MedKG: enabling drug discovery through a
unified biomedical knowledge graph.
Kumari M, Chauhan R, Garg P. Mol Divers. 2025 Mar 14. Online ahead of print.
PMID: 40085402
Web app: http://pitools.niper.ac.in/medkg/
BioMedGraphica: An All-in-One Platform for Biomedical Prior Knowledge and Omic Signaling Graph Generation. Zhang H, Liang S, Xu T, Li W, Huang D, Dong Y, Li G, Miller JP, Goedegebuure SP, Sardiello M, Cooper J, Buchser W, Dickson P, Fields RC, Cruchaga C, Chen Y, Province M, Payne P, Li F. bioRxiv [Preprint]. 2024 Dec 9:2024.12.05.627020. PMID: 39713411
HeteroKGRep: Heterogeneous Knowledge Graph based Drug Repositioning. Ceskoutsé RFT, Bomgni AB, Gnimpieba Zanfack DR, Agany DDM, Thomas BB, Zohim EG. Knowl Based Syst. 2024 Dec 3;305:112638. doi: 10.1016/j.knosys.2024.112638. PMID: 39610660
NetMedPy: A Python package for Large-Scale Network Medicine Screening. Aldana A, Sebek M, Ispirova G, Dorantes-Gilardi R, Barabási AL, Loscalzo J, Menichetti G. bioRxiv [Preprint]. 2024 Sep 8:2024.09.05.611537. doi: 10.1101/2024.09.05.611537. PMID: 39569139
Decoding the Foodome: Molecular Networks Connecting Diet and Health. Menichetti G, Barabási AL, Loscalzo J. Annu Rev Nutr. 2024 Aug;44(1):257-288. doi: 10.1146/annurev-nutr-062322-030557. PMID: 39207880
GutUDB: A comprehensive multiomics database for intestinal diseases.
Bao Y, Chen Y, Lin L, Li J, Liu X, Wang G, Li Y, Lin Y, Chen Y, Zhou L, Qi Y, Xie Y, Lin Z, Sun Z, Fan Y, Jiang J, Zhang F, Chen H, Chu J, Huang J, Chen X, Liang H, Liang S, An S. Imeta. 2024 Apr 27;3(3):e195. doi: 10.1002/imt2.195.
PMID: 38898990
Database: https://intestine.splicedb.net/
LanDis: the disease landscape explorer.
Caniza H, Cáceres JJ, Torres M, Paccanaro A.
Eur J Hum Genet. 2024 Jan 10. doi: 10.1038/s41431-023-01511-9. Online ahead of print.
PMID: 38200084
Web interface:
https://paccanarolab.org/landis/
BioKG: a comprehensive, large-scale biomedical knowledge graph for AI-powered, data-driven biomedical research.
Zhang Y, Sui X, Pan F, Yu K, Li K, Tian S, Erdengasileng A, Han Q, Wang W, Wang J, Wang J, Sun D, Chung H, Zhou J, Zhou E, Lee B, Zhang P, Qiu X, Zhao T, Zhang J.
bioRxiv. 2023 Dec 12:2023.10.13.562216. doi: 10.1101/2023.10.13.562216. Preprint.
PMID: 38168218
Web interface:
https://www.biokde.com/
Food4healthKG: Knowledge graphs for food recommendations based on gut microbiota and mental health. Fu C, Huang Z, van Harmelen F, He T, Jiang X. Artif Intell Med. 2023 Nov;145:102677. PMID: 37925207
BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs. Callaghan J, Xu CH, Xin J, Cano MA, Riutta A, Zhou E, Juneja R, Yao Y, Narayan M, Hanspers K, Agrawal A, Pico AR, Wu C, Su AI. Bioinformatics. 2023 Sep 14:btad570. doi: 10.1093/bioinformatics/btad570. PMID: 37707514
KG-Hub - Building and Exchanging Biological Knowledge Graphs. Caufield JH, Putman T, Schaper K, Unni DR, Hegde H, Callahan TJ, Cappelletti L, Moxon SAT, Ravanmehr V, Carbon S, Chan LE, Cortes K, Shefchek KA, Elsarboukh G, Balhoff J, Fontana T, Matentzoglu N, Bruskiewich RM, Thessen AE, Harris NL, Munoz-Torres MC, Haendel MA, Robinson PN, Joachimiak MP, Mungall CJ, Reese JT. Bioinformatics. 2023 Jun 30:btad418. doi: 10.1093/bioinformatics/btad418. PMID: 37389415
Hetnet connectivity search provides rapid insights into how biomedical entities are related. Himmelstein DS, Zietz M, Rubinetti V, Kloster K, Heil BJ, Alquaddoomi F, Hu D, Nicholson DN, Hao Y, Sullivan BD, Nagle MW, Greene CS. Gigascience. 2022 Dec 28;12:giad047. doi: 10.1093/gigascience/giad047. PMID: 37503959
Preprint:
Neuroscience needs Network Science.
