10
Author(s): Christine Tataru, Maude M. David
Software Mentions: 13
Published: over 4 years ago

10.1371/journal.pone.0079217

A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity
Cited by: 154
Author(s): Adi L. Tarca, Gaurav Bhatti, Roberto Romero
Software Mentions: 12
Published: about 11 years ago

10.1186/s12864-017-4423-x

Integration of multiple networks and pathways identifies cancer driver genes in pan-cancer analysis
Cited by: 31
Author(s): Claudia Cava, Gloria Bertoli, Antonio Colaprico, Catharina Olsen, Gianluca Bontempi, Isabella Castiglioni
Software Mentions: 12
Published: almost 7 years ago

10.3389/fmicb.2019.00697

Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must
Cited by: 28
Author(s): Kimmo Sirén, Sarah S.T. Mak, Chrats Melkonian, Christian Carøe, Jan H. Swiegers, Douwe Molenaar, Ulrich Fischer, M. Thomas P. Gilbert
Software Mentions: 12
Published: over 5 years ago

10.3389/fmicb.2019.02597

New Insights Into Cinnamoyl Esterase Activity of Oenococcus oeni
Cited by: 9
Author(s): Ingrid Collombel, Chrats Melkonian, Douwe Molenaar, Francisco M. Campos, Tim Hogg
Software Mentions: 12
Published: about 5 years ago

10.12688/f1000research.12544.1

Easy and efficient ensemble gene set testing with EGSEA
Cited by: 45
Author(s): Monther Alhamdoosh, Charity W. Law, Tian Li, Julie Sheridan, Milica Ng, Matthew E. Ritchie
Software Mentions: 12
Published: about 7 years ago

10.1371/journal.pone.0075146

NuChart: An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations
Cited by: 29
Author(s): Ivan Merelli, Píetro Lió, Luciano Milanesi
Software Mentions: 12
Published: about 11 years ago

10.1128/mSystems.00404-19

Effects of Antibiotic Pretreatment of an Ulcerative Colitis-Derived Fecal Microbial Community on the Integration of Therapeutic Bacteria <i>In Vitro</i>
Cited by: 13
Author(s): Kaitlyn Oliphant, Kyla Cochrane, Kathleen Schroeter, Michelle Daigneault, Sandi Yen, Elena F. Verdú, Emma Allen‐Vercoe
Software Mentions: 11
Published: almost 5 years ago

10.3389/fgene.2015.00040

Integrating multi-omic features exploiting Chromosome Conformation Capture data
Cited by: 9
Author(s): Ivan Merelli, Fabio Tordini, Maurizio Drocco, Marco Aldinucci, Píetro Lió, Luciano Milanesi
Software Mentions: 11
Published: almost 10 years ago

10.3389/fmicb.2018.01095

CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software
Cited by: 99
Author(s): Toby Wilkinson, Sharon Huws, Joan E. Edwards, Alison H. Kingston‐Smith, Karen Siu-Ting, Martin Hughes, Francesco Rubino, Maximillian Friedersdorff, Christopher J. Creevey
Software Mentions: 10
Published: over 6 years ago

10.1128/mSystems.00493-20

Exometabolite Dynamics over Stationary Phase Reveal Strain-Specific Responses
Cited by: 3
Author(s): John L. Chodkowski, Ashley Shade
Software Mentions: 9
Published: almost 4 years ago

10.1038/s42003-021-01948-y

High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers
Cited by: 9
Author(s): Chrats Melkonian, Lucas Fillinger, Siavash Atashgahi, Ulisses Nunes da Rocha, Eric Kuiper, Brett G. Olivier, Martin Braster, Willi Gottstein, Rick Helmus, John R. Parsons, Hauke Smidt, Marcelle van der Waals, Jan Gerritse, Bernd W. Brandt, Wilfred F. M. Röling, Douwe Molenaar, Rob J.M. van Spanning
Software Mentions: 9
Published: over 3 years ago

