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Reranking candidate gene models with cross-species comparison for improved gene prediction

Qian Liu, Koby Crammer, Fernando CN Pereira, David S Roos
2008 BMC Bioinformatics  
Conclusion: Reranking gene models with cross-species comparison improves gene prediction accuracy.  ...  For each gene locus, we first generate the K best candidate gene models using the gene finder Evigan, and then rerank these models using comparisons with putative orthologous genes from closely-related  ...  We also thank reviewers and editors for very helpful suggestions to make the paper better.  ... 
doi:10.1186/1471-2105-9-433 pmid:18854050 pmcid:PMC2587481 fatcat:t4qx6vmo3jdxnmvhz657u46bkq

An Information Theoretic Approach To Rescoring Peptides Produced By De Novo Peptide Sequencing

John R. Rose, James P. Cleveland, Alvin Fox
2010 Zenodo  
Protein mixtures possibly representing thousands of proteins from multiple species are treated with proteolytic enzymes, cutting the proteins into smaller peptides that are then analyzed generating MS/  ...  This in turn leads to higher accuracy in peptide prediction.  ...  The research was also suported by award #0959427 from the National Science Foundation The experiments were run on an SGI Altix 4700 system, with 128 computing cores and 256GB shared memory funded by NSF  ... 
doi:10.5281/zenodo.1070517 fatcat:crjasqlttvcgznwp3aibrqflim

Symptom-driven idiopathic disease gene identification

Bhuvan Molparia, Phillip H. Pham, Ali Torkamani
2015 Genetics in Medicine  
Conclusion: We have developed a method to prioritize candidate disease-causative genes based on symptoms that would be useful for both the prioritization of candidates and the identification of additional  ...  A recently described method, PHIVE, 35 uses cross-species phenotypic information to prioritize candidate genes in human sequencing studies.  ...  This process relies on the existence of model organisms with the appropriate candidate gene perturbed.  ... 
doi:10.1038/gim.2014.202 pmid:25590976 pmcid:PMC4861313 fatcat:y5hqvixg6nbatcaax745jkawfa

HPO-Shuffle, An Associated Gene Prioritization Strategy and Its Application in Drug Repurposing for the Treatment of Canine Epilepsy

Shuguang Wang, Xiangyu Meng, Yuxing Wang, Yemao Liu, Jingbo Xia
2019 Bioscience Reports  
After applying HPO-Shuffle, the association ranking of epilepsy genes were improved.  ...  In order to discover novel drugs for the treatment of canine epilepsy, multiomics data were analyzed to identify epilepsy associated genes.  ...  Minhui Deng for some early discussion, as well as Mr. Keming Yang, Mr. Songtao Chen and other audiences in HZAU BioNLP seminar for involvement in the long term discussion.  ... 
doi:10.1042/bsr20191247 pmid:31427480 pmcid:PMC6732366 fatcat:xisc7sa5evfbdjk73yphht4csi

A Systems Biology Approach to Transcription Factor Binding Site Prediction

Xiang Zhou, Pavel Sumazin, Presha Rajbhandari, Andrea Califano, Diego Di Bernardo
2010 PLoS ONE  
significant improvements in prediction accuracy.  ...  Recent reverse engineering methods deduce regulatory interactions from large-scale mRNA expression profiles and cross-species conserved regulatory regions in DNA.  ...  and for biochemical validation.  ... 
doi:10.1371/journal.pone.0009878 pmid:20360861 pmcid:PMC2845628 fatcat:6om6bfhyfzet7krboj7srotgqu

Dynamic programming re-ranking for PPI interactor and pair extraction in full-text articles

Richard Tsai, Po-Ting Lai
2011 BMC Bioinformatics  
The curation of such databases can be facilitated by employing textmining systems to identify genes which play the interactor role in PPIs and to map these genes to unique database identifiers (interactor  ...  Using our new re-ranking algorithm, we have been able to improve system performance (AUC iP/R) by 1.84%.  ...  We especially thank the BMC reviewers for their valuable comments, which helped us improve the quality of the paper.  ... 
doi:10.1186/1471-2105-12-60 pmid:21342534 pmcid:PMC3053256 fatcat:3ekq22twqnghxnoubz5pnzt4my

Linking genomics and metabolomics to chart specialized metabolic diversity

Justin J J van der Hooft, Hosein Mohimani, Anelize Bauermeister, Pieter C Dorrestein, Katherine R Duncan, Marnix H Medema
2020 Chemical Society Reviews  
One reason is the relatively low number of natural products with reference MS/MS data to train an appropriate spectral prediction model.  ...  Here, Global Natural Product Social (GNPS) molecular networking improved spectral comparison within and across samples. 11 In general, metabolites with a similar chemical architecture yield similar fragmentation  ... 
doi:10.1039/d0cs00162g pmid:32393943 fatcat:jjkyiefpsrdr5lpj5f6jjyyxnm

Prioritization of Cancer-Related Genomic Variants by SNP Association Network

Changning Liu, Zhenyu Xuan
2015 Cancer Informatics  
We found that random walk with restart (RWR) using SAN (RWR-SAN) can greatly improve the prediction of lung-cancer-associated genes by comparing RWR with the use of network in HPRD (AUC 0.81 vs 0.66).  ...  We used this network to further develop two methods for predicting and prioritizing disease-associated genes from genome-wide association studies (GWASs).  ...  Database (HPRD) network, the prediction based on SAN shows a significant improvement (AUC: 0.81 vs 0.66).  ... 
doi:10.4137/cin.s17288 pmid:25995611 pmcid:PMC4384763 fatcat:axncixzrrbbxpjmbm4akgit7xa