Barabási DL, Bianconi G, Bullmore E, Burgess M, Chung S, Eliassi-Rad T, George D, Kovács IA, Makse H, Papadimitriou C, Nichols TE, Sporns O, Stachenfeld K, Toroczkai Z, Towlson EK, Zador AM, Zeng H, Barabási AL, Bernard A, Buzsáki G.
ArXiv. 2023 May 11:arXiv:2305.06160v2.
PMID: 37214134
Preprint:
BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs.
Callaghan J, Xu CH, Xin J, Cano MA, Riutta A, Zhou E, Juneja R, Yao Y, Narayan M, Hanspers K, Agrawal A, Pico AR, Wu C, Su AI.
ArXiv. 2023 Apr 18:arXiv:2304.09344v1.
PMID: 37131885
Website:
https://explorer.biothings.io/
Code:
https://github.com/biothings/biothings_explorer
Democratizing knowledge representation with BioCypher. Lobentanzer S, Aloy P, Baumbach J, Bohar B, Carey VJ, Charoentong P, Danhauser K, Doğan T, Dreo J, Dunham I, Farr E, Fernandez-Torras A, Gyori BM, Hartung M, Hoyt CT, Klein C, Korcsmaros T, Maier A, Mann M, Ochoa D, Pareja-Lorente E, Popp F, Preusse M, Probul N, Schwikowski B, Sen B, Strauss MT, Turei D, Ulusoy E, Waltemath D, Wodke JAH, Saez-Rodriguez J. Nat Biotechnol. 2023 Jun 19. PMID: 37337100
Drug repurposing: Known knowns to unknown unknowns - Network analysis of the repurposome. Cavalla D, Crichton G. Drug Discov Today. 2023 May 24:103639. PMID: 37236525
From Data to Wisdom: Biomedical Knowledge Graphs for Real-World Data Insights. Hänsel K, Dudgeon SN, Cheung KH, Durant TJS, Schulz WL. J Med Syst. 2023 May 17;47(1):65. PMID: 37195430
Effective holistic characterization of small molecule effects using heterogeneous biological networks. Mangione W, Falls Z, Samudrala R. Front Pharmacol. 2023 Apr 26;14:1113007. PMID: 37180722
Machine learning prediction of the degree of food processing. Menichetti G, Ravandi B, Mozaffarian D, Barabási AL. Nat Commun. 2023 Apr 21;14(1):2312. PMID: 37085506
Mpox Knowledge Graph: a comprehensive representation embedding chemical entities and associated biology of Mpox. Karki R, Gadiya Y, Zaliani A, Gribbon P. Bioinform Adv. 2023 Apr 3;3(1):vbad045. PMID: 37187795
Accelerating network layouts using graph neural networks. Both C, Dehmamy N, Yu R, Barabási AL. Nat Commun. 2023 Mar 21;14(1):1560. PMID: 36944640
The curse and blessing of abundance-the evolution of drug interaction databases and their impact on drug network analysis. Udrescu M, Ardelean SM, Udrescu L. Gigascience. 2022 Dec 28;12(1):giad011. PMID: 36892110
Defining the distance between diseases using SNOMED CT embeddings. Fu M, Yan Y, Olde Loohuis L, Chang TS. J Biomed Inform. 2023 Feb 2:104307. PMID: 36738869
Building a knowledge graph to enable precision medicine.
Chandak P, Huang K, Zitnik M.
Sci Data. 2023 Feb 2;10(1):67.
