WikiPathways: Pathway Editing for the People

Cited by (732)

Items 501–600 of 732

1. Bioinformatics for Dentistry: A secondary database for the genetics of tooth development
   Ava K. Chow, Rachel Low, Jerald Yuan, Karen K Yee, Jaskaranjit Kaur Dhaliwal, Shanice Govia, Nazlee Sharmin · 2024 · PLoS ONE
2. BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform
   Saikat Chowdhury, Noopur Sinha, Piyali Ganguli, Rupa Bhowmick, Vidhi Singh, Sutanu Nandi, Ram Rup Sarkar · 2018 · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics
3. Using Nanopublications to Detect and Explain Contradictory Research Claims
   Imran Asif, Ilaria Tiddi, Alasdair J. G. Gray · 2021 · IEEE International Conference on eScience
4. Using Biological Networks in Protein Function Prediction and Gene Expression Analysis
   Limsoon Wong · 2011 · Internet Mathematics
5. Social pathway annotation: extensions of the systems biology metabolic modelling assistant
   Ismael Navas‐Delgado, Alejandro Real-Chicharro, Miguel Ángel Medina, Francisca Sánchez‐Jiménez, José Francisco Aldana-Montes · 2010 · Briefings in Bioinformatics
6. Identifying Myc Interactors
   Romina Ponzielli, William B. Tu, Igor Jurišica, Linda Z. Penn · 2013 · Methods in molecular biology
7. Modeling Biological Systems Using Crowdsourcing
   Szymon Wąsik · 2018 · Foundations of Computing and Decision Sciences
8. Comparison of the effects of pachymic acid, moronic acid and hydrocortisone on the polysome loading of RNAs in lipopolysaccharide-treated THP-1 macrophages
   Tomohito Kakegawa, Lucia Satiko Yoshida, Mariko Takada, Mari Noguchi, Ken Yasukawa, Hiromi Takano‐Ohmuro · 2018 · Journal of Natural Medicines
9. Pathway Analysis for Cancer Research and Precision Oncology Applications
   Alessandro La Ferlita, Salvatore Alaimo, Alfredo Ferro, Alfredo Pulvirenti · 2022 · Advances in experimental medicine and biology
10. Molecular biology gets wikified
    Heidi K. Ledford · 2008 · Nature
11. Systems biomedicine of primary and metastatic colorectal cancer reveals potential therapeutic targets
    Mehran Piran, Mehrdad Piran, Neda Sepahi, Ali Ghanbariasad, Amir Rahimi · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
12. BioHackJP 2023 Report R3: Expand the pathway analysis environment to non-model organisms
    Alexander R. Pico, Hiromasa Ono, Ryo Nozu, Naoya Oec, Hidemasa U. Bono · 2023
13. The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data
    Taha Mohseni Ahooyi, Benjamin J. Stear, J. Alan Simmons, Vincent T. Metzger, Praveen Kumar, John Erol Evangelista, Daniel J. B. Clarke, Zhuorui Xie, Hee-Su Kim, Sherry L. Jenkins et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
14. Differential Protein-Coding Gene Expression Profile in Patients with Prostate Cancer
    Lorena Albarracín, Maylin Almonte Becerril, Enmanuel Isidoro Guerrero Quiroz, Josué Rivadeneira, Marcelino Telechea‐Fernández, Elizabeth Guzmán, Fanny Calderón, María José Hernández, Támara Otzen, Carlos Manterola et al. · 2024 · Biomedicines
15. Genomics guiding personalized first-line immunotherapy response in lung and bladder tumors
    Jenifer Brea Iglesias, María Gallardo‐Gómez, Ana Oitabén, Martín Lázaro-Quintela, Luis León‐Mateos, João M. Alves, Manuel Pino-González, Laura Juaneda‐Magdalena, Carmé García-Benito, Ihab Abdulkader et al. · 2025 · Journal of Translational Medicine
16. Drugst.One DREAM - Drug Repurposing through Expert Annotation and Modification