10.7717/peerj.7495

Metabolic alterations in pea leaves during arbuscular mycorrhiza development
Cited by: 21
Author(s): O. Y. Shtark, Roman Puzanskiy, G. S. Avdeeva, Andrey P. Yurkov, Galina Smolikova, Vladislav V. Yemelyanov, Marina S. Kliukova, А. Л. Шаварда, А. А. Кирпичникова, А. И. Жернаков, Alexey М. Afonin, И. А. Тихонович, В. А. Жуков, М. Ф. Шишова
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0201830

Exposure to a firefighting overhaul environment without respiratory protection increases immune dysregulation and lung disease risk
Cited by: 14
Author(s): Stephen J. Gainey, Gavin P. Horn, Albert E. Towers, Maci L. Oelschlager, Vincent L. Tir, Jenny Drnevich, Kenneth W. Fent, Stephen Kerber, Denise L. Smith, Gregory G. Freund
Software Mentions: 7
Published: over 6 years ago

10.18632/aging.101912

The widespread increase in inter-individual variability of gene expression in the human brain with age
Cited by: 19
Author(s): Veronika R. Kedlian, Handan Melike Dönertaş, Janet M. Thornton
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pcbi.1006042

The Pathway Coexpression Network: Revealing pathway relationships
Cited by: 40
Author(s): Yered Pita-Juárez, Gabriel Altschuler, Sokratis Kariotis, Wenbin Wei, Katjuša Koler, Claire Green, Rudolph E. Tanzi, Winston Hide
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pone.0246695

Analysis of lung transcriptome in calves infected with Bovine Respiratory Syncytial Virus and treated with antiviral and/or cyclooxygenase inhibitor
Cited by: 5
Author(s): Maxim Lebedev, Heather McEligot, Victoria Mutua, Paul Walsh, Francisco R. Carvallo Chaigneau, Laurel J. Gershwin
Software Mentions: 6
Published: almost 4 years ago

10.3390/plants10061033

Metabolic Alterations in Pisum sativum Roots during Plant Growth and Arbuscular Mycorrhiza Development
Cited by: 13
Author(s): O. Y. Shtark, Roman Puzanskiy, G. S. Avdeeva, Vladislav V. Yemelyanov, А. Л. Шаварда, Daria A. Romanyuk, Marina S. Kliukova, А. А. Кирпичникова, И. А. Тихонович, Vladimir A. Zhukov, М. Ф. Шишова
Software Mentions: 6
Published: over 3 years ago

10.1186/s13321-020-00447-2

DTiGEMS+: drug–target interaction prediction using graph embedding, graph mining, and similarity-based techniques
Cited by: 54
Author(s): Maha A. Thafar, Rawan S. Olayan, Haitham Ashoor, Somayah Albaradei, Vladimir B. Bajic, Xin Gao, Takashi Gojobori, Magbubah Essack
Software Mentions: 6
Published: over 4 years ago

10.3389/fimmu.2018.01868

Silent Witness: Dual-Species Transcriptomics Reveals Epithelial Immunological Quiescence to Helminth Larval Encounter and Fostered Larval Development
Cited by: 11
Author(s): Friederike Ebner, Mathias Kuhring, Aleksandar Radonić, Ankur Midha, Bernhard Y. Renard, Susanne Hartmann
Software Mentions: 5
Published: over 6 years ago

10.3389/fimmu.2019.00527

Immunometabolic Signatures Predict Risk of Progression to Active Tuberculosis and Disease Outcome
Cited by: 37
Author(s): Fergal J. Duffy, January Weiner, Scott G. Hansen, David L. Tabb, Sara Suliman, Ethan Thompson, Jeroen Maertzdorf, Steven G. Smith, Gerard Tromp, Shreemanta K. Parida, Drew Dover, Michael K. Axthelm, Jayne S. Sutherland, Hazel M. Dockrell, Tom H. M. Ottenhoff, Thomas J. Scriba, Louis J. Picker, Gerhard Walzl, Stefan H. E. Kaufmann, Daniel E. Zak
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-018-5411-5