PMID: 36732524
Website: https://zitniklab.hms.harvard.edu/projects/PrimeKG
Code: https://github.com/mims-harvard/PrimeKG
Hetnet connectivity search provides rapid insights into how two biomedical entities are related. Himmelstein DS, Zietz M, Rubinetti V, Kloster K, Heil BJ, Alquaddoomi F, Hu D, Nicholson DN, Hao Y, Sullivan BD, Nagle MW, Greene CS. bioRxiv. 2023 Jan 7:2023.01.05.522941. Preprint. PMID: 36711546
Exploration and comparison of molecular mechanisms across diseases using MINERVA Net. Gawron P, Smula E, Schneider R, Ostaszewski M. Protein Sci. 2023 Feb;32(2):e4565. PMID: 36648161
Mining hidden knowledge: embedding models of cause-effect relationships curated from the biomedical literature. Krämer A, Green J, Billaud JN, Pasare NA, Jones M, Tugendreich S. Bioinform Adv. 2022 Apr 7;2(1):vbac022. PMID: 36699407
Time-aware Embeddings of Clinical Data using a Knowledge Graph. Soman K, Nelson CA, Cerono G, Baranzini SE. Pac Symp Biocomput. 2023;28:97-108. PMID: 36540968
A network medicine approach for identifying diagnostic and prognostic biomarkers and exploring drug repurposing in human cancer. Zhang L, Fan S, Vera J, Lai X. Comput Struct Biotechnol J. 2022 Nov 29;21:34-45. PMID: 36514340
A biomedical open knowledge network harnesses the power of AI to understand deep human biology. Baranzini SE, Börner K, Morris J, Nelson CA, Soman K, Schleimer E, Keiser M, Musen M, Pearce R, Reza T, Smith B, Herr BW 2nd, Oskotsky B, Rizk-Jackson A, Rankin KP, Sanders SJ, Bove R, Rose PW, Israni S, Huang S. AI Mag. 2022 Spring;43(1):46-58. PMID: 36093122
Research gaps and opportunities in precision nutrition: an NIH workshop report. Lee BY, Ordovás JM, et al. Am J Clin Nutr. 2022 Sep 2:nqac237. PMID: 36055772
Visualizing novel connections and genetic similarities across diseases using a network-medicine based approach. Ferolito B, do Valle IF, Gerlovin H, Costa L, Casas JP, Gaziano JM, Gagnon DR, Begoli E, Barabási AL, Cho K. Sci Rep. 2022 Sep 1;12(1):14914. PMID: 36050444
KG-Predict: A knowledge graph computational framework for drug repurposing. Gao Z, Ding P, Xu R. J Biomed Inform. 2022 Jul 12;132:104133. PMID: 35840060
The heterogeneous pharmacological medical biochemical network PharMeBINet.
Königs C, Friedrichs M, Dietrich T. Sci Data. 2022 Jul 11;9(1):393.
PMID: 35821017
Web app for database access:
https://pharmebi.net/#/
Comprehensive characterization of human-virus protein-protein interactions reveals disease comorbidities and potential antiviral drugs.
Li S, Zhou W, Li D, Pan T, Guo J, Zou H, Tian Z, Li K, Xu J, Li X, Li Y.
Comput Struct Biotechnol J. 2022 Mar 7;20:1244-1253.
PMID: 35356543
Website:
HVPPI (Human-Virus Protein-Protein Interaction) database
OpenCell: Endogenous tagging for the cartography of human cellular organization.
Cho NH, Cheveralls KC, Brunner AD, Kim K, Michaelis AC, Raghavan P, Kobayashi H, Savy L, Li JY, Canaj H, Kim JYS, Stewart EM, Gnann C, McCarthy F, Cabrera JP, Brunetti RM, Chhun BB, Dingle G, Hein MY, Huang B, Mehta SB, Weissman JS, Gómez-Sjöberg R, Itzhak DN, Royer LA, Mann M, Leonetti MD.
Science. 2022 Mar 11;375(6585):eabi6983.
PMID: 35271311
Website:
opencell.czbiohub.org
Task-driven knowledge graph filtering improves prioritizing drugs for repurposing. Ratajczak F, Joblin M, Ringsquandl M, Hildebrandt M. BMC Bioinformatics. 2022 Mar 4;23(1):84. PMID: 35246025
TransDiscovery: Discovering Biotransformation from Human Microbiota by Integrating Metagenomic and Metabolomic Data. Yan D, Cao L, Zhou M, Mohimani H. Metabolites. 2022 Jan 26;12(2):119. PMID: 35208194
Executable network of SARS-CoV-2-host interaction predicts drug combination treatments. Howell R, Clarke MA, Reuschl AK, Chen T, Abbott-Imboden S, Singer M, Lowe DM, Bennett CL, Chain B, Jolly C, Fisher J. NPJ Digit Med. 2022 Feb 14;5(1):18. PMID: 35165389
MIMOSA2: A metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data.
