Article
Biochemical Research Methods
Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Young-Ki Paik, Ileana M. Cristea, Fernando J. Corrales, Cecilia Lindskog, Susan Weintraub, Michael H. A. Roehrl, Siqi Liu, Nuno Bandeira, Sudhir Srivastava, Yu-Ju Chen, Ruedi Aebersold, Robert L. Moritz, Eric W. Deutsch
Summary: The 2021 Metrics of the HUPO Human Proteome Project (HPP) reveal significant progress in detecting protein expression in the human genome. The number of missing proteins has decreased, and the utilization of proteomics in biological and clinical research continues to expand and integrate effectively with other omics platforms. This represents a promising advancement in understanding the human proteome and its potential applications in healthcare.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Charles Pineau, Nicolle H. Packer, Ileana M. Cristea, Cecilia Lindskog, Susan T. Weintraub, Sandra Orchard, Michael H. A. Roehrl, Edouard Nice, Siqi Liu, Nuno Bandeira, Yu-Ju Chen, Tiannan Guo, Ruedi Aebersold, Robert L. Moritz, Eric W. Deutsch
Summary: According to the 2022 metrics of the HUPO Human Proteome Project (HPP), protein expression has been detected for 93.2% of the predicted proteins in the human genome. The number of missing proteins has been reduced, indicating experimental progress and reclassification. Proteomics continues to yield significant findings in biological and clinical studies and integrates with other omics platforms.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Chemistry, Analytical
Taran Driver, Nikhil Bachhawat, Ruediger Pipkorn, Leszek J. Frasinski, Jon P. Marangos, Marina Edelson-Averbukh, Vitali Averbukh
Summary: The study introduces a protein database search engine based on 2D-PC-MS method, which can accurately identify protein sequences by matching theoretical and experimentally detected correlating fragments, with high structural specificity. This search engine is not only suitable for peptide identification, but also for intact protein identification.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Mustafa S. Pir, Halil Bilgin, Ahmet Sayici, Furkan M. Torun, Pei Zhao, Yahong Kang, Sebiha Cevik, Oktay Kaplan
Summary: ConVarT is an integrated search engine that helps match variants between humans, mice, and Caenorhabditis elegans. Analyzing phenotypic variants from mice and C. elegans can provide clues about the functional consequences of human genetic variants.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Georg J. Pirklbauer, Christian E. Stieger, Manuel Matzinger, Stephan Winkler, Karl Mechtler, Viktoria Dorfer
Summary: Cross-linking mass spectrometry (XL-MS) has enabled insights into protein structures and interactions, with cleavable cross-linkers further reducing search space and promoting proteome-wide studies. However, some search engines struggle with validating identified cross-linked peptides and estimating false discovery rates (FDR). The new search engine MS Annika provides realistic FDR estimates without the need for arbitrary score cutoffs, offering on average 44% more identifications at a similar or better true FDR compared to other tools.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Hematology
Mary L. Clarke, Roza B. Lemma, David S. Walton, Giacomo Volpe, Boris Noyvert, Odd S. Gabrielsen, Jon Frampton
Summary: MYB is crucial for gene regulation in hematopoietic hierarchy and maintaining normal hematopoietic stem cells (HSC). Genetic dysregulation of MYB is involved in leukemias, while inherited noncoding variants of MYB contribute to various hematological conditions. However, the mechanism linking MYB levels to disease predisposition, especially age-related disease initiation, remains unknown. Our mouse model of Myb insufficiency shows development of MPN, myelodysplasia, and leukemia in later life, mimicking the age profile of human diseases. In young Myb-insufficient mice, we observe altered proteasomal activity and elevated proliferation indicators, suggesting an imbalance in proteostasis contributing to disease initiation.
Article
Computer Science, Software Engineering
Luca Di Grazia, Paul Bredl, Michael Pradel
Summary: This paper introduces DiffSearch, a search engine that returns a set of code changes matching a given query, using a query language with wildcards and placeholders and a tree-based matching algorithm. The approach indexes and maps code changes into a feature space for efficient searching. The implementation for Java, JavaScript, and Python responds within seconds, achieving high recall rates and outperforming regular expression-based and GitHub searches. The approach is valuable for finding relevant code changes and gathering real-world bug fix datasets.
IEEE TRANSACTIONS ON SOFTWARE ENGINEERING
(2023)
Article
Materials Science, Biomaterials
Chao Liu, Ting Wu, Xin Shu, Shang-Tong Li, Daniel R. Wang, Nanxi Wang, Rong Zhou, Hao Yang, Hong Jiang, Ivo A. Hendriks, Pengyun Gong, Long Zhang, Michael L. Nielsen, Kui Li, Lei Wang, Bing Yang
Summary: The software OpenUaa is developed for identifying protein crosslinks generated by genetically encoded unnatural amino acids and endogenous protein conjugation, dramatically improving identification sensitivity and coverage. Integrating GECX with OpenUaa enabled the successful identification of the direct interactome of thioredoxin in Escherichia coli cells and significantly improved the coverage of SUMOylated peptides.