Bacterial and viral pathogen-associated molecular patterns induce divergent early transcriptomic landscapes in a bovine macrophage cell line
Cited by: 6
Author(s): Felix N. Toka, Kiera Dunaway, Felicia Smaltz, Lidia Szulc-Dąbrowska, Jenny Drnevich, Matylda Barbara Mielcarska, Magdalena Bossowska-Nowicka, Matthias Schweizer
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12859-017-1674-0

Ranking metrics in gene set enrichment analysis: do they matter?
Cited by: 47
Author(s): Joanna Żyła, Michał Marczyk, January Weiner, Joanna Polańska
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pgen.1008783

Conditional antagonism in co-cultures of Pseudomonas aeruginosa and Candida albicans: An intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics
Cited by: 23
Author(s): Georgia Doing, Katja Koeppen, Patricia Occipinti, Colleen E. Harty, Deborah A. Hogan
Software Mentions: 5
Published: over 4 years ago

10.3389/fnins.2016.00071

BBBomics-Human Blood Brain Barrier Transcriptomics Hub
Cited by: 28
Author(s): Krishna R. Kalari, Kevin J. Thompson, Asha Nair, Xiaojia Tang, Matthew A. Bockol, Navya Jhawar, Suresh Kumar Swaminathan, Val J. Lowe, Karunya K. Kandimalla
Software Mentions: 5
Published: over 8 years ago

10.3389/fmicb.2021.647977

Probiotic Yeasts and Vibrio anguillarum Infection Modify the Microbiome of Zebrafish Larvae
Cited by: 12
Author(s): Orlando Vargas, María Soledad Gutiérrez, Mario Caruffo, Benjamín Valderrama, Daniel A. Medina, Katherine García, Angélica Reyes-Jara, Mauricio Toro, Carmen G. Feijóo, Paola Navarrete
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.67714

The cryptic gonadotropin-releasing hormone neuronal system of human basal ganglia
Cited by: 13
Author(s): Katalin Skrapits, Miklós Sárvári, Imre Farkas, Balázs Göcz, Szabolcs Takács, Éva Rumpler, Viktória Váczi, Csaba Vastagh, Gergely Rácz, András Matolcsy, Norbert Solymosi, Szilárd Póliska, Blanka Tóth, Ferenc Erdélyi, Gábor Szabó, Michael D. Culler, Cécile Allet, Ludovica Cotellessa, Vincent Prévot, Paolo Giacobini, Erik Hrabovszky
Software Mentions: 5
Published: over 3 years ago

10.3390/cells10071821

Plasma Metabolome Profiling Identifies Metabolic Subtypes of Pancreatic Ductal Adenocarcinoma
Cited by: 8
Author(s): Ujjwal Mukund Mahajan, Ahmed Alnatsha, Qi Li, Bettina Oehrle, Florian Weiß, Matthias Sendler, Marius Distler, Waldemar Uhl, Tim Fahlbusch, Elisabetta Goni, Georg Beyer, Ansgar M. Chromik, M. Bahra, Fritz Klein, Christian Pilarsky, Robert Grützmann, Markus M. Lerch, Kirsten Lauber, Nicole Christiansen, Beate Kamlage, Ivonne Regel, Julia Mayerle
Software Mentions: 4
Published: over 3 years ago

10.3390/genes11090983

MicroRNAs Modulate the Pathogenesis of Alzheimer’s Disease: An In Silico Analysis in the Human Brain
Cited by: 12
Author(s): Agnese Gugliandolo, Luigi Chiricosta, Virginia Boccardi, Patrizia Mecocci, Placido Bramantı, Emanuela Mazzon
Software Mentions: 4
Published: over 4 years ago

10.3390/genes10100745

Differential Gene Expression in Articular Cartilage and Subchondral Bone of Neonatal and Adult Horses
Cited by: 4
Author(s): Ann M. Kemper, Jenny Drnevich, Molly E. McCue, Annette M. McCoy
Software Mentions: 4
Published: about 5 years ago