    Lisa Spindler, Johannes Kersting, Quirin Manz, Michael Hartung, Andreas Maier, Zeinab M. Mamdouh, Zina Piper, Ana Isabel Casas, Harald H.H.W. Schmidt, Jan Baumbach et al. · 2025 · British Journal of Pharmacology
17. Exploring the omnigenic architecture of selected complex traits
    Florin Ratajczak, Matthias Heinig, Pascal Falter‐Braun · 2025 · The American Journal of Human Genetics
18. Maternal medication use in pregnancy and offspring ASD risk: A prescription-wide, target-informed study
    Nina Zaks, Arad Kodesh, Nicole Zatorski, Yifan Wang, Stephen Z. Levine, Sven Sandin, Abraham Reichenberg, Avner Schlessinger, Magdalena Janecka · 2025 · European Psychiatry
19. Nanocitation: Complete and Interoperable Citations of Nanopublications
    Erika Fabris, Tobias Kuhn, Gianmaria Silvello · 2020 · Communications in computer and information science
20. RDFizing the biosynthetic pathway of E.coli O-antigen to enable semantic sharing of microbiology data
    Sunmyoung Lee, Tamiko Ono, Kiyoko Flora Aoki-Kinoshita · 2021 · BMC Microbiology
21. Metabolomics
    Peter Natesan Pushparaj · 2019 · Springer eBooks
22. Over-representation analysis of angiogenic factors in immunosuppressive mechanisms in neoplasms and neurological conditions during COVID-19
    Sujash S. Chatterjee, B.S. Sanjeev · 2023 · Microbial Pathogenesis
23. Hematopoiesis after anti-CD117 monoclonal antibody treatment in the settings of wild-type and Fanconi anemia mice
    Morgane Denis, Leah Swartzrock, Hana Willner, Quenton Rashawn Bubb, Ethan Haslett, Yan Yi Chan, Anzhi Chen, Mark R. Krampf, Agnieszka D. Czechowicz · 2024 · Haematologica
24. A machine learning framework for extracting information from biological pathway images in the literature
    Mun Su Kwon, Junkyu Lee, Hyun Uk Kim · 2024 · Metabolic Engineering
25. Explainable Machine Learning Models Using Robust Cancer Biomarkers Identification from Paired Differential Gene Expression
    Elisa Díaz de la Guardia‐Bolívar, Juan Emilio Martínez-Manjón, David Pérez-Filgueiras, Igor Jorge Sergio Zwir, Coral del Val · 2024 · International Journal of Molecular Sciences
26. Literature-Based Knowledge Discovery from Relationship Associations Based on a DL Ontology Created from MeSH
    Steven B. Kraines, Weisen Guo, Daisuke Hoshiyama, Takaki Makino, Haruo Mizutani, Yoshihiro Okuda, Yo Shidahara, Toshihisa Takagi · 2013 · Communications in computer and information science
27. A graphical models approach for comparing gene sets
    Maria Sofia Massa, Monica Chiogna, Chiara Romualdi · 2010 · Contributions to statistics
28. Multisource biological pathway consolidation
    Mark S. Doderer, Zachry Anguiano, Uthra Suresh, Dashnamoorthy Ravi, Alexander J.R. Bishop, Yidong Chen · 2011 · IEEE International Workshop on Genomic Signal Processing and Statistics
29. Emerging Applications of Metabolomics to Polyphenols and CVD Biomarker Discovery
    Rosa Vázquez‐Fresno, Sara Tulipani, Olha Khymenets, Mireia Urpí-Sardà, Mar Garcia‐Aloy, Montse Rabassa, María Boto‐Ordóñez, Maria Rotchés-Ribalta, Rafaël Llorach, Cristina Andrés‐Lacueva · 2013 · Polyphenols in Human Health and Disease
30. Quantitative Biological Models as Dynamic, User-Generated Online Content
    J. R. Lawson, Catherine M. Lloyd, Ting Yu, Poul F. Nielsen · 2009 · World Congress on Medical Physics and Biomedical Engineering, September 7 - 12, 2009, Munich, Germany
31. Processing of Mass Spectrometry Data in Clinical Applications
    Dario Di Silvestre, Pietro Brunetti, Pierluigi Mauri · 2012 · Translational bioinformatics
