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  3. Oocyte quality decreases with aging, thereby increasing errors in fertilization, chromosome segregation, and embryonic cleavage. Oocyte appearance also changes with aging, suggesting a functional relationship ...

    Authors: Momoko Imakubo, Jun Takayama, Hatsumi Okada and Shuichi Onami

    Citation: BMC Bioinformatics 2021 22:73

    Content type: Research article

    Published on:

  4. Bioimaging techniques offer a robust tool for studying molecular pathways and morphological phenotypes of cell populations subjected to various conditions. As modern high-resolution 3D microscopy provides acce...

    Authors: Grzegorz Bokota, Jacek Sroka, Subhadip Basu, Nirmal Das, Pawel Trzaskoma, Yana Yushkevich, Agnieszka Grabowska, Adriana Magalska and Dariusz Plewczynski

    Citation: BMC Bioinformatics 2021 22:72

    Content type: Software

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  5. Specialized data structures are required for online algorithms to efficiently handle large sequencing datasets. The counting quotient filter (CQF), a compact hashtable, can efficiently store k-mers with a skew...

    Authors: Moustafa Shokrof, C. Titus Brown and Tamer A. Mansour

    Citation: BMC Bioinformatics 2021 22:71

    Content type: Methodology article

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  6. The quantity of genomic data is expanding at an increasing rate. Tools for phylogenetic analysis which scale to the quantity of available data are required. To address this need, we present cognac, a user-frie...

    Authors: Ryan D. Crawford and Evan S. Snitkin

    Citation: BMC Bioinformatics 2021 22:70

    Content type: Software

    Published on:

  8. The clustering of data produced by liquid chromatography coupled to mass spectrometry analyses (LC-MS data) has recently gained interest to extract meaningful chemical or biological patterns. However, recent i...

    Authors: Olga Permiakova, Romain Guibert, Alexandra Kraut, Thomas Fortin, Anne-Marie Hesse and Thomas Burger

    Citation: BMC Bioinformatics 2021 22:68

    Content type: Methodology article

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  9. The search for statistically significant relationships between molecular markers and outcomes is challenging when dealing with high-dimensional, noisy and collinear multivariate omics data, such as metabolomic...

    Authors: Alina Peluso, Robert Glen and Timothy M. D. Ebbels

    Citation: BMC Bioinformatics 2021 22:67

    Content type: Research article

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  10. Conformational transitions are implicated in the biological function of many proteins. Structural changes in proteins can be described approximately as the relative movement of rigid domains against each other...

    Authors: Truong Khanh Linh Dang, Thach Nguyen, Michael Habeck, Mehmet Gültas and Stephan Waack

    Citation: BMC Bioinformatics 2021 22:66

    Content type: Methodology article

    Published on:

  11. The advancement of SMRT technology has unfolded new opportunities of genome analysis with its longer read length and low GC bias. Alignment of the reads to their appropriate positions in the respective referen...

    Authors: Angana Chakraborty, Burkhard Morgenstern and Sanghamitra Bandyopadhyay

    Citation: BMC Bioinformatics 2021 22:64

    Content type: Methodology article

    Published on:

  15. Current high-throughput technologies—i.e. whole genome sequencing, RNA-Seq, ChIP-Seq, etc.—generate huge amounts of data and their usage gets more widespread with each passing year. Complex analysis pipelines ...

    Authors: Daniele Dall’Olio, Nico Curti, Eugenio Fonzi, Claudia Sala, Daniel Remondini, Gastone Castellani and Enrico Giampieri

    Citation: BMC Bioinformatics 2021 22:60

    Content type: Research article

    Published on:

  17. Hub transcription factors, regulating many target genes in gene regulatory networks (GRNs), play important roles as disease regulators and potential drug targets. However, while numerous methods have been deve...

    Authors: Julia Åkesson, Zelmina Lubovac-Pilav, Rasmus Magnusson and Mika Gustafsson

    Citation: BMC Bioinformatics 2021 22:58

    Content type: Methodology article

    Published on:

  18. Mass spectrometry imaging (MSI) is a family of acquisition techniques producing images of the distribution of molecules in a sample, without any prior tagging of the molecules. This makes it a very interesting...

    Authors: Florent Grélard, David Legland, Mathieu Fanuel, Bastien Arnaud, Loïc Foucat and Hélène Rogniaux

    Citation: BMC Bioinformatics 2021 22:56

    Content type: Research article

    Published on:

  19. Identification and selection of protein particles in cryo-electron micrographs is an important step in single particle analysis. In this study, we developed a deep learning-based particle picking network to a...