Article
Geochemistry & Geophysics
Jiyan Xue, Sihong Wu, Qinghua Huang, Li Zhao, Nicholas Sarlis, Panayiotis A. Varotsos
Summary: Geoelectric data are valuable for short-term earthquake prediction, but identifying anomalies in this data can be challenging due to the large volumes and noise disturbance. In this study, we develop a real-time automatic search engine (RASE) that uses an unsupervised convolutional denoising network (UCN) and a supervised LSTM prediction network (SLN) to detect anomalous signals. Experiments show that the RASE provides accurate and efficient detection results within seconds, and the combination of UCN and SLN gives the highest accuracy. This search engine reduces human labor and maximizes the potential of geoelectric field observation in earthquake monitoring and disaster prevention.
IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING
(2023)
Article
Biochemical Research Methods
Chen Zhou, Shuaijian Dai, Yuanqiao Lin, Sheng Lian, Xiaodan Fan, Ning Li, Weichuan Yu
Summary: In this paper, a comprehensive cross-linking search method called ECL-PF is proposed for cleavable XL-MS data analysis, which can improve the sensitivity of protein-protein interaction detection and protein structure probing.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Siti Hajar Amir, Mohd Hafis Yuswan, Wan Mohd Aizat, Muhammad Kamaruzaman Mansor, Mohd Nasir Mohd Desa, Yus Aniza Yusof, Lai Kok Song, Shuhaimi Mustafa
Summary: This study evaluated the performance of different search engines in halal analysis and found that combining different search engines can provide a comprehensive protein list, which is helpful for future precise halal analysis.
JOURNAL OF PROTEOMICS
(2021)
Article
Multidisciplinary Sciences
Mikihito Shibata, Kartik Pattabiraman, Sydney K. Muchnik, Navjot Kaur, Yury M. Morozov, Xiaoyang Cheng, Stephen G. Waxman, Nenad Sestan
Summary: Comparative analysis of human and macaque transcriptomic data identified transient upregulation of CBLN2 gene expression in the prefrontal cortex during midfetal development, coinciding with synaptogenesis initiation. Species differences in CBLN2 expression and laminar distribution may be partly due to Hominini-specific deletions containing SOX5-binding sites within a retinoic acid-responsive CBLN2 enhancer. Humanization of the mouse Cbln2 enhancer promotes increased and ectopic Cbln2 expression, suggesting a genetic and molecular basis for the disproportionate increase in dendritic spines in the Hominini prefrontal cortex and its potential linkage to neuropsychiatric disorder pathogenesis.
Article
Biochemistry & Molecular Biology
Ayush Malik, Anupam Banerjee, Abantika Pal, Pralay Mitra
Summary: De-novo protein design explores unexplored sequence space and an efficient search algorithm is proposed for better sequence-structure compatibility in protein design. The algorithm exhibits good performance with low deviations and high recapitulation of core residues, while introducing new molecular functions.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemical Research Methods
Nanette Christie, Chanaka Mannapperuma, Raphael Ployet, Karen van der Merwe, Niklas Mahler, Nicolas Delhomme, Sanushka Naidoo, Eshchar Mizrachi, Nathaniel R. Street, Alexander A. Myburg
Summary: Affordable high-throughput DNA and RNA sequencing technologies are enabling genomic analysis of plant and animal populations, allowing for new systems genetics approaches to study complex traits. Developing intuitive tools to browse and analyze resulting large-scale genetic and genomic datasets remains a significant challenge.
