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  3. Gene and protein interaction experiments provide unique opportunities to study the molecular wiring of a cell. Integrating high-throughput functional genomics data with this information can help identifying ne...

    Authors: Viola Fanfani, Fabio Cassano and Giovanni Stracquadanio

    Citation: BMC Bioinformatics 2020 21:476

    Content type: Software

    Published on:

  4. Single individual haplotype problem refers to reconstructing haplotypes of an individual based on several input fragments sequenced from a specified chromosome. Solving this problem is an important task in com...

    Authors: Fatemeh Zamani, Mohammad Hossein Olyaee and Alireza Khanteymoori

    Citation: BMC Bioinformatics 2020 21:475

    Content type: Methodology article

    Published on:

  5. Identifying frequently mutated regions is a key approach to discover DNA elements influencing cancer progression. However, it is challenging to identify these burdened regions due to mutation rate heterogeneit...

    Authors: Jing Zhang, Jason Liu, Patrick McGillivray, Caroline Yi, Lucas Lochovsky, Donghoon Lee and Mark Gerstein

    Citation: BMC Bioinformatics 2020 21:474

    Content type: Methodology article

    Published on:

  6. Phenotypes such as height and intelligence, are thought to be a product of the collective effects of multiple phenotype-associated genes and interactions among their protein products. High/low degree of intera...

    Authors: Mikhail G. Dozmorov, Kellen G. Cresswell, Silviu-Alin Bacanu, Carl Craver, Mark Reimers and Kenneth S. Kendler

    Citation: BMC Bioinformatics 2020 21:473

    Content type: Methodology article

    Published on:

  7. Optimality principles have been used to explain the structure and behavior of living matter at different levels of organization, from basic phenomena at the molecular level, up to complex dynamics in whole pop...

    Authors: Nikolaos Tsiantis and Julio R. Banga

    Citation: BMC Bioinformatics 2020 21:472

    Content type: Methodology article

    Published on:

  8. Microbial communities have become an important subject of research across multiple disciplines in recent years. These communities are often examined via shotgun metagenomic sequencing, a technology which can o...

    Authors: Alexander Eng, Adrian J. Verster and Elhanan Borenstein

    Citation: BMC Bioinformatics 2020 21:471

    Content type: Software

    Published on:

  9. Many studies prove that miRNAs have significant roles in diagnosing and treating complex human diseases. However, conventional biological experiments are too costly and time-consuming to identify unconfirmed m...

    Authors: Lei Zhang, Bailong Liu, Zhengwei Li, Xiaoyan Zhu, Zhizhen Liang and Jiyong An

    Citation: BMC Bioinformatics 2020 21:470

    Content type: Methodology article

    Published on:

  10. Common and complex traits are the consequence of the interaction and regulation of multiple genes simultaneously, therefore characterizing the interconnectivity of genes is essential to unravel the underlying ...

    Authors: Akram Yazdani, Raul Mendez-Giraldez, Azam Yazdani, Michael R. Kosorok and Panos Roussos

    Citation: BMC Bioinformatics 2020 21:469

    Content type: Research article

    Published on:

  12. Genomic profiling of solid human tumors by projects such as The Cancer Genome Atlas (TCGA) has provided important information regarding the somatic alterations that drive cancer progression and patient surviva...

    Authors: Xingyu Zheng, Christopher I. Amos and H. Robert Frost

    Citation: BMC Bioinformatics 2020 21:467

    Content type: Methodology article

    Published on:

  13. Homology based methods are one of the most important and widely used approaches for functional annotation of high-throughput microbial genome data. A major limitation of these methods is the absence of well-ch...

    Authors: Swati Sinha, Andrew M. Lynn and Dhwani K. Desai

    Citation: BMC Bioinformatics 2020 21:466

    Content type: Research article

    Published on:

  15. Genome browsers are widely used for locating interesting genomic regions, but their interactive use is obviously limited to inspecting short genomic portions. An ideal interaction is to provide patterns of reg...

    Authors: Arnaud Ceol, Piero Montanari, Ilaria Bartolini, Stefano Ceri, Paolo Ciaccia, Marco Patella and Marco Masseroli

    Citation: BMC Bioinformatics 2020 21:464

    Content type: Software

    Published on:

  16. Repetitive sequences account for a large proportion of eukaryotes genomes. Identification of repetitive sequences plays a significant role in many applications, such as structural variation detection and genom...

    Authors: Xingyu Liao, Xin Gao, Xiankai Zhang, Fang-Xiang Wu and Jianxin Wang

    Citation: BMC Bioinformatics 2020 21:463

    Content type: Methodology article

    Published on:

  18. Linkage disequilibrium (LD) analysis is broadly utilized in genetics to understand the evolutionary and demographic history and helps geneticists identify genes associated with interested inherited traits, suc...