    Authors: Nguyen Phuoc Nguyen, Ilker Ersoy, Jacob Gotberg, Filiz Bunyak and Tommi A. White

    Citation: BMC Bioinformatics 2021 22:55

    Content type: Methodology article

    Published on:

  23. An inverted repeat is a DNA sequence followed downstream by its reverse complement, potentially with a gap in the centre. Inverted repeats are found in both prokaryotic and eukaryotic genomes and they have bee...

    Authors: Hayam Alamro, Mai Alzamel, Costas S. Iliopoulos, Solon P. Pissis and Steven Watts

    Citation: BMC Bioinformatics 2021 22:51

    Content type: Software

    Published on:

  24. In the last decade, Genome-wide Association studies (GWASs) have contributed to decoding the human genome by uncovering many genetic variations associated with various diseases. Many follow-up investigations i...

    Authors: Haohan Wang, Fen Pei, Michael M. Vanyukov, Ivet Bahar, Wei Wu and Eric P. Xing

    Citation: BMC Bioinformatics 2021 22:50

    Content type: Methodology article

    Published on:

  25. Microbiomes consist of bacteria, viruses, and other microorganisms, and are responsible for many different functions in both organisms and the environment. Past analyses of microbiomes focused on using correla...

    Authors: Daniella Vo, Shayal Charisma Singh, Sara Safa and Debashis Sahoo

    Citation: BMC Bioinformatics 2021 22:49

    Content type: Research article

    Published on:

  26. Various databases on genetically modified organisms (GMOs) exist, all with their specific focus to facilitate access to information needed for, e. g., the assistance in risk assessment, the development of dete...

    Authors: Paulien Adamse, Emilie Dagand, Karen Bohmert-Tatarev, Daniela Wahler, Manoela Miranda, Esther J. Kok and Joachim Bendiek

    Citation: BMC Bioinformatics 2021 22:48

    Content type: Database

    Published on:

  27. Survival analysis is an important part of cancer studies. In addition to the existing Cox proportional hazards model, deep learning models have recently been proposed in survival prediction, which directly int...

    Authors: Jiarui Feng, Heming Zhang and Fuhai Li

    Citation: BMC Bioinformatics 2021 22:47

    Content type: Methodology article

    Published on:

  28. The development of genetically modified crops (GM) includes the discovery of candidate genes through bioinformatics analysis using genomics data, gene expression, and others. Proteins of unknown function (PUFs...

    Authors: Marcos José Andrade Viana, Adhemar Zerlotini and Mauricio de Alvarenga Mudadu

    Citation: BMC Bioinformatics 2021 22:46

    Content type: Database

    Published on:

  29. Several bioinformatics pipelines have been developed to detect sequences from viruses that integrate into the human genome because of the health relevance of these integrations, such as in the persistence of v...

    Authors: Elisa Pischedda, Cristina Crava, Martina Carlassara, Susanna Zucca, Leila Gasmi and Mariangela Bonizzoni

    Citation: BMC Bioinformatics 2021 22:45

    Content type: Methodology article

    Published on:

  30. Differential expression and feature selection analyses are essential steps for the development of accurate diagnostic/prognostic classifiers of complicated human diseases using transcriptomics data. These step...

    Authors: Liangqun Lu, Kevin A. Townsend and Bernie J. Daigle Jr.

    Citation: BMC Bioinformatics 2021 22:44

    Content type: Methodology article

    Published on:

  31. Transposable elements (TEs) constitute a significant part of eukaryotic genomes. Short interspersed nuclear elements (SINEs) are non-autonomous TEs, which are widely represented in mammalian genomes and also f...

    Authors: Yulia M. Suvorova, Anastasia M. Kamionskaya and Eugene V. Korotkov

    Citation: BMC Bioinformatics 2021 22:42

    Content type: Methodology article

    Published on:

  32. The drive to understand how microbial communities interact with their environments has inspired innovations across many fields. The data generated from sequence-based analyses of microbial communities typicall...

    Authors: Charlie M. Carpenter, Daniel N. Frank, Kayla Williamson, Jaron Arbet, Brandie D. Wagner, Katerina Kechris and Miranda E. Kroehl

    Citation: BMC Bioinformatics 2021 22:41

    Content type: Software

    Published on:

  33. Generating and analysing single-cell data has become a widespread approach to examine tissue heterogeneity, and numerous algorithms exist for clustering these datasets to identify putative cell types with shar...

