Article
Multidisciplinary Sciences
Shaun M. Kandathil, Joe G. Greener, Andy M. Lau, David T. Jones
Summary: The study presents a deep learning-based method for predicting protein structure, which reduces preprocessing time and directly outputs main chain coordinates. The approach is fast, easy to use, and produces accurate structural models. It enables large-scale modeling of proteins on minimal hardware.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Oncology
Manli Tan, Shangzhi Gao, Xiao Ru, Maolin He, Jinmin Zhao, Li Zheng
Summary: This study offers a satisfactory 10-GPCRs model signature to predict the prognosis of osteosarcoma, and provides candidate targets with approved drugs.
FRONTIERS IN ONCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Kishan Thambu, Victoria Glomb, Rolando Hernandez Trapero, Julio C. Facelli
Summary: Microproteins are a novel and expanding group of small proteins encoded by less than 100-150 codons, translated from small open reading frames (smORFs). Research results show that these microproteins have different amino acid compositions, similar structural characteristics, and fewer small-molecule ligand binding sites compared to regular proteins.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Abdo A. Elfiky, Ibrahim M. Ibrahim
Summary: Recent studies have shown the association between the Zika virus and the host cell membrane receptor GRP78. Utilizing structural bioinformatics and molecular dynamics simulations, the research predicts the binding site of the ZIKV envelope protein with GRP78, shedding light on the viral recognition mechanism.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Endocrinology & Metabolism
Wataru Nemoto, Yoshihiro Yamanishi, Vachiranee Limviphuvadh, Shunsuke Fujishiro, Sakie Shimamura, Aoi Fukushima, Hiroyuki Toh
Summary: The GGIP web server provides a web application for predicting GPCR-GPCR interaction pairs using a support vector machine. Users can input two sequences in FASTA format to receive predictions without the need for login. This server utilizes the GGIP software, which is currently the only method for predicting GPCR interaction pairs.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Biochemical Research Methods
Wenshan Wu, Zelu Huang, Weijia Kong, Hui Peng, Wilson Wen Bin Goh
Summary: This article summarizes the PROTREC method and explores the impact of different hyper-parameters on missing protein prediction. The results show that selecting different PROTREC score selection methods can improve the recovery rate of missing proteins, but may lead to a reduction in the number of predicted and validated proteins. It is also found that PROTREC can perform well independently.
Article
Multidisciplinary Sciences
Wenkai Wang, Chenjie Feng, Renmin Han, Ziyi Wang, Lisha Ye, Zongyang Du, Hong Wei, Fa Zhang, Zhenling Peng, Jianyi Yang
Summary: This study develops trRosettaRNA, a deep learning-based approach for predicting RNA 3D structures. Blind tests demonstrate that the automated predictions compete effectively with top human predictions on natural RNAs. However, accurately predicting structures for synthetic RNAs remains a challenging problem.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Saisai Sun, Wenkai Wang, Zhenling Peng, Jianyi Yang
Summary: Recent studies have shown that deep neural networks can accurately predict inter-residue contact/distance in protein structures, while fewer studies have focused on predicting RNA inter-nucleotide 3D closeness. A new algorithm named RNAcontact, based on deep residual neural networks and utilizing covariance information and predicted secondary structure, was proposed and demonstrated to achieve high precision in predicting RNA inter-nucleotide 3D closeness. These predicted 3D closenesses can provide critical information for RNA structure determination and folding, leading to more accurate models compared to approaches that do not consider 3D closeness.
Article
Biochemistry & Molecular Biology
Hongfei Ci, Xufeng Wang, Keyu Shen, Wei Du, Jiaming Zhou, Yan Fu, Qiongzhu Dong, Huliang Jia
Summary: This study identified key genes associated with angiogenesis in hepatocellular carcinoma (HCC) and explored therapeutic targets to improve patient prognosis. A risk score model based on 14 angiogenesis-related genes was developed and shown to predict overall survival in HCC patients. The study also predicted that the anti-angiogenic drug Crizotinib may be more effective in high-risk patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Charles Christoffer, Vijay Bharadwaj, Ryan Luu, Daisuke Kihara
Summary: Protein-protein docking is a useful tool for modeling protein complex structures and understanding their functional mechanisms. Despite the increasing number of known protein structures, there are still cases where the structures of proteins for docking are unknown. This study integrated the AttentiveDist method for protein structure prediction into the LZerD docking webserver, allowing users to submit protein sequences and obtain full-complex atomic models without providing any structure themselves.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biology
Congyu Lu, Zheng Zhang, Zena Cai, Zhaozhong Zhu, Ye Qiu, Aiping Wu, Taijiao Jiang, Heping Zheng, Yousong Peng
Summary: This study focuses on predicting hosts for prokaryotic viruses, introducing a Gaussian model software tool that outperforms previous computational methods, facilitating the rapid identification of hosts for newly identified prokaryotic viruses.
