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Section edited by Frank Eisenhaber and Sandor Pongor

The Bioinformatics section will be the publishing channel for scientific articles that report about theoretical, computational and data analysis approaches applied to biological, medical and other life science related problems, and the results and insights that have been achieved with them. Special emphasis is given to manuscripts that deal with biological mechanism interpretation to biomolecular sequence data and data from other experimental high-throughput techniques. This section also covers all fields of bioinformatics and computational biology that might not be handled by other subsections of Biology Direct. Hypotheses are welcome as long as they are based on rigorous scientific standards and as they fit existing data. Manuscripts describing new methods or software developments need to demonstrate that a major improvement has been achieved, and this has led to either improved accuracy by orders of magnitude, lowered resource consumption and/or some new biological insight.

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  1. Drug-induced liver injury (DILI) is a major safety concern characterized by a complex and diverse pathogenesis. In order to identify DILI early in drug development, a better understanding of the injury and mod...

    Authors: Anika Liu, Moritz Walter, Peter Wright, Aleksandra Bartosik, Daniela Dolciami, Abdurrahman Elbasir, Hongbin Yang and Andreas Bender
    Citation: Biology Direct 2021 16:6
  2. The human proteins TMTC1, TMTC2, TMTC3 and TMTC4 have been experimentally shown to be components of a new O-mannosylation pathway. Their own mannosyl-transferase activity has been suspected but their actual en...

    Authors: Birgit Eisenhaber, Swati Sinha, Chaitanya K. Jadalanki, Vladimir A. Shitov, Qiao Wen Tan, Fernanda L. Sirota and Frank Eisenhaber
    Citation: Biology Direct 2021 16:4
  3. Drug-induced liver injury (DILI) is one of the primary problems in drug development. Early prediction of DILI can bring a significant reduction in the cost of clinical trials. In this work we examined whether ...

    Authors: Wojciech Lesiński, Krzysztof Mnich, Agnieszka Kitlas Golińska and Witold R. Rudnicki
    Citation: Biology Direct 2021 16:2
  4. Composition of microbial communities can be location-specific, and the different abundance of taxon within location could help us to unravel city-specific signature and predict the sample origin locations accu...

    Authors: Runzhi Zhang, Alejandro R. Walker and Susmita Datta
    Citation: Biology Direct 2021 16:1
  5. The transamidase complex is a molecular machine in the endoplasmic reticulum of eukaryotes that attaches a glycosylphosphatidylinositol (GPI) lipid anchor to substrate proteins after cleaving a C-terminal prop...

    Authors: Chinh Tran-To Su, Swati Sinha, Birgit Eisenhaber and Frank Eisenhaber
    Citation: Biology Direct 2020 15:14
  6. AMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand complexes using Autodock Vina and AutoDock4, including the option of using the Autodock4Zn force...

    Authors: Mario S. Valdés-Tresanco, Mario E. Valdés-Tresanco, Pedro A. Valiente and Ernesto Moreno
    Citation: Biology Direct 2020 15:12
  7. Glioma is one of the most common malignant brain tumors and exhibits low resection rate and high recurrence risk. Although a large number of glioma studies powered by high-throughput sequencing technologies ha...

    Authors: Lin Liu, Guangyu Wang, Liguo Wang, Chunlei Yu, Mengwei Li, Shuhui Song, Lili Hao, Lina Ma and Zhang Zhang
    Citation: Biology Direct 2020 15:10
  8. Accurate classification of different Burkholderia cepacia complex (BCC) species is essential for therapy, prognosis assessment and research. The taxonomic status of BCC remains problematic and an improved knowled...

    Authors: Yuan Jin, Jianglin Zhou, Jing Zhou, Mingda Hu, Qi Zhang, Na Kong, Hongguang Ren, Long Liang and Junjie Yue
    Citation: Biology Direct 2020 15:6
  9. Drug-induced liver injury (DILI) is a major concern in drug development, as hepatotoxicity may not be apparent at early stages but can lead to life threatening consequences. The ability to predict DILI from in...

    Authors: Marco Chierici, Margherita Francescatto, Nicole Bussola, Giuseppe Jurman and Cesare Furlanello
    Citation: Biology Direct 2020 15:3
  10. Drug-induced liver injury (DILI) is a serious concern during drug development and the treatment of human disease. The ability to accurately predict DILI risk could yield significant improvements in drug attrit...

    Authors: G. Rex Sumsion, Michael S. Bradshaw III, Jeremy T. Beales, Emi Ford, Griffin R. G. Caryotakis, Daniel J. Garrett, Emily D. LeBaron, Ifeanyichukwu O. Nwosu and Stephen R. Piccolo
    Citation: Biology Direct 2020 15:1
  11. Patients diagnosed as diffuse large B cell lymphoma (DLBCL) with CD5 positive normally have a worse outcome and poorly respond to the regulatory treatment strategy.