EILEEN: A recommendation system for scientific publications and grants [article]

Daniel E. Acuna, Kartik Nagre, Priya Matnani
2022 arXiv   pre-print
We describe EILEEN's architecture for ingesting and processing documents and modeling the recommendation system and keyphrase estimator.  ...  This article describes EILEEN (Exploratory Innovator of LitEraturE Networks), a recommendation system for scientific publications and grants with open source code and datasets.  ...  a model to rerank this initial set of candidates.  ... 
arXiv:2110.09663v2 fatcat:bbm2xa2nkzd7hds4l6a7yuqhk4

Pretrained Transformers for Text Ranking: BERT and Beyond

Andrew Yates, Rodrigo Nogueira, Jimmy Lin
2021 Proceedings of the 14th ACM International Conference on Web Search and Data Mining  
In the context of text ranking, these models produce high quality results across many domains, tasks, and settings.  ...  The goal of text ranking is to generate an ordered list of texts retrieved from a corpus in response to a query for a particular task.  ...  We'd like to thank the following people for comments on earlier drafts of this work: Maura Grossman, Sebastian Hofstätter, Xueguang Ma, and Bhaskar Mitra.  ... 
doi:10.1145/3437963.3441667 fatcat:6teqmlndtrgfvk5mneq5l7ecvq

BioCreative II Workshop Proceedings

Lynette, Martin, Alfonso
2007 Zenodo  
Conditional Random Fields and n-Gram Language Models for Gene Mention Recognition 85 Tackling the BioCreative2 Gene Mention task with Conditional Random Fields and Syntactic Parsing 89 Named Entity Recognition  ...  II Gene Mention Tagging System at IBM Watson 105 Rich Feature Set, Unifi cation of Bidirectional Parsing and Dictionary Filtering for High F-Score Gene Mention Tagging 109 High-Recall Gene Mention Recognition  ...  Acknowledgements We would like to thank Santiago Schnell for graciously providing us with additional proteomics related articles not containing protein-protein interaction information.  ... 
doi:10.5281/zenodo.4274543 fatcat:3sa3fvgngffjrblxzgswof42tq

A Common Dataset for Genomic Analysis of Livestock Populations

Matthew A. Cleveland, John M. Hickey, Selma Forni
2012 G3: Genes, Genomes, Genetics  
livestock species.  ...  This dataset was useful for comparing methods for genomic prediction using real data.  ...  In this situation, selection candidates can be genotyped for a small panel (e.g. ,1,000 SNP) and 60k genotypes imputed to improve the predictive power.  ... 
doi:10.1534/g3.111.001453 pmid:22540034 pmcid:PMC3337471 fatcat:kp3hpgicozanreofvqddbrc3hm

FLT3 inhibitor design using molecular docking based virtual screening for acute myeloid leukemia

Padmini Gokhale, In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore – 452010, Madhya Pradesh, India, Aashish Pratap Singh Chauhan, Anushka Arora, Natasha Khandekar, Anuraj Nayarisseri, Sanjeev Kumar Singh
2019 Bioinformation  
It is of interest to identify new compounds against FLT3 with improved activity using molecular docking and virtual screening.  ...  A comparative study of both the compounds using a drug-drug comparison, ADMET studies, boiled egg plot and pharmacophore parameters and properties confirmed the result and predicted the ligand to be an  ...  Comparative ADMET profile study of the compounds and the control A relative ADMET profile comparison was carried out for selected inhibitors by taking the predicted probability values of parameters such  ... 
doi:10.6026/97320630015104 pmid:31435156 pmcid:PMC6677903 fatcat:mpp3r5lthbaatmgbfiu3rjck3q

Peptide-Spectra Matching from Weak Supervision [article]

Samuel S. Schoenholz and Sean Hackett and Laura Deming and Eugene Melamud and Navdeep Jaitly and Fiona McAllister and Jonathon O'Brien and George Dahl and Bryson Bennett and Andrew M. Dai and Daphne Koller
2018 arXiv   pre-print
In particular, we achieve a 43% improvement over standard matching methods and a 10% improvement over a combination of the matching method and an industry standard cross-spectra reranking tool.  ...  Our resulting model is much better at identifying peptides with spectra than the model used to generate its training data.  ...  For each species we assemble a list of candidate peptides by direct enumeration.  ... 
arXiv:1808.06576v2 fatcat:ara5vlkdpje2nhcoigvnovzxha

MKRMDA: multiple kernel learning-based Kronecker regularized least squares for MiRNA–disease association prediction

Xing Chen, Ya-Wei Niu, Guang-Hui Wang, Gui-Ying Yan
2017 Journal of Translational Medicine  
Methods: In this work, we developed a novel computational model of multiple kernels learning-based Kronecker regularized least squares for MiRNA-disease association prediction (MKRMDA), which could reveal  ...  In another two kinds of case studies for new diseases without any known associated miRNAs and diseases only with known associations in HMDDv1.0 database, the verified ratios of two different cancers were  ...  Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.  ... 
doi:10.1186/s12967-017-1340-3 pmid:29233191 pmcid:PMC5727873 fatcat:nc2tpxmdxbdsbet5gqqn63jn7q
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