    Authors: You Tang, Zhuo Li, Chao Wang, Yuxin Liu, Helong Yu, Aoxue Wang and Yao Zhou

    Citation: BMC Bioinformatics 2020 21:461

    Content type: Software

    Published on:

  20. High-throughput sequencing can establish the functional capacity of a microbial community by cataloging the protein-coding sequences (CDS) present in the metagenome of the community. The relative performance o...

    Authors: Jonathan Louis Golob and Samuel Schwartz Minot

    Citation: BMC Bioinformatics 2020 21:459

    Content type: Research article

    Published on:

  21. The pathogenesis of asthma is a complex process involving multiple genes and pathways. Identifying biomarkers from asthma datasets, especially those that include heterogeneous subpopulations, is challenging. P...

    Authors: Shaoke Lou, Tianxiao Li, Daniel Spakowicz, Xiting Yan, Geoffrey Lowell Chupp and Mark Gerstein

    Citation: BMC Bioinformatics 2020 21:457

    Content type: Research article

    Published on:

  24. MicroRNAs (miRNAs) are non-coding RNAs with regulatory functions. Many studies have shown that miRNAs are closely associated with human diseases. Among the methods to explore the relationship between the miRNA...

    Authors: Tian-Ru Wu, Meng-Meng Yin, Cui-Na Jiao, Ying-Lian Gao, Xiang-Zhen Kong and Jin-Xing Liu

    Citation: BMC Bioinformatics 2020 21:454

    Content type: Methodology article

    Published on:

  25. Bayesian factorization methods, including Coordinated Gene Activity in Pattern Sets (CoGAPS), are emerging as powerful analysis tools for single cell data. However, these methods have greater computational cos...

    Authors: Thomas D. Sherman, Tiger Gao and Elana J. Fertig

    Citation: BMC Bioinformatics 2020 21:453

    Content type: Software

    Published on:

  26. Any two unrelated people differ by about 20,000 missense mutations (also referred to as SAVs: Single Amino acid Variants or missense SNV). Many SAVs have been predicted to strongly affect molecular protein fun...

    Authors: Jiajun Qiu, Dmitrii Nechaev and Burkhard Rost

    Citation: BMC Bioinformatics 2020 21:452

    Content type: Research article

    Published on:

  27. DNA methylation is an important epigenetic modification that plays a critical role in most eukaryotic organisms. Parental alleles in haploid genomes may exhibit different methylation patterns, which can lead t...

    Authors: Qiangwei Zhou, Ze Wang, Jing Li, Wing-Kin Sung and Guoliang Li

    Citation: BMC Bioinformatics 2020 21:451

    Content type: Software

    Published on:

  28. The vast majority of microbiome research so far has focused on the structure of the microbiome at a single time-point. There have been several studies that measure the microbiome from a particular environment ...

    Authors: Toby Kenney, Junqiu Gao and Hong Gu

    Citation: BMC Bioinformatics 2020 21:450

    Content type: Research article

    Published on:

  29. Multimodal imaging that combines mass spectrometry imaging (MSI) with Raman imaging is a rapidly developing multidisciplinary analytical method used by a growing number of research groups. Computational tools ...

    Authors: Stefania Alexandra Iakab, Lluc Sementé, María García-Altares, Xavier Correig and Pere Ràfols

    Citation: BMC Bioinformatics 2020 21:448

    Content type: Software

    Published on:

  30. Recent studies have shown that N6-methyladenosine (m6A) plays a critical role in numbers of biological processes and complex human diseases. However, the regulatory mechanisms of most methylation sites remain unc...

    Authors: Lin Zhang, Shutao Chen, Jingyi Zhu, Jia Meng and Hui Liu

    Citation: BMC Bioinformatics 2020 21:447

    Content type: Research article

    Published on:

  31. Repertoire analysis of patient-derived recombinant monoclonal antibodies is an important tool to study the role of B cells in autoimmune diseases of the human brain and beyond. Current protocols for generation...

    Authors: S. Momsen Reincke, Harald Prüss and Jakob Kreye

    Citation: BMC Bioinformatics 2020 21:446

    Content type: Software

    Published on:

  32. As a machine learning method with high performance and excellent generalization ability, extreme learning machine (ELM) is gaining popularity in various studies. Various ELM-based methods for different fields ...

    Authors: Liang-Rui Ren, Ying-Lian Gao, Jin-Xing Liu, Junliang Shang and Chun-Hou Zheng

    Citation: BMC Bioinformatics 2020 21:445

    Content type: Methodology article

    Published on:

  35. Identification of genes responsible for anatomical entities is a major requirement in many fields including developmental biology, medicine, and agriculture. Current wet lab techniques used for this purpose, s...