BMC BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Eduardo A. De La Toba, Krishna D. B. Anapindi, Jonathan V. Sweedler
Summary: Protein database search engines are crucial for mass spectrometry-based peptidomic analyses. In this study, four different search engines were compared, with PEAKS found to have the highest number of peptide and neuropeptide identifications. It was also discovered that errors in precursor and fragment ion m/z were the primary factors influencing incorrect peptide assignments.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Fuyi Li, Yanan Wang, Chen Li, Tatiana T. Marquez-Lago, Andre Leier, Neil D. Rawlings, Gholamreza Haffari, Jerico Revote, Tatsuya Akutsu, Kuo-Chen Chou, Anthony W. Purcell, Robert N. Pike, Geoffrey Webb, A. Ian Smith, Trevor Lithgow, Roger J. Daly, James C. Whisstock, Jiangning Song
BRIEFINGS IN BIOINFORMATICS
(2019)
Article
Biochemistry & Molecular Biology
Nkumbu L. Sikanyika, Helena C. Parkington, A. Ian Smith, Sanjaya Kuruppu
NEUROCHEMICAL RESEARCH
(2019)
Article
Multidisciplinary Sciences
Anja Greule, Thierry Izore, Dumitrita Iftime, Julien Tailhades, Melanie Schoppet, Yongwei Zhao, Madeleine Peschke, Iftekhar Ahmed, Andreas Kulik, Martina Adamek, Robert Ja Goode, Ralf B. Schittenhelm, Joe A. Kaczmarski, Colin J. Jackson, Nadine Ziemert, Elizabeth H. Krenske, James J. De Voss, Evi Stegmann, Max J. Cryle
NATURE COMMUNICATIONS
(2019)
Article
Biochemistry & Molecular Biology
Milda Kaniusaite, Robert J. A. Goode, Ralf B. Schittenhelm, Thomas M. Makris, Max J. Cryle
ACS CHEMICAL BIOLOGY
(2019)
Article
Biochemical Research Methods
Anup D. Shah, Robert J. A. Goode, Cheng Huang, David R. Powell, Ralf B. Schittenhelm
JOURNAL OF PROTEOME RESEARCH
(2020)
Article
Chemistry, Organic
Julien Tailhades, Yongwei Zhao, Melanie Schoppet, Anja Greule, Robert J. A. Goode, Ralf B. Schittenhelm, James J. De Voss, Max J. Cryle
Article
Chemistry, Organic
Yongwei Zhao, Robert J. A. Goode, Ralf B. Schittenhelm, Julien Tailhades, Max J. Cryle
JOURNAL OF ORGANIC CHEMISTRY
(2020)
Article
Chemistry, Multidisciplinary
Julien Tailhades, Yongwei Zhao, Y. T. Candace Ho, Anja Greule, Iftekhar Ahmed, Melanie Schoppet, Ketav Kulkarni, Rob J. A. Goode, Ralf B. Schittenhelm, James J. De Voss, Max J. Cryle
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2020)
Article
Biochemistry & Molecular Biology
Milda Kaniusaite, Julien Tailhades, Tiia Kittila, Christopher D. Fage, Robert J. A. Goode, Ralf B. Schittenhelm, Max J. Cryle
Summary: The biosynthesis of glycopeptide antibiotics demonstrates the exceptional ability of nonribosomal peptide synthesis to generate diverse and complex structures. An important study on the NRPS assembly lines involved in synthesizing GPAs revealed that they function as dynamic peptide assembly lines, allowing for flexible control over amino acid modifications and peptide formation, which is beneficial for the redesign of important biosynthetic systems.
Article
Genetics & Heredity
Fuyi Li, Andre Leier, Quanzhong Liu, Yanan Wang, Dongxu Xiang, Tatsuya Akutsu, Geoffrey Webb, A. Ian Smith, Tatiana Marquez-Lago, Jian Li, Jiangning Song
GENOMICS PROTEOMICS & BIOINFORMATICS
(2020)
Article
Biochemistry & Molecular Biology
Milda Kaniusaite, Tiia Kittila, Robert J. A. Goode, Ralf B. Schittenhelm, Max J. Cryle
ACS CHEMICAL BIOLOGY
(2020)
Article
Multidisciplinary Sciences
Thierry Izore, Y. T. Candace Ho, Joe A. Kaczmarski, Athina Gavriilidou, Ka Ho Chow, David L. Steer, Robert J. A. Goode, Ralf B. Schittenhelm, Julien Tailhades, Manuela Tosin, Gregory L. Challis, Elizabeth H. Krenske, Nadine Ziemert, Colin J. Jackson, Max J. Cryle
Summary: Non-ribosomal peptide synthetases (NRPSs) are essential for assembling complex natural products, with condensation domains playing a central role in chain assembly. Structural snapshots of a condensation domain bound to an aminoacyl-PCP substrate reveal a mechanism for controlling substrate access and tuning selectivity, without requiring a distinct pocket for side chain selection during peptide assembly.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Christina R. Hall, Philippa C. Griffin, Andrew J. Lonie, Jeffrey H. Christiansen
Summary: The authors have implemented a hybrid training approach to address the need for bioinformatics training among biologists in Australia. This method combines guidance from experienced trainers with webinar-style delivery and concurrent hands-on practical exercises. It has been successfully used internationally to train over 800 researchers in various bioinformatics topics and software platforms, and can be adapted to different locations and settings.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Milda Kaniusaite, Robert J. A. Goode, Julien Tailhades, Ralf B. Schittenhelm, Max J. Cryle
Article
Chemistry, Multidisciplinary
Milda Kaniusaite, Julien Tailhades, Edward A. Marschall, Robert J. A. Goode, Ralf B. Schittenhelm, Max J. Cryle