32. Bioinformatics Methods for Interpreting Toxicogenomics Data
    Kristina Maria Hettne, Jos C. S. Kleinjans, Rob H. Stierum, André Boorsma, Jan A. Kors · 2014 · Elsevier eBooks
33. Integrative Analysis of Proteomics Data to Obtain Clinically Relevant Markers
    Nathan Salomonis · 2017 · Methods in molecular biology
34. Incomplete autophagy and increased cholesterol synthesis during neuronal cell death caused by a synthetic cannabinoid, CP-55,940
    Hikari Tachibana, Moeka Nomura, Takeshi Funakoshi, Kana Unuma, Toshihiko Aki, Koichi Uemura · 2024 · NeuroToxicology
35. Using BioPAX-Parser (BiP) to Annotate Lists of Biological Entities with Pathway Data
    Giuseppe Agapito, Mario Cannataro · 2020 · Lecture notes in computer science
36. Visualization of omics data for systems
    Sean I O’Donoghue, Nitin S. Baliga, Alexander Goesmann, Matthew Hibbs, Hiroaki Kitano, Oliver Kohlbacher, Heiko Neuweger, Reinhard Schneider, Dan Tenenbaum, Anne‐Claude Gavin · 2010
37. A model of social collaboration in Molecular Biology knowledge bases
    Luna De Ferrari, Stuart Aitken, Igor Goryanin, Jano I. Van Hemert · 2009
38. Cataloguing and linking publicly available biomedical SPARQL endpoints for federation - addressing aPosteriori data integration
    Syed Muhammad Ali Hasnain · 2017 · Arrow@dit (Dublin Institute of Technology)
39. Data Processing, Metabolomic Databases and Pathway Analysis
    Oliver Fiehn, Tobias Kind, Dinesh Kumar Barupal · 2017 · Wiley eBooks
40. Comparative Multi-omic Mapping of Human Pancreatic Islet Endoplasmic Reticulum and Cytokine Stress Responses Provides Insights into Type 2 Diabetes Genetics
    Eishani Kumar Sokolowski, Romy Kursawe, Vijay Selvam, Redwan M. Bhuiyan, Asa Thibodeau, Chi George Zhao, Cassandra Nichole Spracklen, Duygu Ucar, Michael L. Stitzel · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
41. VIOLIN: A modular framework for scalable reconciliation of heterogeneous interaction graphs
    Haomiao Luo, Casey Hansen, Niloofar Arazkhani, Cheryl A. Telmer, Difei Tang, Gaoxiang Zhou, Peter Spirtes, Nataša Miškov-Živanov · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
42. Symphonies of metabolomics
    Denise Slenter · 2024
43. Oxytocin receptor controls promiscuity and development in prairie voles
    Ruchira Sharma, Kristen M. Berendzen, Amanda Everitt, Belinda Wang, Gina Williams, Shuyu Wang, Kara Quine, Rose Larios, Kimberly L. P. Long, Nerissa E. G. Hoglen et al. · 2025 · eLife
44. Enhancing schizophrenia phenotype prediction from genotype data through knowledge-driven deep neural network models
    Daniel Martins, Maryam Abbasi, Conceição Egas, Joel Perdiz Arrais · 2024 · Genomics
45. Unveiling Shared Gene Regulatory Networks and Pathways in Bipolar Disorder and Alzheimer’s Disease: Identifying Novel Therapeutic Targets and Drug Candidates
    Urmi Bose, Mehedi Hasan Rooman, Touhid Bhuiyan, Mohammad Sarwar Hossain Mollah, Md. Mehedi Hassan, Bikash Kumar Paul · 2024 · IEEE International Conference on Biomedical Engineering, Computer and Information Technology for Health (BECITHCON)
46. Unraveling LINE ‐1 retrotransposition in head and neck squamous cell carcinoma
    Jenifer Brea Iglesias, Ana Oitabén, Sonia Zumalave, Bernardo Rodríguez–Martín, María Gallardo‐Gómez, Martín Santamarina, Ana Pequeño‐Valtierra, Laura Juaneda‐Magdalena, Ramón García‐Escudero, José Luis López-Cedrún et al. · 2025 · Molecular Oncology
47. Decoding the transcriptome from bulk RNA of infection-naïve versus imprinted patients with SARS-CoV-2 Omicron B.1.1.529