Noecker C, Eng A, Muller E, Borenstein E.
Bioinformatics. 2022 Jan 6:btac003.
PMID: 34999748
Web server: http://elbo-spice.cs.tau.ac.il/shiny/MIMOSA2shiny/
R package: http://www.borensteinlab.com/software_MIMOSA2.html
Human exposome assessment platform.
Merino Martinez R, Müller H, Negru S, Ormenisan A, Arroyo Mühr LS, Zhang X, Trier Møller F, Clements MS, Kozlakidis Z, Pimenoff VN, Wilkowski B, Boeckhout M, Öhman H, Chong S, Holzinger A, Lehtinen M, van Veen EB, Bała P, Widschwendter M, Dowling J, Törnroos J, Snyder MP, Dillner J.
Environ Epidemiol. 2021 Dec 3;5(6):e182. doi: 10.1097/EE9.0000000000000182.
PMID: 34909561
https://www.humanexposome.eu/about/
Combinatorial, additive and dose-dependent drug-microbiome associations. Forslund SK, Chakaroun R, Zimmermann-Kogadeeva M, et al. Nature. 2021 Dec;600(7889):500-505. doi: 10.1038/s41586-021-04177-9. PMID: 34880489
The RareDis corpus: A corpus annotated with rare diseases, their signs and symptoms.
Martínez-deMiguel C, Segura-Bedmar I, Chacón-Solano E, Guerrero-Aspizua S.
J Biomed Inform. 2021 Dec 5;125:103961.
PMID: 34879250
Data:
https://github.com/isegura/NLP4RARE-CM-UC3M
Reconciling Signaling Pathway Databases with Network Topologies.
Rubel T, Singh P, Ritz A.
Pac Symp Biocomput. 2022;27:211-222.
PMID: 34890150
Data: https://github.com/Reed-CompBio/pathway-reconciliation
Network medicine for disease module identification and drug repurposing with the NeDRex platform. Sadegh S, Skelton J, Anastasi E, Bernett J, Blumenthal DB, Galindez G, Salgado-Albarrán M, Lazareva O, Flanagan K, Cockell S, Nogales C, Casas AI, Schmidt HHHW, Baumbach J, Wipat A, Kacprowski T. Nat Commun. 2021 Nov 25;12(1):6848. PMID: 34824199
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, [...] Auffray C, Balling R, Schneider R; COVID-19 Disease Map Community. Mol Syst Biol. 2021 Oct;17(10):e10387. PMID: 34664389
Gut-microbiota-microglia-brain interactions in Alzheimer's disease: knowledge-based, multi-dimensional characterization. Wang Q, Davis PB, Qi X, Chen SG, Gurney ME, Perry G, Doraiswamy PM, Xu R. Alzheimers Res Ther. 2021 Oct 20;13(1):177. PMID: 34670619
Network neighbors of viral targets and differentially expressed genes in COVID-19 are drug target candidates. Zambrana C, Xenos A, Böttcher R, Malod-Dognin N, Pržulj N. Sci Rep. 2021 Sep 23;11(1):18985. PMID: 34556735
Bioaccumulation of therapeutic drugs by human gut bacteria. Klünemann M, Andrejev S, Blasche S, Mateus A, Phapale P, Devendran S, Vappiani J, Simon B, Scott TA, Kafkia E, Konstantinidis D, Zirngibl K, Mastrorilli E, Banzhaf M, Mackmull MT, Hövelmann F, Nesme L, Brochado AR, Maier L, Bock T, Periwal V, Kumar M, Kim Y, Tramontano M, Schultz C, Beck M, Hennig J, Zimmermann M, Sévin DC, Cabreiro F, Savitski MM, Bork P, Typas A, Patil KR. Nature. 2021 Sep;597(7877):533-538. PMID: 34497420
CADA: phenotype-driven gene prioritization based on a case-enriched knowledge graph.