Article
Oncology
Lisi Luo, Yufang Li, Chumei Huang, Yujing Lin, Yonghui Su, Hong Cen, Yutong Chen, Siqi Peng, Tianyi Ren, Rongzhi Xie, Linjuan Zeng
Summary: This study identified 163 genes associated with overall survival of PDAC patients, established a 7-gene prediction model, and validated the genes through different experimental methods. The results showed that the model had good predictive ability in three datasets, especially in TNM stages I and II subgroups.
AMERICAN JOURNAL OF CANCER RESEARCH
(2021)
Article
Biochemical Research Methods
Yi-Heng Zhu, Jun Hu, Fang Ge, Fuyi Li, Jiangning Song, Yang Zhang, Dong-Jun Yu
Summary: The study developed a machine learning model to predict protein crystallization propensity and implemented two predictors, DCFCrystal with multiple stages and MDCFCrystal specially designed for membrane proteins. Experimental results showed that these predictors outperformed other state-of-the-art protein crystallization propensity predictors by significantly increasing Matthew's correlation coefficient values.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Raphael Mourad
Summary: This study proposes a versatile regression framework for accurately identifying and analyzing the three-dimensional organization of the genome, including differential borders and rearrangements. The results highlight the significance of this method in identifying new genomic features and transcription factors and comparing favorably with current state-of-the-art methods.
BMC BIOINFORMATICS
(2022)
Article
Biology
Phasit Charoenkwan, Nalini Schaduangrat, Mohammad Ali Moni, Pietro Lio, Balachandran Manavalan, Watshara Shoombuatong
Summary: This study presents a novel computational method, SAPPHIRE, for accurately identifying thermophilic proteins (TPPs) using sequence information. The method combines different feature encodings and machine learning algorithms to train baseline models and extract key information of TPPs. SAPPHIRE outperforms existing methods in terms of predictive performance and achieves higher accuracy and correlation coefficient.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Review
Clinical Neurology
Ellen Rijckmans, Katrien Stouffs, Anna C. Jansen, Stefanie Brock
Summary: This article discusses the clinical manifestations and neurological examination methods of malformations of cortical development (MCD), as well as their associations with MCD subtype and genotype. Detailed clinical information is crucial for interpreting genetic variants, and neurological examination can assist in diagnosis and interpretation of genetic testing. The findings of this study are applicable in clinical practice.
EUROPEAN JOURNAL OF PAEDIATRIC NEUROLOGY
(2022)
Article
Genetics & Heredity
Nuno Maia, Sven Potelle, Hamide Yildirim, Sandrine Duvet, Shyam K. Akula, Celine Schulz, Elsa Wiame, Alexander Gheldof, Katherine O'Kane, Abbe Lai, Karen Sermon, Maia Proisy, Philippe Loget, Tania Attie-Bitach, Chloe Quelin, Ana Maria Fortuna, Ana Rita Soares, Arjan P. M. de Brouwer, Emile Van Schaftingen, Marie-Cecile Nassogne, Christopher A. Walsh, Katrien Stouffs, Paula Jorge, Anna C. Jansen, Francois Foulquier
Summary: This study reports on six individuals, including two fetuses, with bi-allelic pathogenic variants in MAN2C1 gene from four different families. These individuals exhibit dysmorphic features, congenital anomalies, and brain abnormalities. The pathogenicity of MAN2C1 variants is confirmed, and it is demonstrated that these variants lead to accumulation and delay in the processing of fOSs in cells.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Clinical Neurology
Siddharth Banka, Abigail Bennington, Martin J. Baker, Ellen Rijckmans, Giuliana D. Clemente, Nurhuda Mohamad Ansor, Hilary Sito, Pritha Prasad, Kwame Anyane-Yeboa, Lauren Badalato, Boyan Dimitrov, David Fitzpatrick, Anna C. E. Hurst, Anna C. Jansen, Melissa A. Kelly, Ian Krantz, Claudine Rieubland, Meredith Ross, Natasha L. Rudy, Javier Sanz, Katrien Stouffs, Zhuo Luan Xu, Angeliki Malliri, Marcelo G. Kazanietz, Tom H. Millard
Summary: RAC1 is a crucial GTPase involved in neurodevelopmental disorders. This study reveals that certain variants in RAC1 can activate downstream signaling pathways, leading to abnormal neuronal morphology and a distinct neurodevelopmental disorder.