    Authors: Qingyuan Qu, Ying Li, Xiaosheng Fang, Lingyan Zhang, Chao Xue, Xueling Ge, Xin Wang and Yujie Jiang
    Citation: Biology Direct 2019 14:23
  12. Recently high-throughput technologies have been massively used alongside clinical tests to study various types of cancer. Data generated in such large-scale studies are heterogeneous, of different types and fo...

    Authors: Iliyan Mihaylov, Maciej Kańduła, Milko Krachunov and Dimitar Vassilev
    Citation: Biology Direct 2019 14:22
  13. Metaproteomics allows to decipher the structure and functionality of microbial communities. Despite its rapid development, crucial steps such as the creation of standardized protein search databases and reliab...

    Authors: Johannes Werner, Augustin Géron, Jules Kerssemakers and Sabine Matallana-Surget
    Citation: Biology Direct 2019 14:21
  14. Accumulating evidence suggests that the human microbiome impacts individual and public health. City subway systems are human-dense environments, where passengers often exchange microbes. The MetaSUB project pa...

    Authors: Chengsheng Zhu, Maximilian Miller, Nick Lusskin, Yannick Mahlich, Yanran Wang, Zishuo Zeng and Yana Bromberg
    Citation: Biology Direct 2019 14:19
  15. Neuroblastoma is one of the most common types of pediatric cancer. In current neuroblastoma prognosis, patients can be stratified into high- and low-risk groups. Generally, more than 90% of the patients in the...

    Authors: Yatong Han, Xiufen Ye, Chao Wang, Yusong Liu, Siyuan Zhang, Weixing Feng, Kun Huang and Jie Zhang
    Citation: Biology Direct 2019 14:16
  16. The availability of hundreds of city microbiome profiles allows the development of increasingly accurate predictors of the origin of a sample based on its microbiota composition. Typical microbiome studies inv...

    Authors: Carlos S. Casimiro-Soriguer, Carlos Loucera, Javier Perez Florido, Daniel López-López and Joaquin Dopazo
    Citation: Biology Direct 2019 14:15
  17. Integrating the rich information from multi-omics data has been a popular approach to survival prediction and bio-marker identification for several cancer studies. To facilitate the integrative analysis of mul...

    Authors: So Yeon Kim, Hyun-Hwan Jeong, Jaesik Kim, Jeong-Hyeon Moon and Kyung-Ah Sohn
    Citation: Biology Direct 2019 14:8
  18. Rubber tree (Hevea brasiliensis) acts as an important tropic economic crop and rubber tree anthracnose, mainly caused by Colletotrichum gloeosporioides, is one of the most common fungal disease, which leads to se...

    Authors: Hongyan Yin, Xiaodong Zhang, Bei Zhang, Hongli Luo and Chaozu He
    Citation: Biology Direct 2019 14:7
  19. Splice sites prediction has been a long-standing problem in bioinformatics. Although many computational approaches developed for splice site prediction have achieved satisfactory accuracy, further improvement ...

    Authors: Ying Zeng, Hongjie Yuan, Zheming Yuan and Yuan Chen
    Citation: Biology Direct 2019 14:6
  20. Protein-protein interactions are crucial for normal biological processes and to regulate cellular reactions that affect gene expression and function. Several previous studies have emphasized the roles of resid...

    Authors: Srinivasan Jayashree, Pavalam Murugavel, Ramanathan Sowdhamini and Narayanaswamy Srinivasan
    Citation: Biology Direct 2019 14:1
  21. Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein s...

    Authors: Gayatri Kumar, Richa Mudgal, Narayanaswamy Srinivasan and Sankaran Sandhya
    Citation: Biology Direct 2018 13:8
  22. There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow...

    Authors: Daniel H. Huson, Benjamin Albrecht, Caner Bağcı, Irina Bessarab, Anna Górska, Dino Jolic and Rohan B. H. Williams
    Citation: Biology Direct 2018 13:6
  23. High-throughput methodologies such as microarrays and next-generation sequencing are routinely used in cancer research, generating complex data at different omics layers. The effective integration of omics data c...

    Authors: Margherita Francescatto, Marco Chierici, Setareh Rezvan Dezfooli, Alessandro Zandonà, Giuseppe Jurman and Cesare Furlanello
    Citation: Biology Direct 2018 13:5
  24. The experience with running various types of classification on the CAMDA neuroblastoma dataset have led us to the conclusion that the results are not always obvious and may differ depending on type of analysis...

