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In This Issue

2002 Comparative and Functional Genomics  
approaches for mammalian systems and a solid-phase peptide tagging method for proteomics.  ...  Other recent papers have reported on a mechanism for genome size reduction in Arabidopsis, comparisons and verifications of large-scale protein-protein interaction datasets, developments in RNA interference  ...  approaches for mammalian systems and a solid-phase peptide tagging method for proteomics.  ... 
doi:10.1002/cfg.210 fatcat:4yem7bx62vhlhiric7gqwokory

Identification of Potential Biomarkers using Improved Ranked Guided Iterative Feature Elimination

Wen Xin Ng, Weng Howe Chan
2021 International Journal of Innovative Computing  
The performance of the classification is measured in terms of accuracy and compared with existing methods.  ...  Experiments are done using two gene expression datasets for prostate cancer and central nervous system.  ...  ACKNOWLEDGMENT The authors acknowledged Universiti Teknologi Malaysia (UTM) for providing the facilities and funding for this research.  ... 
doi:10.11113/ijic.v11n1.288 fatcat:mhefgch3vjakhdrwcnkbltym7u

Transcriptional Profiling of Host Cell Responses to Virulent Haemophilus parasuis: New Insights into Pathogenesis

Shulin Fu, Jing Guo, Ruizhi Li, Yinsheng Qiu, Chun Ye, Yu Liu, Zhongyuan Wu, Ling Guo, Yongqing Hou, Chien-An Hu
2018 International Journal of Molecular Sciences  
Our study provides new insights for understanding the interaction between bacterial and host cells, and analyzed, in detail, the possible mechanisms that lead to vascular damage induced by H. parasuis.  ...  The transcriptome results showed that when PAVECs were infected with H. parasuis for 24 h, 281 differentially expressed genes (DEGs) were identified; of which, 236 were upregulated and 45 downregulated  ...  The red genes were upregulated. 2. 4 . 4 Analysis of the Association among DEGs of the Main Pathways Using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) Figure 4 . 4 KEGG  ... 
doi:10.3390/ijms19051320 pmid:29710817 pmcid:PMC5983834 fatcat:hzwuvcwhdrehzcqsgwqufx36ua

Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society

Manuela Helmer-Citterich, Rita Casadio, Alessandro Guffanti, Giancarlo Mauri, Luciano Milanesi, Graziano Pesole, Giorgio Valle, Cecilia Saccone
2005 BMC Bioinformatics  
The BITS2005 Conference brought together about 200 Italian scientists working in the field of  ...  Acknowledgements We thank the Fondazione Giuliano Preparata for supporting this Supplement.  ...  We also thank the BMC Bioinformatics Editorial Office for their efficient and kind support.  ... 
doi:10.1186/1471-2105-6-s4-s1 fatcat:xnqmjj5nurendicaf4hbbde7ka

Comprehensive predictions of target proteins based on protein-chemical interaction using virtual screening and experimental verifications

Hiroki Kobayashi, Hiroko Harada, Masaomi Nakamura, Yushi Futamura, Akihiro Ito, Minoru Yoshida, Shun-ichiro Iemura, Kazuo Shin-ya, Takayuki Doi, Takashi Takahashi, Tohru Natsume, Masaya Imoto (+1 others)
2012 BMC Chemical Biology  
for identifying target proteins of small molecules.  ...  Results: We applied our protocol of predicting target proteins combining in silico screening and experimental verification for incednine, which inhibits the anti-apoptotic function of Bcl-xL by an unknown  ...  This work was also supported by Grant-in-Aid for Scientific Research (A) No.23241066 from the Ministry of Education, Culture, Sports, Science and Technology of Japan.  ... 
doi:10.1186/1472-6769-12-2 pmid:22480302 pmcid:PMC3471015 fatcat:maax3huuevhphjepyaqfmnoi7a

A Comprehensive Resource of Interacting Protein Regions for Refining Human Transcription Factor Networks

