GLiDe: a web-based genome-scale CRISPRi sgRNA design tool for prokaryotes.

Authors: Xiang, Tongjun^1,2 (AUTHOR), Feng, Huibao^1,3 (AUTHOR) fhb_14@163.com, Xing, Xin-hui^1,4,5 (AUTHOR), Zhang, Chong^1,4 (AUTHOR) chongzhang@tsinghua.edu.cn

Source: BMC Bioinformatics. 1/3/2025, Vol. 26 Issue 1, p1-14. 14p.

Subject Terms: *CRISPRS, *INTERNET servers, *ROBUST control, *QUALITY control, *BINDING sites

Meta-2OM: A multi-classifier meta-model for the accurate prediction of RNA 2′-O-methylation sites in human RNA.

Authors: Harun-Or-Roshid, Md.¹ (AUTHOR), Pham, Nhat Truong² (AUTHOR), Manavalan, Balachandran² (AUTHOR) kurata@bio.kyutech.ac.jp, Kurata, Hiroyuki¹ (AUTHOR) kurata@bio.kyutech.ac.jp

Source: PLoS ONE. 6/26/2024, Vol. 19 Issue 6, p1-27. 27p.

Subject Terms: *TRANSFER RNA, *INTERNET servers, *RNA modification & restriction, *MACHINE learning, *RNA, *NATURAL language processing, *SMALL nuclear RNA, *NATURAL immunity

m6A-TCPred: a web server to predict tissue-conserved human m⁶A sites using machine learning approach.

Authors: Tu, Gang¹ (AUTHOR), Wang, Xuan^1,2 (AUTHOR) xuan.wang@liverpool.ac.uk, Xia, Rong³ (AUTHOR), Song, Bowen⁴ (AUTHOR)

Source: BMC Bioinformatics. 3/25/2024, Vol. 25 Issue 1, p1-12. 12p.

Subject Terms: *INTERNET servers, *MACHINE learning, *EUKARYOTIC cells, *ONLINE databases, *ADENOSINES

High-throughput prediction of enzyme promiscuity based on substrate–product pairs.

Authors: Xing, Huadong¹ (AUTHOR), Cai, Pengli¹ (AUTHOR), Liu, Dongliang¹ (AUTHOR), Han, Mengying¹ (AUTHOR), Liu, Juan² (AUTHOR), Le, Yingying¹ (AUTHOR) qnhu@sibs.ac.cn, Zhang, Dachuan³ (AUTHOR) qnhu@sibs.ac.cn, Hu, Qian-Nan¹ (AUTHOR) qnhu@sibs.ac.cn

Source: Briefings in Bioinformatics. Mar2024, Vol. 25 Issue 2, p1-11. 11p.

Subject Terms: *INTERNET servers, *BASE pairs, *BIOENGINEERING, *ENZYMES, *SYNTHETIC biology, *TRANSFORMER models

Diff-AMP: tailored designed antimicrobial peptide framework with all-in-one generation, identification, prediction and optimization.

Authors: Wang, Rui¹ (AUTHOR), Wang, Tao¹ (AUTHOR), Zhuo, Linlin¹ (AUTHOR) zhuoninnin@163.com, Wei, Jinhang¹ (AUTHOR), Fu, Xiangzheng² (AUTHOR) zhuoninnin@163.com, Zou, Quan³ (AUTHOR) zhuoninnin@163.com, Yao, Xiaojun⁴ (AUTHOR) zhuoninnin@163.com

Source: Briefings in Bioinformatics. Mar2024, Vol. 25 Issue 2, p1-13. 13p.

Subject Terms: *ANTIMICROBIAL peptides, *INTERNET servers, *CONVOLUTIONAL neural networks, *PEPTIDE antibiotics, *REINFORCEMENT learning, *DEEP learning, *DRUG toxicity

CRISPRlnc: a machine learning method for lncRNA-specific single-guide RNA design of CRISPR/Cas9 system.

Authors: Yang, Zitian^1,2 (AUTHOR), Zhang, Zexin¹ (AUTHOR), Li, Jing¹ (AUTHOR), Chen, Wen³ (AUTHOR), Liu, Changning¹ (AUTHOR) liuchangning@xtbg.ac.cn

Source: Briefings in Bioinformatics. Mar2024, Vol. 25 Issue 2, p1-14. 14p.

Subject Terms: *INTERNET servers, *MACHINE learning, *RNA, *LINCRNA, *GENOME editing, *SUPPORT vector machines, *CRISPRS, *NUCLEIC acids

ImmuneMirror: A machine learning-based integrative pipeline and web server for neoantigen prediction.

Authors: Chuwdhury, Gulam Sarwar¹ (AUTHOR), Guo, Yunshan² (AUTHOR), Chiang, Chi-Leung¹ (AUTHOR), Lam, Ka-On¹ (AUTHOR), Kam, Ngar-Woon^1,3 (AUTHOR), Liu, Zhonghua⁴ (AUTHOR) weidai2@hku.hku, Dai, Wei^1,5 (AUTHOR) weidai2@hku.hku

Source: Briefings in Bioinformatics. Mar2024, Vol. 25 Issue 2, p1-12. 12p.

