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ProTranslator: Zero-Shot Protein Function Prediction Using Textual Description ProTranslator:使用文本描述的零射击蛋白质功能预测
Annual International Conference on Research in Computational Molecular Biology Pub Date : 2022-04-20 DOI: 10.1007/978-3-031-04749-7_17
Hanwen Xu, Sheng Wang
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引用次数: 7
Fast, Flexible, and Exact Minimum Flow Decompositions via ILP 通过ILP快速，灵活和精确的最小流量分解
Annual International Conference on Research in Computational Molecular Biology Pub Date : 2022-01-26 DOI: 10.1007/978-3-031-04749-7_14
Fernando H. C. Dias, Lucia Williams, B. Mumey, Alexandru I. Tomescu
{"title":"Fast, Flexible, and Exact Minimum Flow Decompositions via ILP","authors":"Fernando H. C. Dias, Lucia Williams, B. Mumey, Alexandru I. Tomescu","doi":"10.1007/978-3-031-04749-7_14","DOIUrl":"https://doi.org/10.1007/978-3-031-04749-7_14","url":null,"abstract":"","PeriodicalId":160293,"journal":{"name":"Annual International Conference on Research in Computational Molecular Biology","volume":"148 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133057492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Safety and Completeness in Flow Decompositions for RNA Assembly RNA组装流程分解的安全性和完整性
Annual International Conference on Research in Computational Molecular Biology Pub Date : 2022-01-25 DOI: 10.1007/978-3-031-04749-7_11
Shahbaz Khan, Milla Kortelainen, Manuel O. C'aceres, Lucia Williams, Alexandru I. Tomescu
{"title":"Safety and Completeness in Flow Decompositions for RNA Assembly","authors":"Shahbaz Khan, Milla Kortelainen, Manuel O. C'aceres, Lucia Williams, Alexandru I. Tomescu","doi":"10.1007/978-3-031-04749-7_11","DOIUrl":"https://doi.org/10.1007/978-3-031-04749-7_11","url":null,"abstract":"","PeriodicalId":160293,"journal":{"name":"Annual International Conference on Research in Computational Molecular Biology","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121186510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 11
Joint Inference of Repeated Evolutionary Trajectories and Patterns of Clonal Exclusivity or Co-occurrence from Tumor Mutation Trees 肿瘤突变树的重复进化轨迹和克隆独占或共现模式的联合推断
Annual International Conference on Research in Computational Molecular Biology Pub Date : 2021-11-04 DOI: 10.1101/2021.11.04.467347
X. Luo, Jack Kuipers, N. Beerenwinkel
{"title":"Joint Inference of Repeated Evolutionary Trajectories and Patterns of Clonal Exclusivity or Co-occurrence from Tumor Mutation Trees","authors":"X. Luo, Jack Kuipers, N. Beerenwinkel","doi":"10.1101/2021.11.04.467347","DOIUrl":"https://doi.org/10.1101/2021.11.04.467347","url":null,"abstract":"Cancer progression is an evolutionary process shaped by both deterministic and stochastic forces. Multi-region and single-cell sequencing of tumors empower high-resolution reconstruction of the mutational history of each tumor. At the same time, it also highlights the extensive diversity across tumors and patients. Resolving the interactions among mutations and recovering the recurrent evolutionary processes may offer greater opportunities for successful therapeutic strategies. To this end, we present a novel probabilistic framework, called TreeMHN, for joint inference of repeated evolutionary trajectories and patterns of clonal exclusivity or co-occurrence from a cohort of intra-tumor phylogenetic trees. Through simulation studies, we show that TreeMHN outperforms existing alternatives that can only focus on one aspect of the task. By applying our method to an acute myeloid leukemia dataset, we find the most likely evolutionary trajectories and mutational patterns, consistent with and enriching known findings.","PeriodicalId":160293,"journal":{"name":"Annual International Conference on Research in Computational Molecular Biology","volume":"3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128571117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
MosaicFlye: Resolving Long Mosaic Repeats Using Long Reads 马赛克苍蝇:解决长马赛克重复使用长读取
Annual International Conference on Research in Computational Molecular Biology Pub Date : 2020-05-10 DOI: 10.1007/978-3-030-45257-5_16
A. Bankevich, P. Pevzner