    Authors: Pasan C. Fernando, Paula M. Mabee and Erliang Zeng

    Citation: BMC Bioinformatics 2020 21:442

    Content type: Methodology article

    Published on:

  36. Inferring phylogenetic relationships of polyploid species and their diploid ancestors (leading to reticulate phylogenies in the case of an allopolyploid origin) based on multi-locus sequence data is complicate...

    Authors: Ulrich Lautenschlager, Florian Wagner and Christoph Oberprieler

    Citation: BMC Bioinformatics 2020 21:441

    Content type: Software

    Published on:

  38. Mass spectrometry (MS) has become a promising analytical technique to acquire proteomics information for the characterization of biological samples. Nevertheless, most studies focus on the final proteins ident...

    Authors: Shisheng Wang, Hongwen Zhu, Hu Zhou, Jingqiu Cheng and Hao Yang

    Citation: BMC Bioinformatics 2020 21:439

    Content type: Software

    Published on:

  39. Performing a statistical test requires a null hypothesis. In cancer genomics, a key challenge is the fast generation of accurate somatic mutational landscapes that can be used as a realistic null hypothesis fo...

    Authors: Erik N. Bergstrom, Mark Barnes, Iñigo Martincorena and Ludmil B. Alexandrov

    Citation: BMC Bioinformatics 2020 21:438

    Content type: Software

    Published on:

  40. In epigenetics, the change of the combination of histone modifications at the same genomic location during cell differentiation is of great interest for understanding the function of these modifications and th...

    Authors: Dirk Zeckzer, Alrik Hausdorf, Nicole Hinzmann, Lydia Müller and Daniel Wiegreffe

    Citation: BMC Bioinformatics 2020 21:437

    Content type: Software

    Published on:

  41. Discoveries in cellular dynamics and tissue development constantly reshape our understanding of fundamental biological processes such as embryogenesis, wound-healing, and tumorigenesis. High-quality microscopy...

    Authors: Marco Berghoff, Jakob Rosenbauer, Felix Hoffmann and Alexander Schug

    Citation: BMC Bioinformatics 2020 21:436

    Content type: Software

    Published on:

  43. Precise disease module is conducive to understanding the molecular mechanism of disease causation and identifying drug targets. However, due to the fragmentization of disease module in incomplete human interac...

    Authors: Bingbo Wang, Jie Hu, Yajun Wang, Chenxing Zhang, Yuanjun Zhou, Liang Yu, Xingli Guo, Lin Gao and Yunru Chen

    Citation: BMC Bioinformatics 2020 21:433

    Content type: Methodology article

    Published on:

  44. In systems biology, it is of great interest to identify previously unreported associations between genes. Recently, biomedical literature has been considered as a valuable resource for this purpose. While clas...

    Authors: Jin Hyun Nam, Daniel Couch, Willian A. da Silveira, Zhenning Yu and Dongjun Chung

    Citation: BMC Bioinformatics 2020 21:432

    Content type: Methodology article

    Published on:

  46. A typical task in bioinformatics consists of identifying which features are associated with a target outcome of interest and building a predictive model. Automated machine learning (AutoML) systems such as the...

    Authors: Elisabetta Manduchi, Weixuan Fu, Joseph D. Romano, Stefano Ruberto and Jason H. Moore

    Citation: BMC Bioinformatics 2020 21:430

    Content type: Methodology article

    Published on:

  48. Second messengers, c-di-GMP and (p)ppGpp, are vital regulatory molecules in bacteria, influencing cellular processes such as biofilm formation, transcription, virulence, quorum sensing, and proliferation. Whil...

    Authors: Chunrui Xu, Bronson R. Weston, John J. Tyson and Yang Cao

    Citation: BMC Bioinformatics 2020 21(Suppl 14):408

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 14

  49. Machine learning has been utilized to predict cancer drug response from multi-omics data generated from sensitivities of cancer cell lines to different therapeutic compounds. Here, we build machine learning mo...

    Authors: Evan A. Clayton, Toyya A. Pujol, John F. McDonald and Peng Qiu

    Citation: BMC Bioinformatics 2020 21(Suppl 14):364

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 14

  50. The abundance of molecular profiling of breast cancer tissues entailed active research on molecular marker-based early diagnosis of metastasis. Recently there is a surging interest in combining gene expression...

    Authors: Nahim Adnan, Chengwei Lei and Jianhua Ruan

    Citation: BMC Bioinformatics 2020 21(Suppl 14):359

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 14

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