Article
Biochemical Research Methods
Huanyu Tao, Xuejun Zhao, Keqiong Zhang, Peicong Lin, Sheng-You Huang
Summary: In this study, an improved hierarchical peptide docking algorithm, HPEPDOCK2.0, was proposed to predict the binding modes of cyclic peptides with proteins. The algorithm integrates an efficient peptide conformation sampling algorithm and a knowledge-based scoring function, and it showed higher success rate and shorter running time compared to other algorithms.
Article
Chemistry, Multidisciplinary
Stijn M. Agten, Emma E. Watson, Jorge Ripoll-Rozada, Luke J. Dowman, Mike C. L. Wu, Imala Alwis, Shaun P. Jackson, Pedro Jose Barbosa Pereira, Richard J. Payne
Summary: This study presents a rational design of novel trivalent thrombin inhibitors that simultaneously block two exosites and the active site. These engineered hybrids were synthesized using a tandem diselenide-selenoester ligation and native chemical ligation in one-pot, showing potent anticoagulant activity both in vitro and in vivo. The rational engineering approach paves the way for the development of potent and selective inhibitors for various enzymatic targets.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Multidisciplinary Sciences
Duc Tran, Hung Nguyen, Bang Tran, Carlo La Vecchia, Hung N. Luu, Tin Nguyen
Summary: Accurate analysis of single-cell RNA sequencing (scRNA-seq) data is crucial for various research fields, but is often hindered by technical noise and high dropout rates. The hierarchical autoencoder, scDHA, introduced in this study, outperforms existing methods in various aspects of scRNA-seq analysis, including cell segregation and classification.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Beirong Zhang, Zhou Gong, Lili Zhao, Yuxin An, Hang Gao, Jing Chen, Zhen Liang, Maili Liu, Yukui Zhang, Qun Zhao, Lihua Zhang
Summary: Protein dynamics are crucial for their diverse functions, and are significantly influenced by the intracellular environment. This study introduces a hierarchical decoding strategy that uses chemical cross-linking mass spectrometry to investigate protein dynamics in cells. Computational analysis based on distance restraints derived from cross-links is used to infer protein dynamics in vivo.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Idan Hekselman, Lior Kerber, Maya Ziv, Gil Gruber, Esti Yeger-Lotem
Summary: Hereditary diseases often manifest clinically in specific tissues, and understanding these tissues is crucial for comprehending disease mechanisms. However, information about the affected tissues in each disease is not easily accessible. The Organ-Disease Annotations (ODiseA) database provides detailed annotations of diseases and the inflicted tissues, serving as a valuable tool for researchers studying genotype-phenotype relationships of hereditary diseases.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Mathias Wilhelm, Daniel P. Zolg, Michael Graber, Siegfried Gessulat, Tobias Schmidt, Karsten Schnatbaum, Celina Schwencke-Westphal, Philipp Seifert, Niklas de Andrade Kraetzig, Johannes Zerweck, Tobias Knaute, Eva Braeunlein, Patroklos Samaras, Ludwig Lautenbacher, Susan Klaeger, Holger Wenschuh, Roland Rad, Bernard Delanghe, Andreas Huhmer, Steven A. Carr, Karl R. Clauser, Angela M. Krackhardt, Ulf Reimer, Bernhard Kuster
Summary: The authors improved the prediction of non-tryptic peptides using deep learning and data from the ProteomeTools project, enabling various immunological discoveries. Their study demonstrated that accurate identification of HLA peptides can be enhanced, leading to the discovery of additional immunogenic neo-epitopes from patient tumors in published data.
NATURE COMMUNICATIONS
(2021)
Article
Computer Science, Interdisciplinary Applications
Alexandra List, Chang-Jen Lin
Summary: This study examines the use of digital annotations to support undergraduate students in learning from multiple texts. It found that metacognitive monitoring and evaluation strategies contribute to multiple text comprehension and integration.