10.3389/fphys.2021.707116

Transcriptional Time Course After Rotator Cuff Tear
Cited by: 3
Author(s): Laura S Vasquez-Bolanos, Michael C. Gibbons, Severin Ruoss, Isabella T. Wu, Mario Vargas-Vila, Sydnee A Hyman, Mary C. Esparza, Donald C. Fithian, Joseph R. Lane, Anshuman Singh, Chanond A. Nasamran, Kathleen M. Fisch, Samuel R. Ward
Software Mentions: 4
Published: over 3 years ago

10.1038/s41419-020-2289-3

Oncogene-dependent function of BRG1 in hepatocarcinogenesis
Cited by: 21
Author(s): Pan Wang, Xinhua Song, Dan Cao, Kairong Cui, Jingxiao Wang, Kirsten Utpatel, Runze Shang, Haichuan Wang, Li Che, Matthias Evert, Keji Zhao, Diego F. Calvisi, Xin Chen
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2021.718297

Tight Adherence (Tad) Pilus Genes Indicate Putative Niche Differentiation in Phytoplankton Bloom Associated Rhodobacterales
Cited by: 14
Author(s): Ashley Isaac, Ben Francis, Rudolf Amann, Shady A. Amin
Software Mentions: 4
Published: over 3 years ago

10.3390/ijms17091426

Integrative Analysis of Metabolomic, Proteomic and Genomic Data to Reveal Functional Pathways and Candidate Genes for Drip Loss in Pigs
Cited by: 26
Author(s): Julia Welzenbach, Christiane Neuhoff, Hanna Heidt, Mehmet Ulaş Çınar, Christian Looft, K. Schellander, Ernst Tholen, Christine Große‐Brinkhaus
Software Mentions: 4
Published: about 8 years ago

10.1186/s40168-019-0724-4

Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight
Cited by: 65
Author(s): Peng Jiang, Stefan J. Green, George E. Chlipala, Fred W. Turek, Martha Hotz Vitaterna
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0232189

Investigating the epithelial barrier and immune signatures in the pathogenesis of equine insect bite hypersensitivity
Cited by: 10
Author(s): Iva Cvitaš, Simone Oberhänsli, Tosso Leeb, Martina Dettwiler, Eliane J. Müller, Rémy Bruggman, Eliane Marti
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0251396

Fullerenol changes metabolite responses differently depending on the iron status of cucumber plants
Cited by: 5
Author(s): Nikolai P. Bityutskii, Kirill L. Yakkonen, Roman Puzanskiy, Kseniia A. Lukina, А. Л. Шаварда, Konstantin N. Semenov
Software Mentions: 4
Published: over 3 years ago

10.1128/mSystems.00332-18

A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome
Cited by: 110
Author(s): Courtney R. Armour, Stephen Nayfach, Katherine S. Pollard, Thomas J. Sharpton
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-018-37284-1

A gene expression signature in developing Purkinje cells predicts autism and intellectual disability co-morbidity status
Cited by: 12
Author(s): Harry Clifford, Anna Dulneva, Chris P. Ponting, Wilfried Haerty, Esther B. E. Becker
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.5743

Effects of rheumatoid arthritis associated transcriptional changes on osteoclast differentiation network in the synovium
Cited by: 6
Author(s): Shilpa Harshan, Poulami Dey, Srivatsan Ragunathan
Software Mentions: 3
Published: about 6 years ago

10.3390/microorganisms9040760

Extended Evaluation of Viral Diversity in Lake Baikal through Metagenomics
Cited by: 10
Author(s): Tatyana V. Butina, Yu. S. Bukin, Ivan S. Petrushin, Alexey E. Tupikin, Мarsel R. Kabilov, С. И. Беликов
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0149640

Preferentially Expressed Antigen of Melanoma Prevents Lung Cancer Metastasis
Cited by: 14
Author(s): Quan Huang, Haifeng Wei, Zhipeng Wu, Lin Li, Liangfang Yao, Zhengwang Sun, Lei Li, Lin Zx, Wei Xu, Shuai Han, Wenjiao Cao, Yunfei Xu, Dianwen Song, Xianghong Yang, Jianru Xiao
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0186004