{"title":"MosaicFlye: Resolving Long Mosaic Repeats Using Long Reads","authors":"A. Bankevich, P. Pevzner","doi":"10.1007/978-3-030-45257-5_16","DOIUrl":"https://doi.org/10.1007/978-3-030-45257-5_16","url":null,"abstract":"","PeriodicalId":160293,"journal":{"name":"Annual International Conference on Research in Computational Molecular Biology","volume":"9 15 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132559353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Bagging MSA Learning: Enhancing Low-Quality PSSM with Deep Learning for Accurate Protein Structure Property Prediction 袋装MSA学习:用深度学习增强低质量PSSM以准确预测蛋白质结构特性
Annual International Conference on Research in Computational Molecular Biology Pub Date : 2020-05-10 DOI: 10.1007/978-3-030-45257-5_6
Yuzhi Guo, Jiaxiang Wu, Hehuan Ma, Sheng Wang, Junzhou Huang
{"title":"Bagging MSA Learning: Enhancing Low-Quality PSSM with Deep Learning for Accurate Protein Structure Property Prediction","authors":"Yuzhi Guo, Jiaxiang Wu, Hehuan Ma, Sheng Wang, Junzhou Huang","doi":"10.1007/978-3-030-45257-5_6","DOIUrl":"https://doi.org/10.1007/978-3-030-45257-5_6","url":null,"abstract":"","PeriodicalId":160293,"journal":{"name":"Annual International Conference on Research in Computational Molecular Biology","volume":"28 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125180679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 12
PaccMannRL: Designing Anticancer Drugs From Transcriptomic Data via Reinforcement Learning 通过强化学习从转录组学数据设计抗癌药物
Annual International Conference on Research in Computational Molecular Biology Pub Date : 2020-05-10 DOI: 10.1007/978-3-030-45257-5_18
Jannis Born, Matteo Manica, Ali Oskooei, Joris Cadow, María Rodríguez Martínez
{"title":"PaccMannRL: Designing Anticancer Drugs From Transcriptomic Data via Reinforcement Learning","authors":"Jannis Born, Matteo Manica, Ali Oskooei, Joris Cadow, María Rodríguez Martínez","doi":"10.1007/978-3-030-45257-5_18","DOIUrl":"https://doi.org/10.1007/978-3-030-45257-5_18","url":null,"abstract":"","PeriodicalId":160293,"journal":{"name":"Annual International Conference on Research in Computational Molecular Biology","volume":"2009 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125597130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 14
Strain-Aware Assembly of Genomes from Mixed Samples Using Flow Variation Graphs 基于流量变异图的混合样本基因组的菌株感知组装
Annual International Conference on Research in Computational Molecular Biology Pub Date : 2020-05-10 DOI: 10.1007/978-3-030-45257-5_14
J. Baaijens, L. Stougie, A. Schönhuth
{"title":"Strain-Aware Assembly of Genomes from Mixed Samples Using Flow Variation Graphs","authors":"J. Baaijens, L. Stougie, A. Schönhuth","doi":"10.1007/978-3-030-45257-5_14","DOIUrl":"https://doi.org/10.1007/978-3-030-45257-5_14","url":null,"abstract":"","PeriodicalId":160293,"journal":{"name":"Annual International Conference on Research in Computational Molecular Biology","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116764576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 27
Multiple Competition-Based FDR Control and Its Application to Peptide Detection 基于多竞争的FDR控制及其在多肽检测中的应用
Annual International Conference on Research in Computational Molecular Biology Pub Date : 2020-05-10 DOI: 10.1007/978-3-030-45257-5_4
Kristen Emery, Syamand Hasam, William Stafford Noble, U. Keich
{"title":"Multiple Competition-Based FDR Control and Its Application to Peptide Detection","authors":"Kristen Emery, Syamand Hasam, William Stafford Noble, U. Keich","doi":"10.1007/978-3-030-45257-5_4","DOIUrl":"https://doi.org/10.1007/978-3-030-45257-5_4","url":null,"abstract":"","PeriodicalId":160293,"journal":{"name":"Annual International Conference on Research in Computational Molecular Biology","volume":"45 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121154645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 12
Deep Large-Scale Multi-task Learning Network for Gene Expression Inference 基因表达推理的深度大规模多任务学习网络
Annual International Conference on Research in Computational Molecular Biology Pub Date : 2020-05-10 DOI: 10.1007/978-3-030-45257-5_2
Kamran Ghasedi Dizaji, Wei Chen, Heng Huang
{"title":"Deep Large-Scale Multi-task Learning Network for Gene Expression Inference","authors":"Kamran Ghasedi Dizaji, Wei Chen, Heng Huang","doi":"10.1007/978-3-030-45257-5_2","DOIUrl":"https://doi.org/10.1007/978-3-030-45257-5_2","url":null,"abstract":"","PeriodicalId":160293,"journal":{"name":"Annual International Conference on Research in Computational Molecular Biology","volume":"25 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123329622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
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