Peng C, Dieck S, Schmid A, Ahmad A, Knaus A, Wenzel M, Mehnert L, Zirn B, Haack T, Ossowski S, Wagner M, Brunet T, Ehmke N, Danyel M, Rosnev S, Kamphans T, Nadav G, Fleischer N, Fröhlich H, Krawitz P.
NAR Genom Bioinform. 2021 Sep 3;3(3):lqab078. PMID: 34514393
– based on HPO and ClinVar; I didn't understand the details
Code and Data: https://github.com/Chengyao-Peng/CADA
Web service: https://cada.gene-talk.de/webservice/
Network-Based Identification and Experimental Validation of Drug Candidates Toward SARS-CoV-2 via Targeting Virus-Host Interactome. Fang J, Wu Q, Ye F, Cai C, Xu L, Gu Y, Wang Q, Liu AL, Tan W, Du GH. Front Genet. 2021 Sep 1;12:728960. PMID: 34539756
A network-based analysis of disease modules from a taxonomic perspective. Velardi P, Madeddu L, Grani G. IEEE J Biomed Health Inform. 2021 Aug 24;PP. PMID: 34428165
A multimodal framework for improving in silico drug repositioning with the prior knowledge from knowledge graphs. Xiong Z, Huang F, Wang Z, Liu S, Zhang W. IEEE/ACM Trans Comput Biol Bioinform. 2021 Aug 10; PMID: 34375284
Association predictions of genomics, proteinomics, transcriptomics, microbiome, metabolomics, pathomics, radiomics, drug, symptoms, environment factor, and disease networks: A comprehensive approach. Pan Y, Lei X, Zhang Y. Med Res Rev. 2021 Aug 4. doi: 10.1002/med.21847. PMID: 34346083
DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug-target interactions. Hinnerichs T, Hoehndorf R. Bioinformatics. 2021 Jul 28:btab548. PMID: 34320178
Can microbes combat neurodegeneration? Blacher E. Science 09 Jul 2021: Vol. 373, Issue 6551, pp. 172-173
The Transporter Classification Database (TCDB): recent advances. Saier MH Jr, Reddy VS, Tsu BV, Ahmed MS, Li C, Moreno-Hagelsieb G. Nucleic Acids Res. 2016 Jan 4;44(D1):D372-9. PMID: 26546518
Current status and future prospects of drug-target interaction prediction. Ru X, Ye X, Sakurai T, Zou Q, Xu L, Lin C. Brief Funct Genomics. 2021 Jun 29:elab031. PMID: 34189559
Comparative effectiveness of medical concept embedding for feature engineering in phenotyping. Lee J, Liu C, Kim JH, Butler A, Shang N, Pang C, Natarajan K, Ryan P, Ta C, Weng C. JAMIA Open. 2021 Jun 16;4(2):ooab028. PMID: 34142015
Network Module-based Drug Repositioning for Pulmonary Arterial Hypertension. Wang RS, Loscalzo J. CPT Pharmacometrics Syst Pharmacol. 2021 Jun 16. PMID: 34132494
Assembling Disease Networks From Causal Interaction Resources. Cesareni G, Sacco F, Perfetto L. Front Genet. 2021 Jun 11;12:694468. PMID: 34178043
DeepR2cov: deep representation learning on heterogeneous drug networks to discover anti-inflammatory agents for COVID-19. Wang X, Xin B, Tan W, Xu Z, Li K, Li F, Zhong W, Peng S. Brief Bioinform. 2021 Jun 11:bbab226. PMID: 34117734
DrugComb update: a more comprehensive drug sensitivity data repository and analysis portal.
Zheng S, Aldahdooh J, Shadbahr T, Wang Y, Aldahdooh D, Bao J, Wang W, Tang J.
Nucleic Acids Res. 2021 Jun 1:gkab438.
PMID: 34060634
Website:
https://drugcomb.org/
A multiple network-based bioinformatics pipeline for the study of molecular mechanisms in oncological diseases for personalized medicine. Dotolo S, Marabotti A, Rachiglio AM, Esposito Abate R, Benedetto M, Ciardiello F, De Luca A, Normanno N, Facchiano A, Tagliaferri R. Brief Bioinform. 2021 May 28:bbab180.