Inferring gene and protein interactions using PubMed citations and consensus Bayesian networks
Cited by: 11
Author(s): Anthony Deeter, Mark Dalman, Joseph Haddad, Zhong-Hui Duan
Software Mentions: 3
Published: about 7 years ago

10.3389/fcvm.2021.655869

AMPA-Type Glutamate Receptors Associated With Vascular Smooth Muscle Cell Subpopulations in Atherosclerosis and Vascular Injury
Cited by: 5
Author(s): Alessandro L Gallina, Urszula Rykaczewska, Robert Wirka, April S. Caravaca, Vladimir S. Shavva, Mohamad Youness, Glykeria Karadimou, Mariette Lengquist, Anton Razuvaev, Gabrielle Paulsson-Berne, Thomas Quertermous, Anton Gisterå, Stephen Malin, Laura Tarnawski, Ljubica Matic, Peder S. Olofsson
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-018-5417-z

The transcriptome landscape of the carcinogenic treatment response in the blind mole rat: insights into cancer resistance mechanisms
Cited by: 13
Author(s): Robert Altwasser, Arnon Paz, Abraham B. Korol, Irena Manov, Aaron Avivi, Imad Shams
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-017-3571-3

Understanding the response to endurance exercise using a systems biology approach: combining blood metabolomics, transcriptomics and miRNomics in horses
Cited by: 32
Author(s): Núria Mach, Yuliaxis Ramayo-Caldas, Allison Clark, Marco Moroldo, Céline Robert, Éric Barrey, Jesús Maria López, Laurence Le Moyec
Software Mentions: 3
Published: almost 8 years ago

10.3389/fped.2020.00032

Hydrolyzed Fat Formula Increases Brain White Matter in Small for Gestational Age and Appropriate for Gestational Age Neonatal Piglets
Cited by: 5
Author(s): Megan P. Caputo, Jennifer N. Williams, Jenny Drnevich, Emily C. Radlowski, Ryan J. Larsen, Bradley P. Sutton, Brian J. Leyshon, Jamal Hussain, Manabu Nakamura, Matthew J. Kuchan, Tapas Das, Rodney W. Johnson
Software Mentions: 3
Published: almost 5 years ago

10.1200/CCI.19.00097

Evidence-Based Network Approach to Recommending Targeted Cancer Therapies
Cited by: 7
Author(s): Jayaram Kancherla, Shruti Rao, Krithika Bhuvaneshwar, Rebecca B. Riggins, Robert A. Beckman, Subha Madhavan, Héctor Corrada Bravo, Simina M. Boca
Software Mentions: 3
Published: about 4 years ago

10.1155/2021/5596924

Gut Microbiota-Related Effects of Tanhuo Decoction in Acute Ischemic Stroke
Cited by: 22
Author(s): Qian Guo, Xiaoqing Jiang, Can Ni, Linjing Li, Li Chen, Yaqi Wang, Mo Li, Chunhui Wang, Li Gao, Huaiqiu Zhu, Juexian Song
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-020-3371-7

PANEV: an R package for a pathway-based network visualization
Cited by: 15
Author(s): Valentino Palombo, Marco Milanesi, Gabriella Sferra, Stefano Capomaccio, Sandy Sgorlon, Mariasilvia D’Andrea
Software Mentions: 3
Published: almost 5 years ago

10.7554/eLife.42866

The human gut chemical landscape predicts microbe-mediated biotransformation of foods and drugs
Cited by: 36
Author(s): Leah Guthrie, Sarah J. Wolfson, Libusha Kelly
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.14044

PRKAR2B plays an oncogenic role in the castration-resistant prostate cancer
Cited by: 20
Author(s): Jianjun Sha, Wei Xue, Baijun Dong, Jiahua Pan, Xiaorong Wu, Dong Liu, Dongming Liu, Yiran Huang
Software Mentions: 3
Published: almost 8 years ago

