ATG5 and ATG7 Expression Levels Are Reduced in Cutaneous Melanoma and Regulated by NRF1 by Živa Frangež, Deborah Gérard, Zhaoyue He, Marios Gavriil, Yuniel Fernández-Marrero, Yuniel Fernández-Marrero, S. Morteza Seyed Jafari, Robert E. Hunger, Philippe Lucarelli, Shida Yousefi, Thomas Sauter, Lasse Sinkkonen, Hans-Uwe Simon, Hans-Uwe Simon, Hans-Uwe Simon, Hans-Uwe Simon

“…Currently, the mechanisms regulating ATG expression levels in human melanoma remains unknown. Using bioinformatic predictions of transcription factor (TF) binding motifs in accessible chromatin of primary melanocytes, we identified new TFs involved in the regulation of core ATGs. …”
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Comprehensive analysis of cuproptosis-related genes in immune infiltration and development of a novel diagnostic model for acute kidney injury by Yajing Li, Yingxue Ding

“…Nomogram and DCA further confirmed the accuracy of the model in predicting the risk of AKI.Conclusion This study elucidated the role of cuproptosis in AKI and revealed the association between CRGs and infiltrated immune cells through comprehensive bioinformatic techniques. The six-gene cuproptosis-related signature exhibited remarkable predictive efficiency for AKI.…”
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The bacterial response regulator ArcA uses a diverse binding site architecture to regulate carbon oxidation globally. by Dan M Park, Md Sohail Akhtar, Aseem Z Ansari, Robert Landick, Patricia J Kiley

“…We propose that this strategy favors use of catabolic pathways that recycle redox carriers via fermentation akin to lactate production in mammalian cells. Unexpectedly, bioinformatic analysis of the sequences bound by ArcA in ChIP-seq revealed that most ArcA binding sites contain additional direct repeat elements beyond the two required for binding an ArcA dimer. …”
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In Vitro and In Silico Analysis of Bergenia ciliata and Mimosa pudica for Inhibition of α-Amylase by Mahesh Bohara, Sajani Ghaju, Kabita Sharma, Surya Kant Kalauni, Karan Khadayat

“…The biological potential of the reported phytochemicals was also assessed by using bioinformatic tools. Furthermore, the active phytochemicals from these plants were docked with human pancreatic α-amylase to study their inhibitory activities to this enzyme. …”
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Transcriptomic-Based Identification of miR-125a Novel Targets in Human Hepatocarcinoma Cells by Ilenia De Leo, Nicola Mosca, Mariaceleste Pezzullo, Danila Valletta, Francesco Manfrevola, Vincenza Grazia Mele, Rosanna Chianese, Aniello Russo, Nicoletta Potenza

“…The merging of down-regulated genes with results from bioinformatic predictive tools yielded a number of candidate direct targets that were further experimentally validated by luciferase-based reporter assays. …”
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OMIC Technologies and Vaccine Development: From the Identification of Vulnerable Individuals to the Formulation of Invulnerable Vaccines by Nicola Cotugno, Alessandra Ruggiero, Veronica Santilli, Emma Concetta Manno, Salvatore Rocca, Sonia Zicari, Donato Amodio, Manuela Colucci, Paolo Rossi, Ofer Levy, Federico Martinon-Torres, Andrew J. Pollard, Paolo Palma

“…Finally, we will discuss how system biology “OMICs” data can be used to design bioinformatic tools to predict the vaccination outcome providing genetic and molecular “signatures” of protective immune response. …”
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Placental Vimentin Expression in Preeclampsia and Gestational Diabetes Mellitus by Fırat Asir, Suleyman Cemil Oglak, Tugcan Korak, Fatih Tas, Mehmet Yilmaz, Fikri Erdemci, Firat Sahin, Hayat Ayaz, Emine Zeynep Yilmaz, Gokhan Bolluk

“…Vimentin expression was generally recorded as negative in placental villi, fibrinoid substances, and connective tissue cells in the GDM group. Bioinformatic analysis showed that the AGE-RAGE signaling pathway and cancer-related pathways were mainly observed in Vimentin-associated pathways, which finally activate inflammatory pathways in both preeclampsia and GDM. …”
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Predicted Cold Shock Proteins from the Extremophilic Bacterium Deinococcus maricopensis and Related Deinococcus Species by Michael J. LaGier

“…The primary aim of this study was to test whether a representative, desert-dwelling Deinococcus, Deinococcus maricopensis, encodes Csps as part of its genome. Bioinformatic approaches were used to identify a Csp from D. maricopensis LB-34. …”
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Mass cytometry: exploring the immune landscape of systemic autoimmune and inflammatory diseases in the past fourteen years by Aïcha Kante, Aïcha Kante, Mathieu F. Chevalier, Damien Sène, Damien Sène, Jeanne Chauffier, Jeanne Chauffier, Stéphane Mouly, Stéphane Mouly, Benjamin Glenn Chousterman, Benjamin Glenn Chousterman, Fériel Azibani, Benjamin Terrier, Benjamin Terrier, Théo Pezel, Théo Pezel, Cloé Comarmond, Cloé Comarmond

“…We also delve into the bioinformatical approaches applied to mass cytometry to analyze the high volumes of data generated, as well as the impact of the use of complementary single cell RNA sequencing, and their spatial modalities. …”
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Proteomic Profiling and Functional Analysis of B Cell-Derived Exosomes upon Pneumocystis Infection by Dan Ma, Qian-Yu Zhang, Heng-Mo Rong, Kan Zhai, Zhao-Hui Tong

