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Spotlight on… high-resolution biology

New Content Item © Gómez HF et alHigh-resolution imaging and genomic technologies are changing the way we view the environment, cells, chromosomes and molecules. From super-resolution microscopy to cryo-EM to single-cell sequencing, a ‘resolution revolution’ is taking place.  

Here we share recent highlights from the BMC Series journals.

Read the associated blog for highlights.

Single cell genomics

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Computational identification of clonal cells in single-cell CRISPR screens
Yihan Wang, Shiqi Xie, Daniel Armendariz & Gary C. Hon
BMC Genomics volume 23, Article number: 135 (2022)

Evaluation of methods to detect circular RNAs from single-end RNA-sequencing data
Manh Hung Nguyen, Ha-Nam Nguyen & Trung Nghia Vu
BMC Genomics volume 23, Article number: 106 (2022)

baredSC: Bayesian approach to retrieve expression distribution of single-cell data
Lucille Lopez-Delisle & Jean-Baptiste Delisle
BMC Bioinformatics volume 23, Article number: 36 (2022)

A novel graph-based k-partitioning approach improves the detection of gene-gene correlations by single-cell RNA sequencing
Heng Xu, Ying Hu, Xinyu Zhang, Bradley E. Aouizerat, Chunhua Yan & Ke Xu
BMC Genomics volume 23, Article number: 35 (2022)

scDIOR: single cell RNA-seq data IO software
Huijian Feng, Lihui Lin & Jiekai Chen
BMC Bioinformatics volume 23, Article number: 16 (2022)

Transcription factor network analysis based on single cell RNA-seq identifies that Trichostatin-a reverses docetaxel resistance in prostate Cancer
Patricia M. Schnepp, Aqila Ahmed, June Escara-Wilke, Jinlu Dai, Greg Shelley, Jill Keller, Atsushi Mizokami & Evan T. Keller
BMC Cancer volume 21, Article number: 1316 (2021)

Choice of pre-processing pipeline influences clustering quality of scRNA-seq datasets
Inbal Shainer & Manuel Stemmer
BMC Genomics volume 22, Article number: 661 (2021)

QTLs and candidate genes analyses for fruit size under domestication and differentiation in melon (Cucumis melo L.) based on high resolution maps
Qun Lian, Qiushi Fu, Yongyang Xu, Zhicheng Hu, Jing Zheng, Aiai Zhang, Yuhua He, Changsheng Wang, Chuanqiang Xu, Benxue Chen, Jordi Garcia-Mas, Guangwei Zhao & Huaisong Wang
BMC Plant Biology volume 21, Article number: 126 (2021)

DNA barcoding for high resolution sampling

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Airborne environmental DNA metabarcoding detects more diversity, with less sampling effort, than a traditional plant community survey
Mark D. Johnson, Mohamed Fokar, Robert D. Cox & Matthew A. Barnes
BMC Ecology and Evolution volume 21, Article number: 218 (2021)

Developing an efficient DNA barcoding system to differentiate between Lilium species
Yixin Liu, Mingfang Zhang, Xuqing Chen, Xi Chen, Yue Hu, Junlian Gao, Wenqiang Pan, Yin Xin, Jian Wu, Yunpeng Du & Xiuhai Zhang
BMC Plant Biology volume 21, Article number: 465 (2021)

Seeing through sedimented waters: environmental DNA reduces the phantom diversity of sharks and rays in turbid marine habitats
Yin Cheong Aden Ip, Jia Jin Marc Chang, Kelvin K. P. Lim, Zeehan Jaafar, Benjamin J. Wainwright & Danwei Huang
BMC Ecology and Evolution volume 21, Article number: 166 (2021)

Diversity of dinoflagellate assemblages in coastal temperate and offshore tropical waters of Australia
Tahnee Manning, Arjun Venkatesh Thilagaraj, Dmitri Mouradov, Richard Piola, Clare Grandison, Matthew Gordon, Jeff Shimeta & Aidyn Mouradov
BMC Ecology and Evolution volume 21, Article number: 27 (2021)