COMPUTERS & EDUCATION
(2023)
Review
Biochemistry & Molecular Biology
Chris Avery, John Patterson, Tyler Grear, Theodore Frater, Donald J. Jacobs
Summary: Machine learning has been widely applied in computational biology to understand protein function. By integrating machine learning methods into computational models, prediction accuracy and understanding of protein function can be improved. This article discusses the application of machine learning in protein structure prediction, protein engineering, protein-ligand binding, and highlights future opportunities for research.
Article
Chemistry, Multidisciplinary
Rokam Jeong, Jae-Hoon Eom, Jintaek Gong, Minsang Kang, Jaewook Kim, Hee-Seung Lee
Summary: This study reports the first example of programmed radial assembly of anisotropic microparticles derived from a helical foldamer with a C-terminal cysteine residue. Surface-exposed thiols play a crucial role in facilitating interparticle hydrogen bonding to form higher-order structures in an aqueous solution.
Article
Food Science & Technology
Gang Wu, Jianzhong Zhou, Linlin Fan, Xiaoli Liu, Ying Wang, Caie Wu
Summary: This study analyzed the differentially expressed proteins in fresh blackberry wine and aged blackberry wine, and identified the sources of protein causing haze formation. The majority of proteins associated with polyphenols and haze in blackberry wine were found to come from Saccharomyces cerevisiae, mold, and blackberry raw materials. This study provides valuable information for addressing haze formation caused by proteins.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Leticia Matilla-Cuenca, Agustina Taglialegna, Carmen Gil, Alejandro Toledo-Arana, Inigo Lasa, Jaione Valle
Summary: Biofilm engineering is a controllable method to create living structures with programmable functionalities. This study uses facultative amyloid-like protein Bap to decorate the extracellular biofilm matrix or the bacterial cell surface with functional domains or proteins. By modulating pH, the localization of functional tags can be changed. A tool for trapping and covalently immobilizing molecules at bacterial cell surface or biofilm matrix is built based on Bap features. The cell wall of various Gram-positive bacteria can be functionalized through the addition of recombinant Bap-amyloid domain.
NPJ BIOFILMS AND MICROBIOMES
(2022)
Article
Chemistry, Multidisciplinary
Rashik Ahmed, Jinfeng Huang, Madoka Akimoto, Tongyu Shi, Giuseppe Melacini
Summary: The study demonstrates that temperature has a significant impact on N-15 - R-2, effectively identifying self-association sites. Through agglomerative clustering, the experiment systematically examines the network of residues involved in self-association and extracts the hierarchy of alpha S self-association sites.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biotechnology & Applied Microbiology
Christopher Chevillard, Axelle Amen, Solene Besson, Dalil Hannani, Isabelle Bally, Valentin Dettling, Evelyne Gout, Christophe J. Moreau, Marlyse Buisson, Salome Gallet, Daphna Fenel, Emilie Vassal-Stermann, Guy Schoehn, Pascal Poignard, Marie-Claire Dagher, Pascal Fender
Summary: In this study, a previously designed ADDomer VLP platform was adapted to display multimeric array of large antigens using the SpyTag/SpyCatcher system. By decorating the newly designed VLP with glycosylated receptor binding domain of SARS-CoV-2, significant specific humoral response and strong neutralization titers were induced, surpassing those of COVID-19 convalescent patients.
Article
Chemistry, Multidisciplinary
Isra S. Hassan, Jack T. Fuller, Vanessa N. Dippon, Angeline N. Ta, Michael W. Danneman, Brian R. McNaughton, Anastassia N. Alexandrova, Tomislav Rovis
Summary: We present a computationally-guided protein engineering approach to enhance the catalytic activity of monomeric streptavidin Rh(iii) artificial metalloenzyme in the enantioselective coupling reaction. The improvement in turnover number (TON) is found to be correlated with the calculated distances between the Rh(iii) metal and surrounding residues, highlighting the additional control capability of the artificial metalloenzyme through through-space interactions in metal-catalyzed transformations.