    Sissy Therese Sonnleitner, Samira Walder, Eva Hinterbichler, Ludwig Knabl, Roswitha Poernbacher, Gernot Walder · 2025 · Microbiology Spectrum
48. Accumulation of Lymphoid Progenitors with Defective B Cell Differentiation and of Putative Natural Killer Progenitors in Aging Human Bone Marrow
    Laura Poisa-Beiro, Jonathan J. M. Landry, Aleksandr Cherdintsev, Michael Kardorff, Volker Eckstein, Laura Villacorta, Judith B. Zaugg, Anne‐Claude Gavin, Vladimı́r Beneš, Simon Raffel et al. · 2025 · International Journal of Molecular Sciences
49. Cell barcoding reveals lineage-dependent outcomes in hiPSC cardiac differentiation
    Sogu Sohn, Daylin Morgan, Cody J. Callahan, Katelyn Dockery, Amy Brock, Janet Zoldan · 2026 · Stem Cells
50. Comprehensive evaluation of plasma biomarkers in patients with abdominal aortic aneurysm using high-throughput, label-free quantitative proteomic profiling
    Merry L. Lindsey, Emily I. Chen, Pushkar Shivam, Pius N. Nde, David Horn, Santosh Renuse, Amirmansoor Hakimi, B. Timothy Baxter, Michael C. Terrin, Jon S. Matsumura et al. · 2025 · American Journal of Physiology-Heart and Circulatory Physiology
51. Aging promotes a RAGE-dependent increase in breast cancer metastasis
    Philip Miller, Sunita Chopra, Melinda Magna, Jiaxiang Tao, Carlos Benitez, Thomas Heist, Nanette Hahr Bishopric, Jeanne S. Mandelblatt, Julia Panov, Joyce M. Slingerland et al. · 2026 · Communications Biology
52. The Wnt signaling network in cancer
    Johanna Apfel-Starke, Jignesh R. Parikh, Patricia Reischmann, Rob M. Ewing, Oliver Josef Müller, Yu Xia, Isabel M. Dominguez · 2015 · Cambridge University Press eBooks
53. Comprehensive human membrane protein database
    Min‐Sung Kim, Gwan‐Su Yi · 2012 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
54. Wiki-Genome: A model-driven genome data management environment
    Martínez Ferrandis, A. Gandolfo Maria · 2012 · International Conference on Research Challenges in Information Science (RCIS)
55. Systemic Analysis of Regulated Functional Networks
    Luis Francisco Hernández Sánchez, Elise Aasebø, Frode Selheim, Frode S. Berven, Helge Ræder, Harald Barsnes, Marc Vaudel · 2015 · Methods in molecular biology
56. Metabolic Pathway Databases: A Word of Caution
    Miranda D. Stobbe · 2015 · Methods in pharmacology and toxicology
57. Modelling Molecular Mechanisms of Cancer Pathogenesis: Virtual Patients, Real Opportunities
    Hans Lehrach, Thomas Kessler, Lesley Ann Ogilvie, Moritz Schütte, Christoph Wierling · 2017 · Springer eBooks
58. Fundamentals of Mass Spectrometry-Based Metabolomics
    Emilio S. Rivera, Marissa A. Jones, Emma R. Guiberson, Jeremy L. Norris · 2020 · NATO science for peace and security series. A, Chemistry and biology
59. Databases and Bioinformatics Tools for Data Mining
    Pallabi Pati, Sushil Kumar Rathore, Manoj Kumar Gupta · 2021 · Springer eBooks
60. Comparative Analysis of 3D-Culture System for Murine Neonatal Heart Regeneration: A Systematic Approach for Big Gene Expression Data
    Julia Tzu-Ya Weng, Yi-Cheng Chen, Pei‐Chann Chang, Shin-Ping Huang, Yu-Wei Chiu · 2014 · Lecture notes in computer science
61. Development of a Secondary Dental-Specific Database for Active Learning of Genetics in Dentistry Programs
    Nazlee Sharmin, Ava K. Chow, Shanice Govia · 2022 · Healthcare Informatics Research
62. Growing Directed Acyclic Graphs: Optimization Functions for Pathway Reconstruction Algorithms
