Bioinformatics

In this topical collection (101 articles)

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1. Research

   PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues

   Sandeep Singh, Harinder Singh, Abhishek Tuknait, Kumardeep Chaudhary… Article:73

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2. Research

   Quantitative proteomics signature profiling based on network contextualization

   Wilson Wen Bin Goh, Tiannan Guo, Ruedi Aebersold, Limsoon Wong Article:71

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3. Research

   Prognostic value of cross-omics screening for kidney clear cell renal cancer survival

   Slavica Dimitrieva, Ralph Schlapbach, Hubert Rehrauer Article:68

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4. Research

   Inter-platform concordance of gene expression data for the prediction of chemical mode of action

   Chathura Siriwardhana, Susmita Datta, Somnath Datta Article:67

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5. Research

   Sensitivity, specificity, and reproducibility of RNA-Seq differential expression calls

   Paweł P. Łabaj, David P. Kreil Article:66

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6. Research

   Exploring the importance of cancer pathways by meta-analysis of differential protein expression networks in three different cancers

   Sinjini Sikdar, Somnath Datta, Susmita Datta Article:65

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7. Research

   xHMMER3x2: Utilizing HMMER3’s speed and HMMER2’s sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation

   Choon-Kong Yap, Birgit Eisenhaber, Frank Eisenhaber, Wing-Cheong Wong Article:63

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8. Review

   RNA motif discovery: a computational overview

   Avinash Achar, Pål Sætrom Article:61

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9. Research

   The human disease network in terms of dysfunctional regulatory mechanisms

   Jing Yang, Su-Juan Wu, Wen-Tao Dai, Yi-Xue Li, Yuan-Yuan Li Article:60

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10. Research

    MicroRNA-derived network analysis of differentially methylated genes in schizophrenia, implicating GABA receptor B1 [GABBR1] and protein kinase B [AKT1]

    Vadim Gumerov, Hedi Hegyi Article:59

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11. APPLICATION NOTE

    CLIP-GENE: a web service of the condition specific context-laid integrative analysis for gene prioritization in mouse TF knockout experiments

    Benjamin Hur, Sangsoo Lim, Heejoon Chae, Seokjun Seo, Sunwon Lee… Article:57

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12. Research

    IPC – Isoelectric Point Calculator

    Lukasz P. Kozlowski Article:55

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13. Application note

    TMFoldWeb: a web server for predicting transmembrane protein fold class

    Dániel Kozma, Gábor E. Tusnády Article:54

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14. Application note

    KGCAK: a K-mer based database for genome-wide phylogeny and complexity evaluation

    Dapeng Wang, Jiayue Xu, Jun Yu Article:53

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15. Research

    Weighted-SAMGSR: combining significance analysis of microarray-gene set reduction algorithm with pathway topology-based weights to select relevant genes

    Suyan Tian, Howard H. Chang, Chi Wang Article:50

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16. Discovery notes

    Detection of a common chimeric transcript between human chromosomes 7 and 16

    Wenwen Fang, Yong Wei, Yibin Kang, Laura F Landweber Article:49

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17. Research

    “Phylogenetic and evolutionary analysis of functional divergence among Gamma glutamyl transpeptidase (GGT) subfamilies”

    Ved Vrat Verma, Rani Gupta, Manisha Goel Article:49

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18. Research

    modPDZpep: a web resource for structure based analysis of human PDZ-mediated interaction networks

    Neetu Sain, Debasisa Mohanty Article:48

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19. Research

    Comparative genomic analysis of the WRKY III gene family in populus, grape, arabidopsis and rice

    Yiyi Wang, Lin Feng, Yuxin Zhu, Yuan Li, Hanwei Yan, Yan Xiang Article:48

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20. Discovery notes

    AID/APOBEC cytosine deaminase induces genome-wide kataegis

    Artem G Lada, Alok Dhar, Robert J Boissy, Masayuki Hirano… Article:47

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