Article
Biochemical Research Methods
Jian Gao, Bin Hu, Lei Chen
Summary: The study introduced a network computational method to identify novel phenotypic annotations of proteins, which was executed through constructing a heterogeneous network. Results showed the superior performance and utility of the method compared to other network methods.
CURRENT BIOINFORMATICS
(2021)
Article
Oncology
Guy Kelman, Nadav Brandes, Michal Linial
Summary: This article presents a new cancer portal that quantifies and presents gene selection in tumors across 33 cancer types and pan-cancer based on the biochemical functional effects of mutations at the protein level. Users can view known and overlooked cancer genes through the portal's simple visual interface.
Article
Biochemical Research Methods
Nadav Brandes, Dan Ofer, Yam Peleg, Nadav Rappoport, Michal Linial
Summary: Self-supervised deep language modeling has achieved unprecedented success with natural language tasks, and the authors introduce a new deep language model called ProteinBERT specifically designed for proteins, which efficiently handles long sequences and achieves near or even better performance than other methods, providing an effective framework for rapid training of protein predictors.
Article
Cardiac & Cardiovascular Systems
Nadav Rappoport, Gal Aviel, David M. Shahian, Amit Korach, Shai Carmi, John F. Keaney, Oz M. Shapira
Summary: This study aimed to quantify the risk trend of resternotomy coronary artery bypass grafting (CABG) over the past 2 decades. The outcomes of consecutive resternotomy CABG patients and randomly selected first-time CABG patients reported to a cardiac surgery database were compared. The risk-adjusted odds ratios for mortality and morbidity declined significantly over time.
ANNALS OF THORACIC SURGERY
(2023)
Article
Multidisciplinary Sciences
Richard K. Perez, M. Grace Gordon, Meena Subramaniam, Min Cheol Kim, George C. Hartoularos, Sasha Targ, Yang Sun, Anton Ogorodnikov, Raymund Bueno, Andrew Lu, Mike Thompson, Nadav Rappoport, Andrew Dahl, Cristina M. Lanata, Mehrdad Matloubian, Lenka Maliskova, Serena S. Kwek, Tony Li, Michal Slyper, Julia Waldman, Danielle Dionne, Orit Rozenblatt-Rosen, Lawrence Fong, Maria Dall'Era, Brunilda Balliu, Aviv Regev, Jinoos Yazdany, Lindsey A. Criswell, Noah Zaitlen, Chun Jimmie Ye
Summary: By using mux-seq technology, we conducted extensive single-cell RNA sequencing on peripheral blood cells from SLE patients and healthy individuals. We found increased expression of type 1 interferon-stimulated genes in monocytes, reduced naive CD4(+) T cells, and expanded cytotoxic CD8(+) T cells in SLE patients. The cell type-specific expression features could predict the case-control status and classify patients into two molecular subtypes. Furthermore, we linked SLE-associated genetic variants to cell type-specific expression using genotyping data.
Article
Health Care Sciences & Services
Ido Blass, Tali Sahar, Adi Shraibman, Dan Ofer, Nadav Rappoport, Michal Linial
Summary: This study aimed to develop a model for endometriosis based on the UK-biobank data and re-assess the contribution of known risk factors to this condition. By using machine learning algorithms, an effective prediction model was achieved. The study found that women diagnosed with endometriosis had more diagnoses of other diseases prior to the diagnosis. Using the explainable AI tool SHAP, informative features related to endometriosis were identified.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Article
Psychiatry
Hyojung Paik, Junehawk Lee, Chan-Seok Jeong, Jun Sung Park, Jeong Ho Lee, Nadav Rappoport, Younghoon Kim, Hee-Young Sohn, Chulman Jo, Jimin Kim, Seong Beom Cho
Summary: Observations have confirmed the comorbidity between heart diseases and cognitive impairment. Genetic variants in APOB and ADIPOQ genes were found to have a pleiotropic effect on both diseases. Integrating healthcare records and genetic evidence can help understand the molecular underpinnings of heart disease and associated cognitive impairment.