    Authors: Anna Leśniewska, Joanna Zyprych-Walczak, Alicja Szabelska-Beręsewicz and Michal J. Okoniewski
    Citation: Biology Direct 2018 13:3
  25. Though earlier works on modelling transcript abundance from vertebrates to lower eukaroytes have specifically singled out the Zip’s law, the observed distributions often deviate from a single power-law slope. ...

    Authors: Wing-Cheong Wong, Hong-kiat Ng, Erwin Tantoso, Richie Soong and Frank Eisenhaber
    Citation: Biology Direct 2018 13:2
  26. The Clusters of Orthologous Groups (COGs) of proteins systematize evolutionary related proteins into specific groups with similar functions. However, the available databases do not provide means to assess the ...

    Authors: Daria V. Dibrova, Kirill A. Konovalov, Vadim V. Perekhvatov, Konstantin V. Skulachev and Armen Y. Mulkidjanian
    Citation: Biology Direct 2017 12:29
  27. In prokaryotic genomes, functionally coupled genes can be organized in conserved gene clusters enabling their coordinated regulation. Such clusters could contain one or several operons, which are groups of co-...

    Authors: Olesya I. Klimchuk, Kirill A. Konovalov, Vadim V. Perekhvatov, Konstantin V. Skulachev, Daria V. Dibrova and Armen Y. Mulkidjanian
    Citation: Biology Direct 2017 12:26
  28. Programmed ribosomal frameshifting (PRF) is a gene expression mechanism which enables the translation of two N-terminally coincident, C-terminally distinct protein products from a single mRNA. Many viruses uti...

    Authors: Adam M. Dinan, John F. Atkins and Andrew E. Firth
    Citation: Biology Direct 2017 12:24
  29. Bacterial species present in multispecies microbial communities often react to the same chemical signal but at vastly different concentrations. The existence of different response thresholds with respect to th...

    Authors: János Juhász, Dóra Bihary, Attila Jády, Sándor Pongor and Balázs Ligeti
    Citation: Biology Direct 2017 12:22
  30. Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided b...

    Authors: Kuang-Lim Chan, Tatiana V. Tatarinova, Rozana Rosli, Nadzirah Amiruddin, Norazah Azizi, Mohd Amin Ab Halim, Nik Shazana Nik Mohd Sanusi, Nagappan Jayanthi, Petr Ponomarenko, Martin Triska, Victor Solovyev, Mohd Firdaus-Raih, Ravigadevi Sambanthamurthi, Denis Murphy and Eng-Ti Leslie Low
    Citation: Biology Direct 2017 12:21
  31. Much effort is underway to build and upgrade databases and tools related to occurrence, diversity, and characterization of CRISPR-Cas systems. As microbial communities and their genome complements are unearthe...

    Authors: Alice Toms and Rodolphe Barrangou
    Citation: Biology Direct 2017 12:20
  32. We report a comprehensive computational dissection of the domain architecture of the SAMD9 family proteins that are involved in antivirus and antitumor response in humans. We show that the SAMD9 protein family...

    Authors: Sergei L. Mekhedov, Kira S. Makarova and Eugene V. Koonin
    Citation: Biology Direct 2017 12:13
  33. The protein Gcn1 (General control non-derepressible 1) is found in virtually all eukaryotes, and is a key component of the general amino acid control signal transduction pathway. This pathway is best known for...

    Authors: Ramachandran Rakesh, Rangachari Krishnan, Evelyn Sattlegger and Narayanaswamy Srinivasan
    Citation: Biology Direct 2017 12:12
  34. TRIF is a key protein in antiviral innate immunity, operating downstream of TLRs. TRIF activation leads to the production of interferon-β and pro-inflammatory cytokines. There is evidence from experiments to s...

    Authors: Jarjapu Mahita and Ramanathan Sowdhamini
    Citation: Biology Direct 2017 12:9
  35. Recent developments of high throughput sequencing technologies allow the characterization of the microbial communities inhabiting our world. Various metagenomic studies have suggested using microbial taxa as p...

    Authors: Mustafa Alshawaqfeh, Ahmad Bashaireh, Erchin Serpedin and Jan Suchodolski
    Citation: Biology Direct 2017 12:4
  36. It is believed that all cancers occur due to the mutation or change in one or more genes. In order to investigate the significance of the biological pathways which are interrupted by these genetic mutations, w...

    Authors: Sinjini Sikdar, Somnath Datta and Susmita Datta
    Citation: Biology Direct 2016 11:65

Annual Journal Metrics

  • 2022 Citation Impact
    5.5 - 2-year Impact Factor
    3.8 - 5-year Impact Factor
    0.893 - SNIP (Source Normalized Impact per Paper)
    1.117 - SJR (SCImago Journal Rank)

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