    Authors: Ryan B. Patterson-Cross, Ariel J. Levine and Vilas Menon

    Citation: BMC Bioinformatics 2021 22:39

    Content type: Methodology article

    Published on:

  34. Due to the complexity of the biological systems, the prediction of the potential DNA binding sites for transcription factors remains a difficult problem in computational biology. Genomic DNA sequences and expe...

    Authors: Chen Chen, Jie Hou, Xiaowen Shi, Hua Yang, James A. Birchler and Jianlin Cheng

    Citation: BMC Bioinformatics 2021 22:38

    Content type: Software

    Published on:

  35. IsomiRs are miRNA variants that vary in length and/or sequence when compared to their canonical forms. These variants display differences in length and/or sequence, including additions or deletions of one or m...

    Authors: Ana M. Vasconcelos, Maria Beatriz Carmo, Beatriz Ferreira, Inês Viegas, Margarida Gama-Carvalho, António Ferreira and Andreia J. Amaral

    Citation: BMC Bioinformatics 2021 22:37

    Content type: Software

    Published on:

  37. Assigning chromatin states genome-wide (e.g. promoters, enhancers, etc.) is commonly performed to improve functional interpretation of these states. However, computational methods to assign chromatin state suf...

    Authors: Tara Eicher, Jany Chan, Han Luu, Raghu Machiraju and Ewy A. Mathé

    Citation: BMC Bioinformatics 2021 22:35

    Content type: Methodology article

    Published on:

  39. Predicting the response of cancer cell lines to specific drugs is an essential problem in personalized medicine. Since drug response is closely associated with genomic information in cancer cells, some large p...

    Authors: Akram Emdadi and Changiz Eslahchi

    Citation: BMC Bioinformatics 2021 22:33

    Content type: Methodology article

    Published on:

  43. Drug repositioning is an emerging approach in pharmaceutical research for identifying novel therapeutic potentials for approved drugs and discover therapies for untreated diseases. Due to its time and cost eff...

    Authors: Tamer N. Jarada, Jon G. Rokne and Reda Alhajj

    Citation: BMC Bioinformatics 2021 22:28

    Content type: Research article

    Published on:

  44. Currently, large-scale gene expression profiling has been successfully applied to the discovery of functional connections among diseases, genetic perturbation, and drug action. To address the cost of an ever-e...

    Authors: Lingpeng Kong, Yuanyuan Chen, Fengjiao Xu, Mingmin Xu, Zutan Li, Jingya Fang, Liangyun Zhang and Cong Pian

    Citation: BMC Bioinformatics 2021 22:27

    Content type: Methodology article

    Published on:

  45. Brain Computer Interfaces (BCIs) translate the activity of the nervous system to a control signal which is interpretable for an external device. Using continuous motor BCIs, the user will be able to control a ...

    Authors: Mehrdad Kashefi and Mohammad Reza Daliri

    Citation: BMC Bioinformatics 2021 22:26

    Content type: Research article

    Published on:

  46. Diverse microbiome communities drive biogeochemical processes and evolution of animals in their ecosystems. Many microbiome projects have demonstrated the power of using metagenomics to understand the structur...

    Authors: Eliza Dhungel, Yassin Mreyoud, Ho-Jin Gwak, Ahmad Rajeh, Mina Rho and Tae-Hyuk Ahn

    Citation: BMC Bioinformatics 2021 22:25

    Content type: Software

    Published on:

  47. Long non-coding RNAs (lncRNAs) regulate diverse biological processes via interactions with proteins. Since the experimental methods to identify these interactions are expensive and time-consuming, many computa...

    Authors: Dipan Shaw, Hao Chen, Minzhu Xie and Tao Jiang

    Citation: BMC Bioinformatics 2021 22:24

    Content type: Methodology article

    Published on:

  48. Copy number alterations (CNAs), due to their large impact on the genome, have been an important contributing factor to oncogenesis and metastasis. Detecting genomic alterations from the shallow-sequencing data...

    Authors: Xinping Fan, Guanghao Luo and Yu S. Huang

    Citation: BMC Bioinformatics 2021 22:23

    Content type: Methodology article

    Published on:

  49. In this study, we demonstrate that our modified Gene Set Enrichment Analysis (GSEA) method, drug perturbation GSEA (dpGSEA), can detect phenotypically relevant drug targets through a unique transcriptomic enri...

    Authors: Mike Fang, Brian Richardson, Cheryl M. Cameron, Jean-Eudes Dazard and Mark J. Cameron

    Citation: BMC Bioinformatics 2021 22:22

    Content type: Methodology article

    Published on:

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