Single cell and multi cell imaging

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Computational modeling of PET tracer distribution in solid tumors integrating microvasculature
Niloofar Fasaeiyan, M. Soltani, Farshad Moradi Kashkooli, Erfan Taatizadeh & Arman Rahmim
BMC Biotechnology volume 21, Article number: 67 (2021)

Virtual reality for 3D histology: multi-scale visualization of organs with interactive feature exploration
Kaisa Liimatainen, Leena Latonen, Masi Valkonen, Kimmo Kartasalo & Pekka Ruusuvuori
BMC Cancer volume 21, Article number: 1133 (2021)

Methodology for comprehensive cell-level analysis of wound healing experiments using deep learning in MATLAB
Jan Oldenburg, Lisa Maletzki, Anne Strohbach, Paul Bellé, Stefan Siewert, Raila Busch, Stephan B. Felix, Klaus-Peter Schmitz & Michael Stiehm
BMC Molecular and Cell Biology volume 22, Article number: 32 (2021)

3D-printed microplate inserts for long term high-resolution imaging of live brain organoids
Mariana Oksdath Mansilla, Camilo Salazar-Hernandez, Sally L. Perrin, Kaitlin G. Scheer, Gökhan Cildir, John Toubia, Kristyna Sedivakova, Melinda N. Tea, Sakthi Lenin, Elise Ponthier, Erica C. F. Yeo, Vinay Tergaonkar, Santosh Poonnoose, Rebecca J. Ormsby, Stuart M. Pitson, Michael P. Brown, Lisa M. Ebert & Guillermo A. Gomez
BMC Biomedical Engineering volume 3, Article number: 6 (2021)

Morphological study of embryonic Chd8+/− mouse brains using light-sheet microscopy
Harold F. Gómez, Leonie Hodel, Odyssé Michos & Dagmar Iber
BMC Research Notes volume 14, Article number: 23 (2021)

Molecular imaging

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NanoBRET in C. elegans illuminates functional receptor interactions in real time
Victoria Elisabeth Groß, Miron Mikhailowitsch Gershkovich, Torsten Schöneberg, Anette Kaiser & Simone Prömel
BMC Molecular and Cell Biology volume 23, Article number: 8 (2022)

Lipidomic profiling reveals distinct differences in plasma lipid composition in overweight or obese adolescent students
Ruili Yin, Xiaojing Wang, Kun Li, Ke Yu & Longyan Yang
BMC Endocrine Disorders volume 21, Article number: 201 (2021)

Elucidating bacterial adhesion to mucosal surface by an original AFM approach
Karen Dunker, Sol Gomez de la Torre Canny, Catherine Taylor Nordgård, Etienne Dague, Cécile Formosa-Dague, Ingrid Bakke & Marit Sletmoen
BMC Microbiology volume 21, Article number: 244 (2021)

SEM and TEM for identification of capsular fibrosis and cellular behavior around breast implants – a descriptive analysis
Britta Kuehlmann, Isabel Zucal, Clark Andrew Bonham, Lydia-Marie Joubert & Lukas Prantl
BMC Molecular and Cell Biology volume 22, Article number: 25 (2021)

Pilot study on the effects of preservatives on corneal collagen parameters measured by small angle X-ray scattering analysis
Susyn Joan Kelly, Lizette duPlessis, John Soley, Frazer Noble, Hannah Carolyn Wells & Patrick John Kelly
BMC Research Notes volume 14, Article number: 78 (2021)

Relaxometric learning: a pattern recognition method for T2 relaxation curves based on machine learning supported by an analytical framework
Yasuhiro Date, Feifei Wei, Yuuri Tsuboi, Kengo Ito, Kenji Sakata & Jun Kikuchi
BMC Chemistry volume 15, Article number: 13 (2021)