Review
Clinical Neurology
Stephanie Vanclooster, Stacey Bissell, Agnies M. van Eeghen, Nola Chambers, Liesbeth De Waele, Anna W. Byars, Jamie K. Capal, Sebastian Cukier, Peter Davis, Jennifer Flinn, Sugnet Gardner-Lubbe, Tanjala Gipson, Tosca-Marie Heunis, Dena Hook, J. Christopher Kingswood, Darcy A. Krueger, Aubrey J. Kumm, Mustafa Sahin, Eva Schoeters, Catherine Smith, Shoba Srivastava, Megumi Takei, Robert Waltereit, Anna C. Jansen, Petrus J. de Vries
Summary: TAND is a complex associated with TSC that includes behavioral, psychiatric, intellectual, academic, neuropsychological, and psychosocial manifestations. While there has been an increase in TAND research recently, there is still a need to focus on participants across the lifespan, research sites in low-middle income countries, and non-pharmacological interventions. Studies have shown variability in the quality of cohort studies, with a lack of non-pharmacological interventions and a focus on remote methodologies for addressing knowledge gaps.
JOURNAL OF NEURODEVELOPMENTAL DISORDERS
(2022)
Article
Clinical Neurology
Hanna M. Hulshof, Hugo J. Kuijf, Katarzyna Kotulska, Paolo Curatolo, Bernhard Weschke, Kate Riney, Pavel Krsek, Martha Feucht, Rima Nabbout, Lieven Lagae, Anna Jansen, Wim M. Otte, Maarten H. Lequin, Kamil Sijko, Arianna Benvenuto, Christoph Hertzberg, Barbora Benova, Theresa Scholl, Jessie De Ridder, Eleonora M. A. Aronica, David J. Kwiatkowski, Sergiusz Jozwiak, Elzbieta Jurkiewicz, Kees Braun, Floor E. Jansen
Summary: This study aimed to identify early MRI biomarkers of epilepsy in infants with TSC and associate them with neurodevelopmental outcomes at 2 years of age. The study found that the presence of tubers and higher tuber-brain ratios were associated with the development of clinical seizures, as well as lower cognitive and motor development quotients at 2 years. These results suggest that early MRI findings may guide clinical care for young children with TSC.
Article
Genetics & Heredity
Nienke Bouw, Hanna Swaab, Nicole Tartaglia, Anna C. Jansen, Sophie van Rijn
Summary: This study investigated early signs of social communication and social emotional development in very young children with sex chromosome trisomies (SCT). The results showed that children with SCT had difficulties in early social communication, particularly in responding to others. They also made less frequent eye contact during social interactions. These findings suggest that SCT affects the maturation of the social brain from an early age, highlighting the importance of early monitoring and support for social development in children with SCT.
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
(2022)
Article
Genetics & Heredity
Stefanie Brock, Annie Laquerriere, Florent Marguet, Scott J. Myers, Yuan Hongjie, Diana Baralle, Tim Vanderhasselt, Katrien Stouffs, Kathelijn Keymolen, Sukhan Kim, James Allen, Gil Shaulsky, Jamel Chelly, Pascale Marcorelle, Jacqueline Aziza, Laurent Villard, Elise Sacaze, Marie C. Y. de Wit, Martina Wilke, Grazia Maria Simonetta Mancini, Ute Hehr, Derek Lim, Sahar Mansour, Stephen F. Traynelis, Claire Beneteau, Marie Denis-Musquer, Anna C. Jansen, Andrew E. Fry, Nadia Bahi-Buisson
Summary: This study aimed to further define the phenotypic spectrum of NMDAR-related malformations of cortical development (MCDs). Clinical, radiological, and molecular features of new and previously reported patients were analyzed and neuropathological findings were presented. The study provides new insights into the clinical and imaging features of NMDAR-related MCDs and contributes to our understanding of the underlying pathogenic mechanisms.