“…In this study, using tandem mass tag-based quantitative proteomics coupled with bioinformatic analysis, we attempted to characterize exosomes derived from B lymphocytes in response to PCP. …”
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Efficacy of Next-Generation Sequencing in Identifying Genetic Markers for Prostate Cancer Risk by Fahad H. Alaithan, Raghad H. Alaithan, Tauheed Ahmed

“…DNA samples were extracted from blood and tumor tissues, followed by library preparation and sequencing using an Illumina platform. Bioinformatic analysis was conducted to identify single nucleotide polymorphisms (SNPs), copy number variations (CNVs), and other genetic alterations linked to prostate cancer. …”
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Structural Predictive Model of Presenilin-2 Protein and Analysis of Structural Effects of Familial Alzheimer’s Disease Mutations by Alejandro Soto-Ospina, Pedronel Araque Marín, Gabriel de Jesús Bedoya, Andrés Villegas Lanau

“…From a theoretical analysis, a preliminary bioinformatic study is made to find the phosphorylation patterns in the protein and the hydropathic index according to the polarity and chemical environment. …”
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Methods of yeast genome editing by A. S. Rozanov, V. N. Shlyahtun, L. A. Tekutieva, O. M. Son, S. V. Sizova, S. E. Peltek

“…Many high­throughput methods were developed in the second decade of the XXI century, including those used in genomics, transcriptomics, proteomics, metabolomics, interactomics, etc. Modern bioinformatic databases now allow one to rapidly process the increasing flow of information and model cellular processes. …”
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Molecularly redefining small bowel adenocarcinoma to accelerate precision patient care – protocol of a multicenter observational cohort biomarker study by Rasmus Haunstrup Døssing, Julia Johanna Almer Broman, Colm J. O’Rourke, Elizaveta Mitkina Tabaksblat, Jesper Bøje Andersen, Carsten Palnæs Hansen, Tim Svenstrup Poulsen, Estrid V. S. Høgdall, Jakob Hagen Vasehus Schou, Dan Høgdall

“…Machine learning algorithms will be employed for bioinformatic analyses to interpret molecular data. Ethical approval has been obtained, and patient consent will be secured for the retrospective study component. …”
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Microcephalic osteodysplastic primordial dwarfism type II in four Indian children with PCNT variants by Amit Singh, Mahak Garg, Mohammed Shariq, Preeti Khetarpal, Inusha Panigrahi

“…Data were analyzed using standard bioinformatic algorithms and possible causal variants identified. …”
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Biophysical and biochemical evidence for the role of acetate kinases (AckAs) in an acetogenic pathway in pathogenic spirochetes. by Ranjit K Deka, Shih-Chia Tso, Wei Z Liu, Chad A Brautigam

“…But the lack of citric-acid-cycle enzymes suggested that alternative sources could be utilized, especially in microaerophilic host environments where glycolysis should not be robust. Recent bioinformatic, biophysical, and biochemical evidence supports the existence of an acetogenic energy-conservation pathway in T. pallidum and related treponemal species. …”
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Dataset for comparative analysis of precision metagenomics and traditional methods in urinary tract infection diagnosticsNCBI by Rob E. Carpenter, Sadia Almas, Vaibhav K. Tamrakar, Rahul Sharma

“…The dataset includes 47 urine samples, each analyzed by microbial culture, PCR, and precision metagenomics, followed by bioinformatic classification using the Explify® platform. precision metagenomics identified significantly more uropathogens (62 distinct organisms) compared to PCR (19 organisms) and microbial culture (13 organisms), with 98 % of samples testing positive for polymicrobial infections via precision metagenomics. …”
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Multimodal cadmium resistance and its regulatory networking in Pseudomonas aeruginosa strain CD3 by Soumya Chatterjee, Partha Barman, Chandan Barman, Sukanta Majumdar, Ranadhir Chakraborty

“…Whole-genome-based phylogenetic tools identified CD3 as the closest relative to Pseudomonas aeruginosa DSM50071T. Bioinformatic analyses revealed a complex network of regulations, with BfmR playing a crucial role in the functions of CzcR and CzcS, essential for biofilm formation and receptor signalling pathways. …”
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Structure and Expression Analyses of SVA Elements in Relation to Functional Genes by Yun-Jeong Kwon, Yuri Choi, Jungwoo Eo, Yu-Na Noh, Jeong-An Gim, Yi-Deun Jung, Ja-Rang Lee, Heui-Soo Kim

“…SINE-VNTR-Alu (SVA) elements are present in hominoid primates and are divided into 6 subfamilies (SVA-A to SVA-F) and active in the human population. Using a bioinformatic tool, 22 SVA element-associated genes are identified in the human genome. …”
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Characterization of the C-terminal tail of the Arc protein. by Melissa Boldridge, Jody Shimabukuro, Keith Nakamatsu, Christian Won, Chad Jansen, Helen Turner, Lei Wang

“…In this study, we characterized the C-terminal tail of Arc using integrated bioinformatic and structural biology techniques. We compared the sequences of Arc proteins in different mammal species and found that the amino-acid composition in the C-terminal tail region has a significantly higher degree of variation rate than the rest of the protein. …”
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