10.18632/oncotarget.24954

Similar expression profiles in CD34+ cells from chronic phase chronic myeloid leukemia patients with and without deep molecular responses to nilotinib
Cited by: 0
Author(s): Ami B. Patel, Thoralf Lange, Anthony D. Pomicter, Christopher J. Conley, Christina A. Harrington, Kimberly R. Reynolds, Todd W. Kelley, Thomas O’Hare, Michael W. Deininger
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-021-91560-1

Tumor metabolism and associated serum metabolites define prognostic subtypes of Asian hepatocellular carcinoma
Cited by: 7
Author(s): Yotsawat Pomyen, Anuradha Budhu, Jittiporn Chaisaingmongkol, Marshonna Forgues, Hien Dang, Mathuros Ruchirawat, Chulabhorn Mahidol, Xin Wei Wang
Software Mentions: 2
Published: over 3 years ago

10.1186/s11658-018-0120-2

Systematic analysis of genes involved in oral cancer metastasis to lymph nodes
Cited by: 22
Author(s): Xingâan Zhang, Lanfang Zhang, Xiaoyao Tan, Ying Li, Xiaojiao Han, Hua-dong Wang, Huawei Ming, Qiujiang Li, Kang Liu, Gang Feng
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0165581

Identification of Binding Targets of a Pyrrole-Imidazole Polyamide KR12 in the LS180 Colorectal Cancer Genome
Cited by: 10
Author(s): Jason Lin, Kiriko Hiraoka, Tomohiro Watanabe, Tony Kuo, Yoshinao Shinozaki, Atsushi Takatori, Nobuko Koshikawa, Anandhakumar Chandran, Joe Otsuki, Hiroshi Sugiyama, Paul Horton, Hiroki Nagase
Software Mentions: 2
Published: about 8 years ago

10.1038/srep28103

OncoScape: Exploring the cancer aberration landscape by genomic data fusion
Cited by: 9
Author(s): Andreas Schlicker, Magali Michaut, Rubayte Rahman, Lodewyk Wessels
Software Mentions: 2
Published: over 8 years ago

10.3390/cells8111367

Metabolic, Physiological, and Transcriptomics Analysis of Batch Cultures of the Green Microalga Chlamydomonas Grown on Different Acetate Concentrations
Cited by: 20
Author(s): Kenny A. Bogaert, Emilie Perez, Judith Rumin, Axel Giltay, Vincenzo Andrea Riggio, Nadine Coosemans, Michèle Radoux, Gauthier Eppe, R. D. Levine, Françoise Remacle, Claire Remacle
Software Mentions: 2
Published: about 5 years ago

10.1186/s12859-017-2006-0

Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data
Cited by: 144
Author(s): Anna Marco-Ramell, Magalí Palau-Rodriguez, Ania Alay, Sara Tulipani, Mireia Urpí-Sardà, Álex Sánchez-Plà, Cristina Andrés‐Lacueva
Software Mentions: 1
Published: almost 7 years ago

10.3390/molecules23071829

Decomposing the Mechanism of Qishen Granules in the Treatment of Heart Failure by a Quantitative Pathway Analysis Method
Cited by: 16
Author(s): Weiquan Ren, Sheng Gao, Huimin Zhang, Yinglu Ren, Xue Yu, Weili Lin, Shuzhen Guo, Ruixin Zhu, Wei Wang
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2020.627396

Identification of Common Genes and Pathways in Eight Fibrosis Diseases
Cited by: 29
Author(s): Chang Gu, Xin Shi, Xuening Dang, Jiafei Chen, Chunji Chen, Yumei Chen, Xufeng Pan, Tao Huang
Software Mentions: 1
Published: almost 4 years ago

10.3389/fbioe.2019.00339

Screening of Methylation Signature and Gene Functions Associated With the Subtypes of Isocitrate Dehydrogenase-Mutation Gliomas
Cited by: 14
Author(s): Xiaoyong Pan, Tao Zeng, Fei Yuan, Yuhang Zhang, Lei Chen, Liucun Zhu, Sibao Wan, Tao Huang, Yi Cai
Software Mentions: 1
Published: about 5 years ago