    Tunç Başar Köse, Jiarong Li, Anna Ritz · 2023 · Journal of Computational Biology
63. BMP4, SGSH, and SLC11A2 are Predicted to Be Biomarkers of Aging Associated with Programmed Cell Death
    Elif Kubat Öktem · 2023 · Journal of Molecular Neuroscience
64. Probing biological network in concurrent carcinomas and Type-2 diabetes for potential biomarker screening: An advanced computational paradigm
    Abdullah Al Marzan, Shatila Shahi, Md Sakil Arman, Md Zafrul Hasan, Ajit Ghosh · 2023 · Advances in Biomarker Sciences and Technology
65. Pathway Activation Analysis for Pan-Cancer Personalized Characterization Based on Riemannian Manifold
    Xingyi Li, Jun Hao, Junming Li, Zhelin Zhao, Xuequn Shang, Min Li · 2024 · International Journal of Molecular Sciences
66. Enhancers regulate genes linked to severe and mild childhood asthma
    Tahmina Akhter, Enrichetta Mileti, M. Kere, J. Kolmert, J. Konradsen, Gunilla Hedlin, E. Mélen, C. Daub · 2024 · Heliyon
67. Data tells the truth: A Knowledge distillation method for genomic survival analysis by handling censoring
    Xiu-Shen Wei, Heyang Xu, Ye Wu, Xiaoming Liu, Ruru Gao, Jiacheng Liu, Bowen Du · 2024 · Fundamental Research
68. Essential Cancer Proteins and Key Pathway Identification of Cancer through Bioinformatic Analysis
    Trilochan Rout, Anjali Mohapatra, Dillip Kumar Muduly, Madhabananda Kar · 2025 · Procedia Computer Science
69. Software Platform for Metabolic Network Reconstruction of Mycobacterium tuberculosis
    Samik Ghosh, Yukiko Matsuoka, Yoshiyuki Asai, Hiroaki Kitano, Anshu Bhardwaj, Vinod Scaria, Rohit Vashisht, Anup D. Shah, Anupam Kumar Mondal, Priti Vishnoi et al. · 2012 · Springer eBooks
70. Graph pattern mining techniques to identify potential model organisms
    Ahmed Ragab Nabhan · 2014 · ScholarWorks -A service of University of Vermont Libraries (University of Vermont)
71. Methodologies and Applications of Proteomics for Study of Yeast Strains: An Update
    Maria Priscila Franco Lacerda, M. Marcelino, Natália Manuela Strohmayer Lourencetti, Álvaro de Baptista Neto, Edwil Aparecida de Lucca Gattás, Maria José Soares Mendes‐Giannini, Ana Marisa Fusco‐Almeida · 2019 · Current Protein and Peptide Science
72. Data Quality Issues in Current Nanopublications
    Imran Asif, Yun-Heh Chen-Burger, Alasdair J. G. Gray · 2019 · International Conference on e-Science
73. Biological pathway analysis
    Mario Cannataro, Pietro Hiram Guzzi, Giuseppe Agapito, Chiara Zucco, Marianna Milano · 2022 · Elsevier eBooks
74. Data Mining of Plant Metabolic Pathways
    James N. D. Battey, Nikolai V. Ivanov · 2013 · Methods and principles in medicinal chemistry
75. Integrated analysis of variants and pathways in genome-wide association studies using polygenic models of disease
    Peter S. Carbonetto, Matthew Stephens · 2012 · arXiv (Cornell University)
76. WikiPathways: Community Curation of Biological Pathways
    Alexander R. Pico, Alexander R. Pico · 2010 · Nature Precedings
77. Text mining for metabolic reaction extraction from scientific literature
    Judith E. Risse · 2014
78. Connecting West and East
    Zhang · 2019
79. Role of genomic variants in the response to biologics targeting common autoimmune disorders
    Gordana Lenert · 2016
80. Dexamethasone modulate TWIST mediated EndMT changes in venous EC under acute shear stress. Implications for vein grafts disease
    Shameem S. Ladak, Liam W. McQueen, Kristina Tomkova, Adewale S. Adebayo, M.Saadeh Suleiman, Sarah J. George, Gavin James Murphy, Mustafa Zakkar · 2023 · medRxiv