TRANSLATIONAL PSYCHIATRY
(2022)
Review
Biochemistry & Molecular Biology
Naomi van Wijk, Keren Zohar, Michal Linial
Summary: This review article discusses the role of mature microRNAs (miRNAs) in post-transcriptional regulation and their involvement in key cellular processes. It emphasizes the importance of miRNA storage and translocation in regulating cellular responses to stress and changing conditions. The article also highlights the shared principles of miRNA regulation in oxidative stress, tumorigenesis, viral infection, and synaptic plasticity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Keren Zohar, Eliran Giladi, Tsiona Eliyahu, Michal Linial
Summary: Neurodegenerative disorders, brain injury, and aging lead to reduced ability of brain cells to cope with oxidative stress and inflammation. This study focused on the response to oxidative stress in SH-SY5Y cells and identified several differentially expressed lncRNAs associated with redox homeostasis, energy metabolism, and neurodegenerative diseases. The impact of ladostigil, an antioxidant and anti-inflammatory agent, on lncRNA expression levels was also examined. These findings suggest that lncRNAs may play a role in cellular homeostasis and could be potential targets for drugs that impact cell viability.
Article
Genetics & Heredity
Roei Zucker, Michael Kovalerchik, Michal Linial
Summary: Hypertension is a polygenic disease that affects a large number of adults worldwide. Although the heritability of hypertension is high, our understanding of its underlying mechanisms is limited. In this study, we compared the findings from genome-wide association studies and proteome-wide association studies in patients with essential hypertension. We identified a number of associated genes, many of which were only significant in the gene-based approach. Furthermore, we found that the genetic effects of hypertension are sex-dependent, with stronger effects in females. Our study provides insights into the biology of hypertension and highlights the importance of considering sex-dependent genetic effects.
Article
Biochemistry & Molecular Biology
Keren Zohar, Elyad Lezmi, Fanny Reichert, Tsiona Eliyahu, Shlomo Rotshenker, Marta Weinstock, Michal Linial
Summary: This study found that the combination of bzATP and LPS can induce a sustained and robust inflammatory response in neonatal microglial cells, characterized by the release of pro-inflammatory cytokines and the induction of long noncoding RNAs. Analyzing the transcriptional profile and related signaling pathways, the researchers suggest that neonatal glial cells exhibit a distinctive expression program in which inflammatory-related genes are significantly upregulated.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Computer Science, Artificial Intelligence
Benyamine Abbou, Orna Tal, Gil Frenkel, Robyn Rubin, Nadav Rappoport
Summary: Operating rooms are crucial in hospitals, and we have trained a machine learning model to predict the length of surgeries and improve their productivity and utility. By analyzing extensive clinical and administrative data, our model outperformed traditional models and explained a significant portion of variance in surgery durations.
BIG DATA AND COGNITIVE COMPUTING
(2022)
Article
Genetics & Heredity
Tair Shauli, Nadav Brandes, Michal Linial
Summary: This study introduces human-specific amino acid substitution matrices based on genetic variations in the modern human population, which are fundamentally different from classic cross-species matrices. Moreover, the study also proposes a purifying selection signal in the human proteome.
NAR GENOMICS AND BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Brooke Sheppard, Nadav Rappoport, Po-Ru Loh, Stephan J. Sanders, Noah Zaitlen, Andy Dahl
Summary: The study introduces a model for structured polygenic epistasis called Coordinated Epistasis (CE) and proves that several recent theories of genetic architecture fall under CE. By proposing the Even-Odd (EO) test and calibrating it in various realistic biological models, evidence of CE is found in 18 out of 26 traits in the UK Biobank. The study concludes that CE is a genetic architecture dimension capturing structured, systemic forms of epistasis in complex human traits.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