Etsuko Miyamoto-Sato, Shigeo Fujimori, Masamichi Ishizaka, Naoya Hirai, Kazuyo Masuoka, Rintaro Saito, Yosuke Ozawa, Katsuya Hino, Takanori Washio, Masaru Tomita, Tatsuhiro Yamashita, Tomohiro Oshikubo (+5 others)
2010 PLoS ONE  
Large-scale data sets of protein-protein interactions (PPIs) are a valuable resource for mapping and analysis of the topological and dynamic features of interactome networks.  ...  The core data set (966 IRs; 943 PPIs) displays a verification rate of 70%. Analysis of the IR data set revealed the existence of IRs that interact with multiple partners.  ...  Note that the verification rate of pull-down assays obtained for the IVV method represents a minimum value because the method detects both direct and indirect interactions [19] .  ... 
doi:10.1371/journal.pone.0009289 pmid:20195357 pmcid:PMC2827538 fatcat:wi3safho4jf4nbyhuofo3gdeaq

Effect of training datasets on support vector machine prediction of protein-protein interactions

Siaw Ling Lo, Cong Zhong Cai, Yu Zong Chen, Maxey C. M. Chung
2005 Proteomics  
The prediction results are consistent with observations, suggesting that real sequence is more practically useful in development of SVM classification system for facilitating protein-protein interaction  ...  The use of real protein sequences for training a SVM classification system is expected to give better prediction results in practical cases.  ...  The authors would like to thank Eivind Coward of the Department of Informatics, University of Bergen for sharing the shufflet sequence-randomizing code.  ... 
doi:10.1002/pmic.200401118 pmid:15717327 fatcat:zlfmb2e7w5bcvko5qpuaxb32hu

Extracting Biological Significant Subnetworks from Protein-Protein Interactions Induced by Differentially Expressed Genes of HIV-1 Vpr Variants

Bandana Barman, Anirban Mukhopadhyay
2015 International Journal of System Dynamics Applications  
Identification of protein interaction network is very important to find the cell signaling pathway for a particular disease.  ...  From the 172 differentially expressed genes the authors found protein-protein interaction network with string-db and then clustered (subnetworks) the PPI networks with cytoscape3.0.  ...  The statistical methods with comparing two Poisson means (rates) to detect differentially expressed genes for RNA-seq data (Chen, 2011) is introduced.  ... 
doi:10.4018/ijsda.2015100103 fatcat:up5jd2wkdvette44fraslbuxxy

Comprehensive Analysis of DNA Methylation and Transcriptome to Identify PD-1-Negative Prognostic Methylated Signature in Endometrial Carcinoma

Lu Cao, Xiaoqian Ma, Pengfei Rong, Juan Zhang, Min Yang, Wei Wang, Yang Mi
2022 Disease Markers  
Principal component analysis (PCA) and ROC analysis were conducted. The protein-drug interactions analysis of DMDGs was performed using Network Analyst 3.0 tool.  ...  Methods. Expression profile and methylation profile data of PD-1-negative EC samples were obtained from TCGA.  ...  Acknowledgments This study was supported in part by grants from the National Natural Science Foundation of China (81971721).  ... 
doi:10.1155/2022/3085289 pmid:35634444 pmcid:PMC9133896 fatcat:snzwzbghpfez3jih5e7dzekp4a


Jan Ramon, Fabrizio Costa, Christophe Costa Florencio, Joost Kok
2010 SIGKDD Explorations  
Modern experimentation and data acquisition techniques allow the study of complex interactions in biological systems.  ...  This raises interesting challenges for machine learning and data mining researchers, as the amount of data is huge, some information can not be observed, and measurements may be noisy.  ...  ACKNOWLEDGEMENTS This workshop is partially supported by the Fund for Scientific Research of Flanders. Jan Ramon is a post-doctoral fellow of the K.U.Leuven.  ... 
doi:10.1145/1809400.1809418 fatcat:djjcaumwonawpksoszbood34mm

Identification of Candidate Serum Proteins for Classifying Well-Differentiated Small Intestinal Neuroendocrine Tumors