81. Cell-autonomous GP130 activation suppresses prostate cancer development via STAT3/ARF/p53-driven senescence and confers an immune-active tumor microenvironment
    Christina Sternberg, Tanja Limberger, Martin Raigel, Karolína Trachtová, Michaela Schlederer, Desiree Lindner, Petra Kodajova, Jiaye Yang, Roman Ziegler, Heidi Anne Neubauer et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
82. Donor Age Impairs Vasculogenic Potential of hiPSC-Derived Endothelial Progenitors
    Bryce Larsen, Cody J. Callahan, Arshitha Rayanki, Sara Faulkner, Janet Zoldan · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
83. Inside the sequence universe: the amazing life of data and the people who look after them
    Tahani Nadim · 2012 · Goldsmiths (University of London)
84. Application of Semantic Web Technology to Establish Knowledge Management and Discovery in the Life Sciences
    Aravind Venkatesan · 2014 · NORA - Norwegian Open Research Archives
85. Functional networks of events that modulate phenotypic manifestation of cancer
    Sam Thiagalingam · 2015 · Cambridge University Press eBooks
86. Computational methods for analyzing complex high-throughput data from cancers
    Kristian Ovaska · 2014 · Työväentutkimus Vuosikirja
87. Biological Pathway Analysis: An Overview of Reactome and Other Integrative Pathway Knowledge Bases
    Robin Haw, Marc E. Gillespie, Michael A. Caudy · 2010
88. The etiology of hematologic malignancies in children and adolescents: Pre- and postnatal factors.
    Amy M. Linabery · 2010 · University of Minnesota Digital Conservancy (University of Minnesota)
89. Data Integration with Biological Pathways
    Martijn van Iersel · 2022
90. Applications of Systems Biology Approaches to Target Identification and Validation in Drug Discovery
    Bart S. Hendriks · 2011 · Wiley eBooks
91. Exploratory pathway analysis
    Thomas Kelder · 2011
92. GENOMIC AND TRANSCRIPTOME PROFILING OF EPITHELIAL OVARIAN CANCER
    Rebecca JZ Menzies, Yury V. Bukhman, Nancy F. L. Ng, Patricia Ann Shaw, Tak W. Mak · 2008 · Clinical and investigative medicine
93. Methods for the Analysis of Differential Composition of Gene Expression
    Emmanuel Dimont · 2015 · Digital Access to Scholarship at Harvard (DASH) (Harvard University)
94. Towards a semantic wiki for human and animal cell lines
    Paolo DM Romano, Dan M Bolser · 2013 · EMBnet journal
95. Improving the risk assessment of inherited breast and ovarian cancer : clinical significance of BRCA1/2 variants and risk modifiers
    Rita D. Brandão · 2012
96. Assembly of Logic-Based Diagrams of Biological Pathways
    Tom C. Freeman · 2010 · Systems biology
97. Simple Sequence Repeats in 5′ and 3′ Flanking Sequences of Cell Cycle Genes
    Seema Trivedi · 2013 · Springer eBooks
98. Automated seeding of specialised wiki knowledgebases with BioKb
    Jonathan R. Manning, Ann Hedley, John J. Mullins, Donald R. Dunbar · 2009 · BMC Bioinformatics
99. Concurrent Dynamic Visualizations With Expressive Petri Net Representations to Enrich the Understanding of Biological and Pathological Processes: an Application to Signaling Pathways
    F. Ramos, C. Hallal, A. Nieto, D. García, Jaime Berumen-Campos, David Escarcega · 2012 · Journal of Applied Research and Technology
100. Scientific Mashups: The Issue of Trust in the Aggregation of Web 2.0 Content
     Sara Javanmardi, Yasser Ganjisaffar, Cristina Lopes, Stanley Grant · 2015