Systematic Functional Annotation and Visualization of Biological Networks

Baryshnikova, Anastasia·2016·Cell Systems
DOI 10.1016/j.cels.2016.04.014

Cited by (157)

Items 101–157 of 157

  1. Drug repurposing for Leishmaniasis with Hyperbolic Graph Neural Networks
    Yenson Lau, Jahir M. Gutierrez, Maksims Volkovs, Saba Zuberi · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  2. A global genetic interaction map of a human cell reveals conserved principles of genetic networks
    Maximilian Billmann, Michael Costanzo, Xiang Zhang, Arshia Zernab Hassan, Mahfuzur Rahman, Kevin R. Brown, Katherine Chan, Amy H.Y. Tong, Carles Pons, Henry N. Ward et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  3. Time-resolved functional genomics using deep learning reveals global hierarchical control of autophagy
    Nathalia Chica, Aram Nikolai Andersen, Sara Orellana‐Muñoz, Ignacio Garcia, Aurélie Nguéa P, Sigve Nakken, Pilar Ayuda Durán, Linda Håkensbakken, Sebastian Wolfgang Schultz, Eline Rødningen et al. · 2026 · Nature Cell Biology
  4. Investigating the Network Basis of Negative Genetic Interactions in Saccharomyces cerevisiae with Integrated Biological Networks and Triplet Motif Analysis
    Chi Nam Ignatius Pang, Apurv Goel, Marc Ronald Wilkins · 2018 · Journal of Proteome Research
  5. A pan‐cancer integrative pathway analysis of multi‐omics data
    Henry Linder, Yuping Zhang · 2020 · Quantitative Biology
  6. Trigenic Synthetic Genetic Array (τ-SGA) Technique for Complex Interaction Analysis
    Elena Kuzmin, Brenda Andrews, Charles M. Boone · 2021 · Methods in molecular biology
  7. Genetic background and mistranslation frequency determine the impact of mistranslating tRNASerUGG
    Matthew D. Berg, Yanrui Zhu, Raphaël Loll‐Krippleber, Bryan-Joseph San Luis, Julie L. Genereaux, Charles M. Boone, Judit Villén, Grant W. Brown, Christopher J. Brandl · 2022 · G3 Genes Genomes Genetics
  8. A network view of human immune system and virus-human interaction
    Kang Lai Tang, Jing Yan Tang, Jinfeng Zeng, Wei Shen, Min Zou, Chi Zhang, Qianru Sun, Xiaoyan Ye, Chunwei Li, Caijun Sun et al. · 2022 · Frontiers in Immunology
  9. Replication Timing Networks: A Novel Class of Gene Regulatory Networks
    Juan Carlos Rivera‐Mulia, Sebo Kim, Haitham Gabr, Abhijit Chakraborty, Ferhat Ay, Tamer Kahveci, David M. Gilbert · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  10. Visualization of Biomedical Networks
    Anne-Christin Hauschild, Chiara Pastrello, Andrea E.M. Rossos, Igor Jurišica · 2018 · Elsevier eBooks
  11. MethylSight: Taking a wider view of lysine methylation through computer-aided discovery to provide insight into the human methyl-lysine proteome
    Kyle K. Biggar, Yasser B. Ruiz‐Blanco, François Charih, Qi Fang, Justin Connolly, Kristin Frensemier, Hemanta Adhikary, Shawn S.‐C. Li, James R. Green · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  12. Prioritizing network communities
    Marinka Žitnik, Rok Sosič, Jure Leskovec · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  13. Proteome-wide Prediction of Lysine Methylation Reveals Novel Histone Marks and Outlines the Methyllysine Proteome
    Kyle K. Biggar, François Charih, Huadong Liu, Yasser B. Ruiz‐Blanco, Leanne Stalker, Anand Chopra, Justin Connolly, Hemanta Adhikary, Kristin Frensemier, Marek Galka et al. · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  14. Robustness quantification of a mutant library screen revealed key genetic markers in yeast
    Cecilia Trivellin, Luca Torello Pianale, Lisbeth Olsson A · 2024 · Microbial Cell Factories
  15. The yeast guanine nucleotide exchange factor Sec7 is a bottleneck in spatial protein quality control and detoxifies neurological disease proteins
    Roja Babazadeh, Kara L. Schneider, Arthur Fischbach, Xinxin Hao, Beidong Liu, Thomas Nyström · 2023 · Scientific Reports
  16. Systematic identification of pleiotropic genes from genetic interactions
    Elizabeth N. Koch, Michael Costanzo, Raamesh Deshpande, Brenda Andrews, Charles M. Boone, Chad L. Myers · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  17. AMP-activated protein kinase and adenylate kinase prevent the ATP catastrophe and cytotoxic protein aggregation
    Masak Takaine, Hiromi Imamura, Satoshi Yoshida · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  18. Subgingival microbiota composition is associated with brain health in the general population–the PAROMIND study
    Marvin Petersen, Carolin Walther, Katrin Borof, Guido Heydecke, Thomas Beikler, Malik Alawi, Christian Müller, Felix L. Nägele, Birgit‐Christiane Zyriax, Jens Fiehler et al. · 2026 · EBioMedicine