JOURNAL OF MEDICAL GENETICS
(2023)
Article
Psychiatry
Tosca-Marie Heunis, Stacey Bissell, Anna W. Byars, Jamie K. Capal, Nola Chambers, Sebastian Cukier, Peter E. Davis, Liesbeth De Waele, Jennifer Flinn, Sugnet Gardner-Lubbe, Tanjala Gipson, J. Christopher Kingswood, Darcy A. Krueger, Aubrey J. Kumm, Mustafa Sahin, Eva Schoeters, Catherine Smith, Shoba Srivastava, Megumi Takei, Stephanie Vanclooster, Agnies M. van Eeghen, Robert Waltereit, Anna C. Jansen, Petrus J. de Vries
Summary: The TANDem project aims to reduce the identification and treatment gap for TSC patients and their caregivers regarding TAND. It includes the development and validation of a self-report version of the TAND Checklist, which will be incorporated into a smartphone application. Consensus clinical recommendations for TAND identification and treatment will also be generated, and a global TAND consortium will be established. The project has the potential to empower the TSC community by providing accessible digital solutions and personalized healthcare tools, and to provide healthcare professionals with clinical recommendations for managing TAND.
FRONTIERS IN PSYCHIATRY
(2022)
Article
Biochemistry & Molecular Biology
Mirte Scheper, Alessia Romagnolo, Zein Mersini Besharat, Anand M. Iyer, Romina Moavero, Christoph Hertzberg, Bernhard Weschke, Kate Riney, Martha Feucht, Theresa Scholl, Borivoj Petrak, Alice Maulisova, Rima Nabbout, Anna C. Jansen, Floor E. Jansen, Lieven Lagae, Malgorzata Urbanska, Elisabetta Ferretti, Aleksandra Tempes, Magdalena Blazejczyk, Jacek Jaworski, David J. Kwiatkowski, Sergiusz Jozwiak, Katarzyna Kotulska, Krzysztof Sadowski, Julita Borkowska, Paolo Curatolo, James D. Mills, Eleonora Aronica
Summary: This study used RNA sequencing analysis to define the expression patterns of miRNAs and isomiRs in the serum of patients with TSC, and identified potential circulating molecular biomarkers using ROC curve analysis to discriminate the development of neuropsychiatric comorbidity in TSC patients.
Review
Obstetrics & Gynecology
Annelore Van Der Kelen, Ozlem Okutman, Elodie Javey, Munevver Serdarogullari, Charlotte Janssens, Manjusha S. Ghosh, Bart J. H. Dequeker, Florence Perold, Claire Kastner, Emmanuelle Kieffer, Ingrid Segers, Alexander Gheldof, Frederik J. Hes, Karen Sermon, Willem Verpoest, Stephane Viville
Summary: High-throughput sequencing methods have led to the identification of numerous gene variants in male and female infertility. Evidence-based curation of these genes can improve diagnostic performance and genetic research.
HUMAN REPRODUCTION UPDATE
(2023)
Article
Rheumatology
Matthew A. Sherman, Katherine Pak, Iago A. Pinal-Fernandez, Willy A. N. Flegel, Ira N. W. Targoff, Frederick W. G. Miller, Lisa G. L. Rider, Andrew L. Mammen
Summary: This study investigated the prevalence and clinical features associated with anti-Sp4 autoantibodies in juvenile-onset idiopathic inflammatory myopathies (IIM). The results showed that anti-Sp4 autoantibodies were present in 7% of the juvenile myositis patients and were associated with coexisting anti-TIF1 autoantibodies and a reduced risk of cancer.
ARTHRITIS & RHEUMATOLOGY
(2023)
Letter
Genetics & Heredity
Liene Thys, Diane Beysen, Anna Jansen, Katrien Janssens, Marije Meuwissen
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
(2023)
Review
Genetics & Heredity
Mathilde Gras, Solveig Heide, Boris Keren, Stephanie Valence, Catherine Garel, Sandra Whalen, Anna C. Jansen, Kathelijn Keymolen, Katrien Stouffs, Melanie Jennesson, Celine Poirsier, Gaetan Lesca, Christel Depienne, Caroline Nava, Agnes Rastetter, Aurore Curie, Laurence Cuisset, Vincent Des Portes, Mathieu Milh, Perrine Charles, Cyril Mignot, Delphine Heron
Summary: In this study, the clinical and molecular data of female patients with de novo ARX pathogenic variants were collected and analyzed. The study found that intellectual disability is a common feature in females with this X linked condition, and the clinical spectrum is broad.
JOURNAL OF MEDICAL GENETICS
(2023)
Article
Biochemical Research Methods
Laura D. T. Vo Ngoc, Randy Osei, Katrin Dohr, Catharina Olsen, Sara Seneca, Alexander Gheldof
Summary: EDIR is a database containing the positions of interspersed repeats within the human exome. It has been calculated using an inductive strategy and can be queried through an R/Bioconductor package or a web interface.