A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization. Schultz B, Zaliani A, Ebeling C, Reinshagen J, Bojkova D, Lage-Rupprecht V, Karki R, Lukassen S, Gadiya Y, Ravindra NG, Das S, Baksi S, Domingo-Fernández D, Lentzen M, Strivens M, Raschka T, Cinatl J, DeLong LN, Gribbon P, Geisslinger G, Ciesek S, van Dijk D, Gardner S, Kodamullil AT, Fröhlich H, Peitsch M, Jacobs M, Hoeng J, Eils R, Claussen C, Hofmann-Apitius M. Sci Rep. 2021 May 26;11(1):11049.
Evaluating Disease Similarity Based on Gene Network Reconstruction and Representation. Li Y, Wang K, Wang G. Bioinformatics. 2021 May 12:btab252. PMID: 33978702
The DisGeNET cytoscape app: Exploring and visualizing disease genomics data. Piñero J, Saüch J, Sanz F, Furlong LI. Comput Struct Biotechnol J. 2021 May 11;19:2960-2967. PMID: 34136095
The Coronavirus Network Explorer: mining a large-scale knowledge graph for effects of SARS-CoV-2 on host cell function.
Krämer A, Billaud JN, Tugendreich S, Shiffman D, Jones M, Green J.
BMC Bioinformatics. 2021 May 3;22(1):229.
PMID: 33941085
Website: https://digitalinsights.qiagen.com/coronavirus-network-explorer
Target identification among known drugs by deep learning from heterogeneous networks. Zeng X, Zhu S, Lu W, Liu Z, Huang J, Zhou Y, Fang J, Huang Y, Guo H, Li L, Trapp BD, Nussinov R, Eng C, Loscalzo J, Cheng F. Chem Sci. 2020 Jan 13;11(7):1775-1797. PMID: 34123272
Current status and future perspectives of computational studies on human-virus protein-protein interactions.
Lian X, Yang X, Yang S, Zhang Z. Brief Bioinform. 2021 Mar 8:bbab029.
PMID: 33693490
–
Table 2 is a nice list of host-virus PPI databases, mostly human host
Large-scale metabolic interaction network of the mouse and human gut microbiota.
Lim R, Cabatbat JJT, Martin TLP, Kim H, Kim S, Sung J, Ghim CM, Kim PJ.
Sci Data. 2020 Jun 26;7(1):204.
PMID: 32591517
–
NJC19 network available as
JSON and cys
and in human-readable form in paper
online-only tables and
supplementary table
Knowledge graphs and their applications in drug discovery. MacLean F. Expert Opin Drug Discov. 2021 Apr 12:1-13. PMID: 33843398 Review.
Network medicine framework for identifying drug-repurposing opportunities for COVID-19.
Morselli Gysi D, do Valle Í, Zitnik M, Ameli A, Gan X, Varol O, Ghiassian SD, Patten JJ, Davey RA, Loscalzo J, Barabási AL.
Proc Natl Acad Sci U S A. 2021 May 11;118(19):e2025581118.
PMID: 33906951
–
already presented last year
[HTML slides] when it was a
preprint
Drug target ranking for glioblastoma multiforme. Saraf R, Agah S, Datta A, Jiang X. BMC Biomed Eng. 2021 Apr 26;3(1):7. PMID: 33902757
GADTI: Graph Autoencoder Approach for DTI Prediction From Heterogeneous Network. Liu Z, Chen Q, Lan W, Pan H, Hao X, Pan S. Front Genet. 2021 Apr 9;12:650821. doi: 10.3389/fgene.2021.650821. PMID: 33912218
The microbiome and human cancer. Sepich-Poore GD, Zitvogel L, Straussman R, Hasty J, Wargo JA, Knight R. Science. 2021 Mar 26;371(6536):eabc4552. PMID: 33766858 Review.
Development of a biomarker database toward performing disease classification and finding disease interrelations.
Hossain SF, Huang M, Ono N, Morita A, Kanaya S, Altaf-Ul-Amin M.
Database (Oxford). 2021 Mar 11;2021:baab011.
PMID: 33705530
–
Database: http://www.knapsackfamily.com/Biomarker/top.php
CMBD: a manually curated cancer metabolic biomarker knowledge database.
Chen J, Liu X, Shen L, Lin Y, Shen B.
Database (Oxford). 2021 Mar 9;2021:baaa094.