Subject Terms: *INTERNET servers, *SOMATIC mutation, *MAJOR histocompatibility complex, *RNA sequencing, *GASTROINTESTINAL cancer, *SQUAMOUS cell carcinoma

Anticipating protein evolution with successor sequence predictor.

Authors: Khan, Rayyan Tariq^1,2 (AUTHOR) rayyan.tariq.khan@gmail.com, Kohout, Pavel^1,2 (AUTHOR) pavel.kohout@recetox.muni.cz, Musil, Milos^1,2,3 (AUTHOR) imusilm@fit.vutbr.cz, Rosinska, Monika^1,3 (AUTHOR) rosinska.monika@email.cz, Damborsky, Jiri^1,2 (AUTHOR) jiri@chemi.muni.cz, Mazurenko, Stanislav^1,2 (AUTHOR) mazurenko@mail.muni.cz, Bednar, David^1,2 (AUTHOR) davidbednar1208@gmail.com

Source: Journal of Cheminformatics. 3/21/2025, Vol. 17 Issue 1, p1-12. 12p.

Subject Terms: *SEQUENCE spaces, *INTERNET servers, *AMINO acids, *EVOLUTIONARY models, *RESEARCH personnel, *PROTEIN engineering

Course time scheduling problem for distance education considering server load balancing: a case of an engineering faculty.

Authors: Alakaş, Hacı Mehmet¹ (AUTHOR) hmalagas@kku.edu.tr, Pınarbaşı, Mehmet¹ (AUTHOR), Sarımehmet, Bedirhan¹ (AUTHOR), Eren, Tamer¹ (AUTHOR)

Source: Neural Computing & Applications. Mar2025, Vol. 37 Issue 7, p5635-5653. 19p.

Subject Terms: *COVID-19 pandemic, *INTERNET servers, *SCHEDULING, *POLYNOMIAL time algorithms, *DISTANCE education

A comparative genomic approach to decipher the mutations associated with Nipah viral human isolates from southeast Asia.

Authors: Dsouza, Norine Norbert^1,2, Chellasamy, Selvaa Kumar¹ selvaakumar.c@dypatil.edu

Source: Iranian Journal of Microbiology. Feb2024, Vol. 16 Issue 1, p104-113. 10p.

Subject Terms: *INTERNET servers, *COMPARATIVE method, *NIPAH virus, *COMPARATIVE genomics, *GENETIC mutation, *EXTRACELLULAR matrix proteins, *METAGENOMICS

Geographic Terms: BANGLADESH, MALAYSIA

PredictEFC: a fast and efficient multi-label classifier for predicting enzyme family classes.

Authors: Chen, Lei¹ (AUTHOR) chen_lei1@163.com, Zhang, Chenyu¹ (AUTHOR), Xu, Jing¹ (AUTHOR)

Source: BMC Bioinformatics. 1/30/2024, Vol. 25 Issue 1, p1-27. 27p.

Subject Terms: *INTERNET servers, *ENZYMES, *RANDOM forest algorithms, *CLASSIFICATION algorithms, *STATISTICS, *FEATURE extraction, *FAMILIES, *DIMENSION reduction (Statistics)

A computational model of circRNA-associated diseases based on a graph neural network: prediction and case studies for follow-up experimental validation.

Authors: Niu, Mengting^1,2 (AUTHOR), Wang, Chunyu³ (AUTHOR), Zhang, Zhanguo⁴ (AUTHOR) 15136413177@163.com, Zou, Quan^5,6 (AUTHOR) zouquan@nclab.net

Source: BMC Biology. 1/29/2024, Vol. 22 Issue 1, p1-13. 13p.

Subject Terms: *INTERNET servers, *CIRCULAR RNA, *DEEP learning, *STOMACH cancer, *HEPATOCELLULAR carcinoma, *FORECASTING, *MULTIOMICS

PhyloString: A web server designed to identify, visualize, and evaluate functional relationships between orthologous protein groups across different phylogenetic lineages.

Authors: Dorantes-Torres, Claudia¹ (AUTHOR), Carrera-Reyna, Maricela¹ (AUTHOR), Santos, Walter¹ (AUTHOR), Sánchez-López, Rosana² (AUTHOR), Merino, Enrique¹ (AUTHOR) enrique.merino@ibt.unam.mx

Source: PLoS ONE. 1/26/2024, Vol. 19 Issue 1, p1-24. 24p.

Subject Terms: *INTERNET servers, *WEB design, *NUCLEIC acids, *DATABASES, *PROTEINS, *PROTEIN models

DisoFLAG: accurate prediction of protein intrinsic disorder and its functions using graph-based interaction protein language model.

Authors: Pang, Yihe¹ (AUTHOR), Liu, Bin^1,2 (AUTHOR) bliu@bliulab.net

Source: BMC Biology. 1/2/2024, Vol. 22 Issue 1, p1-15. 15p.