  19. Gene–environment–brain topology reveals clinical subtypes of depression in UK Biobank
    Emma Tassi, Alessandro Pigoni, Nunzio Turtulici, Federica Colombo, Lidia Fortaner-Uyà, Anna Maria Bianchi, Francesco Benedetti, Chiara Fabbri, Benedetta Vai, Paolo Brambilla et al. · 2025 · Scientific Reports
  20. Computational Analysis of the Chaperone Interaction Networks
    Ashwani Kumar, Kamran Rizzolo, Sandra Zilles, Mohan Babu, Walid A. Houry · 2017 · Methods in molecular biology
  21. Construction of Functional Protein Networks Using Domain Profile Associations
    Jung Eun Shim, Insuk Lee · 2019 · Methods in molecular biology
  22. Towards an Integrated Map of Genetic Interactions in Cancer Cells
    Benedikt Rauscher, Florian Heigwer, Luisa Henkel, Thomas Hielscher, Oksana Voloshanenko, Michael Boutros · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  23. Master regulators of genetic interaction networks mediating statin drug response in Saccharomyces cerevisiae vary with genetic background
    Bede P. Busby, Eliatan Niktab, Christina A. Roberts, Namal Coorey, Jeffrey P. Sheridan, Dinindu Senanayake, Andrew B. Munkacsi, Paul H. Atkinson · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  24. Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability
    Mojca Mattiazzi Ušaj, Nil Sahin, Helena Friesen, Carles Pons, Matej Ušaj, Myra Paz David Masinas, Ermira Shuteriqi, Aleksei Shkurin, Patrick Aloy, Quaid Morris et al. · 2023
  25. High-Throughput Evolution Unravels Landscapes of High-Level Antibiotic Resistance Induced by Low-Level Antibiotic Exposure
    Hanqing Wang, Hui Lü, Chao Jiang, Lizhong Zhu, Huijie Lü · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  26. RISK: a next-generation tool for biological network annotation and visualization
    Ira Horecka, H. Röst · 2025 · Bioinform.
  27. Systems-level proteomic profiling reveals modular control of human cervical remodeling during pregnancy
    Yuguo Deng, Zhiguang Zhao, Hanbo Liu, Lu Wu, Yong Zhao, Jinying Yang · 2026 · Biology of Reproduction
  28. Enhancing the interpretability of the mapper algorithm
    Padraig Fitzpatrick, Anna Jurek, Paweł Dłotko · 2026 · Data Mining and Knowledge Discovery
  29. Multi-mode fiber enabled multi-wavelength optical trapping and dynamic manipulation
    Yikun Shen, Chuangye Zhang, Yuquan Zhang, Jiahui Pan, Siwei Chen, Hongyang Xu, Yixuan Chen, Qi Jin, Xiaocong Yuan, Changjun Min · 2026 · Optics & Laser Technology
  30. Topological Data Analysis Based Feature Selection for Predicting Fatigue Strength of Steel Using Machine Learning
    M A Joshi, Dhananjay Joshi · 2020 · IOP Conference Series Materials Science and Engineering
  31. CSN: unsupervised approach for inferring biological networks based on the genome alone
    Maya Galili, Tamir Tuller · 2020 · BMC Bioinformatics
  32. Unsupervised Discovery of Firm-Level Variables in Earnings Call Transcript Embeddings
    Daniel Edmiston, Ziho Park · 2020
  33. Approximate Pattern Matching using Hierarchical Graph Construction and Sparse Distributed Representation
    Aakanksha Mathuria · 2000
  34. Clinical stratification of Major Depressive Disorder in the UK Biobank: A gene-environment-brain Topological Data Analysis
    Emma Tassi, Alessandro Pigoni, Nunzio Turtulici, Federica Colombo, Lidia Fortaner-Uyà, Anna Maria Bianchi, Francesco Benedetti, Chiara Fabbri, Benedetta Vai, Paolo Brambilla et al. · 2024 · medRxiv
  35. Computational analysis of genetic interaction network structures and gene properties
    Elizabeth N. Koch · 2017 · University of Minnesota Digital Conservancy (University of Minnesota)
  36. tmap : topological analysis of population-scale microbiome data
    Tianhua Liao, Yuchen Wei, Mingjing Luo, Guoping Zhao, Haokui Zhou · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  37. Exostosin-1 Glycosyltransferase Regulates Endoplasmic Reticulum Architecture and Dynamics
    Despoina Kerselidou, B. Dohai, D. Nelson, Sarah Daakour, N. De Cock, Dae-Kyum Kim, Julien Olivet, Diana C. El Assal, Ashish Jaiswal, Deeya Saha et al. · 2020 · bioRxiv
  38. Profiling of Disease-Associated Proteins Neighborhood Networks
    Sheheeda Manakkadu, Sourav Dutta, Sam R. Thangiah · 2020
  39. Structural basis for targeting the human T-cell leukemia virus Tax oncoprotein and syntenin-1 interaction using a small molecule
    Sibusiso B. Maseko, Inge Van Molle, Karim Blibek, Christoph Gorgulla, Julien Olivet, Jérémy Blavier, Charlotte Vandermeulen, Stéphanie Skupiewski, Deeya Saha, Thandokuhle Ntombela et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  40. Faculty Opinions recommendation of Genomewide phenotypic analysis of growth, cell morphogenesis, and cell cycle events in Escherichia coli.