Spyros Darmanis, Tao Cui, Kimi Drobin, Su-Chen Li, Kjell Öberg, Peter Nilsson, Jochen M. Schwenk, Valeria Giandomenico, Arun Sreekumar
2013 PLoS ONE  
Results: A set of 20 antibodies suggested promising proteins for further verification based on technically verified statistical significance.  ...  Materials and Methods: Suspension bead arrays targeting 124 unique proteins with antibodies from the Human Protein Atlas were used to profile biotinylated serum samples.  ...  Acknowledgments We thank the whole Biobank Profiling group at Science for Life Laboratory and the entire staff of the Human Protein Atlas for their efforts.  ... 
doi:10.1371/journal.pone.0081712 pmid:24282616 pmcid:PMC3839889 fatcat:p27srlhfxzgrrdmbzjr4umgk6q

Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D

Yun Niu, David Otasek, Igor Jurisica
2009 Computer applications in the biosciences : CABIOS  
Motivation: Identification and characterization of protein-protein interactions (PPIs) is one of the key aims in biological research.  ...  Results: We developed an interaction detection method and explored the usefulness of various features in automatically identifying PPIs in text.  ...  ACKNOWLEDGEMENTS We would like to acknowledge Richard Lu and Frederic Breard for supporting the I 2 D database, Max Kotlyar for providing the predicted interactions and Kevin R.  ... 
doi:10.1093/bioinformatics/btp602 pmid:19850753 pmcid:PMC2796811 fatcat:pns7ielz2zdczdp2ct3bwhtaoy

Discovery of circulating proteins associated to knee radiographic osteoarthritis

Lucía Lourido, Burcu Ayoglu, Juan Fernández-Tajes, Natividad Oreiro, Frauke Henjes, Cecilia Hellström, Jochen M. Schwenk, Cristina Ruiz-Romero, Peter Nilsson, Francisco J. Blanco
2017 Scientific Reports  
A panel consisting of these three proteins had an area under the curve of 0.82 for the classification of OA and control samples.  ...  A linear regression analysis adjusting for sex, age and body mass index (BMI) revealed that three proteins were significantly elevated (P < 0.05) in serum from OA patients compared to controls: C3, ITIH1  ...  Acknowledgements We thank the entire staff of the Human Protein Atlas for producing all the antibodies used in this study.  ... 
doi:10.1038/s41598-017-00195-8 pmid:28273936 pmcid:PMC5427840 fatcat:mhnh6ilmwzavplq555j34wjprq

DeepAcr: Predicting Anti-CRISPR with Deep Learning [article]

Yunxiang Li, Yumeng Wei, Qingxiong Tan, Licheng Zong, Yixuan Wang, Jiayang Chen, Yu Li
2022 bioRxiv   pre-print
As an important group of proteins discovered in phages, anti-CRISPR inhibits the activity of the immune system of bacteria (i.e., CRISPR-Cas), showing great potential for gene editing and phage therapy  ...  To tackle these issues, we propose a novel deep learning method for anti-CRISPR analysis (DeepAcr), which achieves impressive performance.  ...  We adopt the one-vs-rest strategy for AcRanker and PaCRISPR, converting binary classification methods to 5-class classification methods, and compare their performance on the class prediction problem with  ... 
doi:10.1101/2022.04.02.486820 fatcat:odboywqaiza3ne64mku3kocs6y

Information encoded in a network of inflammation proteins predicts clinical outcome after myocardial infarction

Francisco J Azuaje, Sophie Rodius, Lu Zhang, Yvan Devaux, Daniel R Wagner
2011 BMC Medical Genomics  
Methods: We assembled My-Inflamome, a network of protein interactions related to inflammation and prognosis in MI.  ...  Nevertheless, the systems-level characterization of inflammation proteins in MI remains incomplete.  ...  Acknowledgements and funding We thank Malou Gloesener, Loredana Jacobs, Céline Jeanty and Mélanie Vausort for technical assistance.  ... 
doi:10.1186/1755-8794-4-59 pmid:21756327 pmcid:PMC3152897 fatcat:kube6bqurrg37ipt5mstevjjne
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