PMID: 33693668
–
Database: http://www.sysbio.org.cn/CMBD/
Drug repurposing for cancer treatment through global propagation with a greedy algorithm in a multilayer network. Cheng X, Zhao W, Zhu M, Wang B, Wang X, Yang X, Huang Y, Tan M, Li J. Cancer Biol Med. 2021 Apr 24:j.issn.2095-3941.2020.0218. PMID: 33893730
MultiVERSE: a multiplex and multiplex-heterogeneous network embedding approach. Pio-Lopez L, Valdeolivas A, Tichit L, Remy É, Baudot A. Sci Rep. 2021 Apr 22;11(1):8794. doi: 10.1038/s41598-021-87987-1. PMID: 33888761
KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response. Reese JT, Unni D, Callahan TJ, Cappelletti L, Ravanmehr V, Carbon S, Shefchek KA, Good BM, Balhoff JP, Fontana T, Blau H, Matentzoglu N, Harris NL, Munoz-Torres MC, Haendel MA, Robinson PN, Joachimiak MP, Mungall CJ. Patterns (N Y). 2021 Jan 8;2(1):100155. PMID: 33196056
A deep learning framework for high-throughput mechanism-driven phenotype compound screening and its application to COVID-19 drug repurposing. Pham TH, Qiu Y, Zeng J, Xie L, Zhang P. Nat Mach Intell. 2021 Mar;3(3):247-257. PMID: 33796820
The unmapped chemical complexity of our diet.
Barabási AL, Menichetti G, Loscalzo J.
Nature Food 2020;1:33–37.
–
https://github.com/fhooton/FoodMine
Identifying genes in published pathway figure images.
Riutta A, Hanspers K, Pico AR.
bioRxiv preprint 2018; doi: https://doi.org/10.1101/379446
Pathway information extracted from 25 years of pathway figures.
Hanspers K, Riutta A, Summer-Kutmon M, Pico AR.
Genome Biol. 2020 Nov 9;21(1):273. PMID: 33168034
Web app for searching/viewing the ~65K pathway figures:
https://gladstone-bioinformatics.shinyapps.io/shiny-25years
Presentation:
HTML slides
A bit off-topic but interesting:
A wealth of discovery built on the Human Genome Project - by the numbers.
Gates AJ, Gysi DM, Kellis M, Barabási AL.
Nature. 2021 Feb;590(7845):212-215.
PMID: 33568828
Integrated network analysis reveals new genes suggesting COVID-19 chronic effects and treatment. Pavel A, Del Giudice G, Federico A, Di Lieto A, Kinaret PAS, Serra A, Greco D. Brief Bioinform. 2021 Feb 11:bbaa417. Online ahead of print. PMID: 33569598
Gene co-expression in the interactome: moving from correlation toward causation via an integrated approach to disease module discovery. Paci P, Fiscon G, Conte F, Wang RS, Farina L, Loscalzo J. NPJ Syst Biol Appl. 2021 Jan 21;7(1):3. PMID: 33479222
Adverse Drug Reaction Discovery Using a Tumor-Biomarker Knowledge Graph. Wang M, Ma X, Si J, Tang H, Wang H, Li T, Ouyang W, Gong L, Tang Y, He X, Huang W, Liu X. Front Genet. 2021 Jan 12;11:625659. doi: 10.3389/fgene.2020.625659. PMID: 33584816
An analytical method for the identification of cell type-specific disease gene modules. Guan J, Lin Y, Wang Y, Gao J, Ji G. J Transl Med. 2021 Jan 6;19(1):20. PMID: 33407556
A novel similarity score based on gene ranks to reveal genetic relationships among diseases. Luo D, Zhang C, Fu L, Zhang Y, Hu YQ. PeerJ. 2021 Jan 6;9:e10576. PMID: 33505797
Network machine learning maps phytochemically rich "Hyperfoods" to fight COVID-19. Laponogov I, Gonzalez G, Shepherd M, Qureshi A, Veselkov D, Charkoftaki G, Vasiliou V, Youssef J, Mirnezami R, Bronstein M, Veselkov K. Hum Genomics. 2021 Jan 2;15(1):1. PMID: 33386081
MNBDR: A Module Network Based Method for Drug Repositioning. Chen HG, Zhou XH. Genes (Basel). 2020 Dec 27;12(1):E25. PMID: 33375395
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