Subject Terms: *LANGUAGE models, *INTERNET servers, *PROTEIN models, *PROTEIN-protein interactions, *AMINO acid sequence, *PROTEINS

Drug–drug interaction prediction: databases, web servers and computational models.

Authors: Zhao, Yan¹ (AUTHOR), Yin, Jun¹ (AUTHOR), Zhang, Li¹ (AUTHOR), Zhang, Yong¹ (AUTHOR), Chen, Xing² (AUTHOR) xingchen@amss.ac.cn

Source: Briefings in Bioinformatics. Jan2024, Vol. 25 Issue 1, p1-28. 28p.

Subject Terms: *INTERNET servers, *DRUG interactions, *DRUG side effects, *WEB databases, *DRUG efficacy, *PREDICTION models

Identification of genetic associations and functional SNPs of bovine KLF6 gene on milk production traits in Chinese holstein.

Authors: Liu, Yanan¹ (AUTHOR), Han, Bo¹ (AUTHOR), Zheng, Weijie¹ (AUTHOR), Peng, Peng¹ (AUTHOR), Yang, Chendong² (AUTHOR), Jiang, Guie² (AUTHOR), Ma, Yabin² (AUTHOR), Li, Jianming² (AUTHOR), Ni, Junqing² (AUTHOR) 13803337871@163.com, Sun, Dongxiao¹ (AUTHOR) sundx@cau.edu.cn

Source: BMC Genomic Data. 11/28/2023, Vol. 24 Issue 1, p1-13. 13p.

Subject Terms: *INTERNET servers, *COMPOSITION of milk, *MILK yield, *SINGLE nucleotide polymorphisms, *PEROXISOME proliferator-activated receptors, *BINDING sites, *DAIRY cattle, *HOLSTEIN-Friesian cattle

SRplot: A free online platform for data visualization and graphing.

Authors: Tang, Doudou¹ (AUTHOR), Chen, Mingjie² (AUTHOR), Huang, Xinhua³ (AUTHOR), Zhang, Guicheng² (AUTHOR), Zeng, Lin² (AUTHOR), Zhang, Guangsen⁴ (AUTHOR), Wu, Shangjie¹ (AUTHOR), Wang, Yewei⁴ (AUTHOR) wangyewei@csu.edu.cn

Source: PLoS ONE. 11/9/2023, Vol. 18 Issue 11, p1-8. 8p.

Subject Terms: *INTERNET servers, *DATA visualization, *WEB browsers, *TEXT files

Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification.

Authors: Gautam, Anupam^1,2,3 (AUTHOR), Bhowmik, Debaleena^4,5 (AUTHOR), Basu, Sayantani⁶ (AUTHOR), Zeng, Wenhuan^1,7 (AUTHOR), Lahiri, Abhishake^5,8,9 (AUTHOR), Huson, Daniel H^1,2,3 (AUTHOR), Paul, Sandip⁹ (AUTHOR) sandipp@jisiasr.org

Source: Briefings in Bioinformatics. Nov2023, Vol. 24 Issue 6, p1-9. 9p.

Subject Terms: *INTERNET servers, *DATA integration, *BIOMARKERS, *ECOSYSTEM dynamics, *MICROBIAL communities, *MICROBIAL diversity, *METABOLOMICS

Experimental Study of Uncertainty in Comparing Time Scales of National Standards of Kazakhstan and Russia on the Internet Using NTP Servers.

Authors: Smagulov, S. B.^1,2 (AUTHOR) s.smagulov@ksm.kz, Mishagin, K. G.^3,4 (AUTHOR), Kagan, S. N.⁵ (AUTHOR), Semenov, S. A.⁵ (AUTHOR), Bolsynov, M. Y.¹ (AUTHOR), Zhumagali, A. K.^1,2 (AUTHOR)

Source: Russian Physics Journal. Sep2023, Vol. 66 Issue 5, p591-596. 6p.

Subject Terms: *INTERNET servers, *COMPUTER network protocols, *INTERNET, *CONSUMERS

Geographic Terms: KAZAKHSTAN, RUSSIA

Cancer multi-omics-based differential expression analysis and prognostic potential of identified hub targets of myco-metabolites for breast carcinoma and lung carcinoma.

Authors: Shreya, Singh^1,2 (AUTHOR), Mohapatra, Debadatta^1,3 (AUTHOR), Naik, Gaurav Gopal^1,4 (AUTHOR), Kathait, Pooja¹ (AUTHOR), Malang, Soki¹ (AUTHOR), Patel, Pradeep¹ (AUTHOR), Shambhavi¹ (AUTHOR), Alam, Gulzar² (AUTHOR), Sahu, Alakh N.¹ (AUTHOR) ansahu.phe@itbhu.ac.in

Source: Future Journal of Pharmaceutical Sciences. 2/5/2025, Vol. 11 Issue 1, p1-8. 8p.

Subject Terms: *INTERNET servers, *DEATH rate, *PROTEOMICS, *EPIDERMAL growth factor receptors, *CARCINOMA