    Felipe Cava · 2021 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  41. Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability
    Mojca Mattiazzi Ušaj, Nil Sahin, Helena Friesen, Carles Pons, Matej Ušaj, Myra Paz David Masinas, Ermira Shuteriqi, Aleksei Shkurin, Patrick Aloy, Quaid Morris et al. · 2023
  42. Graphlet-based hyperbolic embeddings capture evolutionary dynamics in genetic networks
    Daniel Tello Velasco, Sam F. L. Windels, Mikhail Rotkevich, Noël Malod‐Dognin, Nataša Pržulj · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  43. Genetic interactions of schizophrenia using gene-based statistical epistasis exclusively identify nervous system-related pathways and key hub genes
    Sathish Periyasamy, P. Youssef, S. John, Rangaswamy Thara, Bryan Mowry · 2024 · Frontiers in Genetics
  44. Molecular and functional characterization of tubulin isotypes in budding yeast (Saccharomyces cerevisiae)
    Emmanuel T. Nsamba · 2021
  45. Truncating the spliceosomal ‘rope protein’ Prp45 results in Htz1 dependent phenotypes
    Kateřina Abrhámová, Martina Groušlová, Anna Valentová, Xinxin Hao, Beidong Liu, Martin Převorovský, Ondřej Gahura, František Půta, Per Sunnerhagen, Petr Folk · 2024 · RNA Biology
  46. A Computational Approach to Interpreting the Embedding Space of Dimension Reduction
    Bingyuan Zhang, Kohei Uno, Hayata Kodama, Koichi Himori, Yusuke Matsui · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  47. Visualization of Biomedical Networks
    Giuseppe Agapito, Pietro Cinaglia · 2024 · Elsevier eBooks
  48. Reconstruction of genomic and proteomic scale network structures and functions
    Jyoti Kant Choudhari, Abhinav Kumar Gupta, Shaifali Bhatt, Sonu Kurmi, Usha Chouhan · 2024 · Elsevier eBooks
  49. Oral microbiome profiles relate periodontal disease and brain health - the PAROMIND Study
    Marvin Petersen, Carolin Walther, Katrin Borof, Guido Heydecke, Thomas Beikler, Malik Alawi, Christian Müller, Felix Leonard Nägele, Birgit‐Christiane Zyriax, Jens Fiehler et al. · 2025 · medRxiv
  50. Perturbational fitness analysis of CRISPR screens uncovers information-theoretic relation between gene function and selection
    Aram Nikolai Andersen, Nathalia Chica, Laure Piechaczyk, Sigve Nakken, Manuela Zucknick, Jorrit M. Enserink · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  51. Proximity map for p53 unveils a strong link with PML Nuclear Bodies in HEK293 cells
    Edith De Bruycker, Giel Vandemoortele, Delphine De Sutter, George D. Moschonas, Sven Eyckerman · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  52. Additional file 1 of Robustness quantification of a mutant library screen revealed key genetic markers in yeast
    Cecilia Trivellin, Torello Pianale, Luca, Lisbeth Olsson A · 2024 · Figshare
  53. Discovering Glycosylation-Dependent Protein Function by Thermal Proteome Profiling
    Johannes F. Hevler, Mirat Sojitra, Tomislav Čaval, Michael Schoof, André Mateus, Carolyn Ruth Bertozzi · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  54. Mapping Parkinson’s Disease Progression through Deep Plasma Proteomics and Functional Genomics
    Ji‐Sun Kim, Chanhee Jeong, Maria Seo-Hyun Kim, Hye‐Yeon Kim, Seungmin Lee, Kyeong Beom Jo, Wen Luo, Irina Shlaifer, Su Hyeon Ha, Saba Sane et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  55. The Spatiotemporal Proteome Landscape of Aging: Structural determinants of age-sensitive proteome remodeling
    Seungmin Yoo, Lingraj Vannur, Liying Li, Christopher Young, Qingqing Liu, Zhihui Wen, Ying Zhang, Laurence A. Florens, Kausik Si, Junming Zhuang et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  56. Un nouveau modèle de protection de graphes : problème de l'ensemble de rebouclement éternel
    Nour Dyab · 2023
  57. Fluoroquinolones in Food-Producing Animals: A Natural Language Processing Analysis of Four Decades of Published Literature
    Nuwan Indika Millagaha Gedara, Lisa Ann Tell, Remya Ampadi Ramachandran, Jim Edmond Riviere, Raghavendra G G Amachawadi, Melissa A. Mercer, Douglas D. Shane, Majid Jaberi‐Douraki · 2026 · Antibiotics