10.1042/BSR20211476

Tissue-based metabolomics reveals metabolic signatures and major metabolic pathways of gastric cancer with help of transcriptomic data from TCGA
Cited by: 6
Author(s): Ya Qin Wang, Wenchao Chen, Kun Li, Gang Wu, Wei Zhang, Pei Zhi, Si Qi Feng
Software Mentions: 1
Published: about 3 years ago

10.3390/metabo10110457

Towards a More Reliable Identification of Isomeric Metabolites Using Pattern Guided Retention Validation
Cited by: 13
Author(s): Tobias Opialla, Stefan Kempa, Matthias Pietzke
Software Mentions: 1
Published: about 4 years ago

10.1186/s13569-019-0112-7

Genomic aberrations in cell cycle genes predict progression of KIT-mutant gastrointestinal stromal tumors (GISTs)
Cited by: 24
Author(s): Michael C. Heinrich, Janice Patterson, Carol Beadling, Yuexiang Wang, Maria Dębiec‐Rychter, Barbara Dewaele, Christopher L. Corless, Anette Duensing, Chandrajit P. Raut, Brian P. Rubin, Tamás Ördög, Matt van de Rijn, Jerry Call, Thomas Mühlenberg, Jonathan A. Fletcher, Sebastian Bauer
Software Mentions: 1
Published: over 5 years ago

10.3389/fpls.2021.700555

Differential Contributions of MYCs to Insect Defense Reveals Flavonoids Alleviating Growth Inhibition Caused by Wounding in Arabidopsis
Cited by: 9
Author(s): Dandan Wang, Pai Li, Qiu-Yi Chen, Xueying Chen, Ziwei Yan, Muyang Wang, Ying‐Bo Mao
Software Mentions: 1
Published: over 3 years ago

10.1099/mgen.0.000229

A global genomic approach uncovers novel components for twitching motility-mediated biofilm expansion in Pseudomonas aeruginosa
Cited by: 15
Author(s): Laura M. Nolan, Cynthia B. Whitchurch, Lars Barquist, Marilyn Katrib, Christine J. Boinett, Matthew Mayho, David Goulding, Ian G. Charles, Alain Filloux, Julian Parkhill, Amy K. Cain
Software Mentions: 1
Published: about 6 years ago

10.3390/genes11111252

Transcriptome Analysis of Amyloodinium ocellatum Tomonts Revealed Basic Information on the Major Potential Virulence Factors
Cited by: 4
Author(s): Omkar Byadgi, Fabio Marroni, Ron P. Dirks, Michela Massimo, Donatella Volpatti, Marco Galeotti, Paola Beraldo
Software Mentions: 1
Published: about 4 years ago

10.1002/gcc.22439

Characterisation of the genomic landscape of<i>CRLF2</i>-rearranged acute lymphoblastic leukemia
Cited by: 44
Author(s): Lisa J. Russell, Lisa Jones, Amir Enshaei, Stefano Tonin, Sarra Ryan, Jeyanthy Eswaran, Sirintra Nakjang, Elli Papaemmanuil, José M. C. Tubío, Adele K. Fielding, Ajay Vora, Peter J. Campbell, Anthony V. Moorman, Christine J. Harrison
Software Mentions: 1
Published: almost 8 years ago

10.1093/molbev/msz134

The Impact of Protein Architecture on Adaptive Evolution
Cited by: 40
Author(s): Ana Filipa Moutinho, Fernanda Fontes Trancoso, Julien Y. Dutheil
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-60192-2

Transcriptome analyses reveal the synergistic effects of feeding and eyestalk ablation on ovarian maturation in black tiger shrimp
Cited by: 12
Author(s): Kanchana Sittikankaew, Wirulda Pootakham, Chutima Sonthirod, Duangjai Sangsrakru, Thippawan Yoocha, Jutatip Khudet, Intawat Nookaew, Umaporn Uawisetwathana, Wanilada Rungrassamee, Nitsara Karoonuthaisiri
Software Mentions: 1
Published: over 4 years ago

Projects: bioconductor: KEGGREST

Papers Mentioning KEGGREST 75