Article
Biochemistry & Molecular Biology
Rui-Xiang Li, Ning-Ning Zhang, Bin Wu, Bo OuYang, Hong-Bin Shen
Summary: The multiobjective algorithm Hydra for protein design introduced in this report utilizes two different energy functions to optimize solutions simultaneously. By leveraging the latent quantitative relationship between different amino acid types, the algorithm facilitates the search process, resulting in high accuracy and a high-speed search process.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemical Research Methods
Sylwester Swat, Artur Laskowski, Jan Badura, Wojciech Frohmberg, Pawel Wojciechowski, Aleksandra Swiercz, Marta Kasprzak, Jacek Blazewicz
Summary: This study proposes a new genome-scale de novo assembler, ALGA, based on the overlap graph approach, which can generate more accurate contigs in a short amount of time. ALGA outperforms nine state-of-the-art assemblers in terms of overall quality of genome reconstruction, achieving a good balance between genome coverage, accuracy, and length of resulting sequences.
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
Plant Sciences
Ashwil Klein, Lizex H. H. Husselmann, Achmat Williams, Liam Bell, Bret Cooper, Brent Ragar, David L. Tabb
Summary: Proteomics has been more valuable in model organisms with genome sequence annotations than in nonmodel organisms lacking such annotations. This study aimed to establish a protein sequence set for the nonmodel organism chia using RNA-Seq experiments. The results showed that assembling RNA-Seq datasets for chia resulted in high completeness of transcript sequences, though the number of sequences and genes varied. After six-frame translation, orthologs were detected among other species within the same taxonomic order.
Article
Computer Science, Information Systems
Kimia Behizadi, Nafiseh Jafarzadeh, Ali Iranmanesh
Summary: This paper focuses on the graph-theoretical side of de novo genome assembly algorithms, exploring the construction of various graph data structures and classifying the most significant and recent assemblers based on these structures.
Article
Chemistry, Medicinal
Andrea Mauri, Matteo Bertola
Summary: AlvaBuilder is a software tool that can generate novel molecules with desirable characteristics through a graphical interface. Users can define these characteristics based on molecular descriptors, QSAR/QSPR models predictions, and matching molecular fragments or design compounds similar to a given one. The generated molecules are always syntactically valid as they are composed of fragments from a training dataset selected by the user. In this paper, we demonstrate the use of AlvaBuilder for designing new compounds in a specific case study.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Adam H. Freedman, Michele Clamp, Timothy B. Sackton
Summary: De novo transcriptome assembly is a powerful tool for evolutionary inferences, but it often faces bias and noise issues in data analysis, leading to underestimation of diversity and gene expression estimates. Researchers should look for ways to minimize the impact of bias in transcriptome assemblies.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Multidisciplinary Sciences
Andy Hsien-Wei Yeh, Christoffer Norn, Yakov Kipnis, Doug Tischer, Samuel J. Pellock, Declan Evans, Pengchen Ma, Gyu Rie Lee, Jason Z. Zhang, Ivan Anishchenko, Brian Coventry, Longxing Cao, Justas Dauparas, Samer Halabiya, Michelle DeWitt, Lauren Carter, K. N. Houk, David Baker
Summary: We have successfully designed an artificial luciferase with high selectivity and catalytic efficiency using a deep-learning-based approach. This achievement is a major milestone in computational enzyme design and has broad applications in biomedical research.
Article
Biophysics
Yicen Xiao, Juansheng Ren, Yunjiao Wang, Xiaohan Chen, Shuo Zhou, Minghan Li, Fangyuan Gao, Liyuan Liang, Deqiang Wang, Guangjun Ren, Liang Wang
Summary: This study utilized nanopore as a single-molecule detector to profile rice peptides with diverse properties. By combining bioinformatics, biochemistry, and nanopore analysis, the researchers identified water-soluble peptides and distinguished them at one amino acid resolution. The findings suggest that nanopore can serve as a new generation of mass detector for various omics analysis, particularly in the agricultural field.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Biochemical Research Methods
Tiago Pereira, Maryam Abbasi, Jose Luis Oliveira, Bernardete Ribeiro, Joel Arrais
Summary: This study introduces a deep reinforcement learning framework to generate compounds with specific biological properties and bioavailability in mind. The results show that the method can produce an interesting set of molecules with the desired properties.
Article
Immunology
Roan E. Zaied, Tayaza Fadason, Justin M. O'Sullivan
Summary: In this study, a network analysis approach was used to construct tissue-specific spatial gene regulatory networks for asthma and identify asthma-associated diseases and their molecular mechanisms. The study also analyzed the comorbidity of asthma with other diseases and identified possible therapeutic targets.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Multidisciplinary Sciences
Zander Harteveld, Jaume Bonet, Stephene Rosset, Che Yang, Fabian Sesterhenn, Bruno E. Correia
Summary: De novo protein design is a powerful tool to explore new sequences and structures not found in nature. By using the TopoBuilder method, we were able to design sequences that adopt predicted folds and demonstrated their stability through experimental characterization.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Denis Beslic, Georg Tscheuschner, Bernhard Y. Renard, Michael G. Weller, Thilo Muth
Summary: Monoclonal antibodies are important proteins used in research, therapeutics, and diagnostics. Mass spectrometry-based de novo protein sequencing is a valuable method to obtain amino acid sequences without prior knowledge. Evaluating different sequencing algorithms is crucial for improving accuracy and coverage.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Alfredo Quijano-Rubio, Hsien-Wei Yeh, Jooyoung Park, Hansol Lee, Robert A. Langan, Scott E. Boyken, Marc J. Lajoie, Longxing Cao, Cameron M. Chow, Marcos C. Miranda, Jimin Wi, Hyo Jeong Hong, Lance Stewart, Byung-Ha Oh, David Baker
Summary: Protein switches have been repurposed for biosensor development by inverting the flow of information, creating modular molecular devices with a closed dark state and an open luminescent state. These sensors, based on thermodynamic coupling, require only one target binding domain for direct readout in solution, allowing for the detection of various molecules clinically, including the SARS-CoV-2 spike protein with high sensitivity and a 50-fold higher luminescence signal than background level. The modularity and sensitivity of this platform enable rapid sensor construction for a wide range of analytes, demonstrating the power of de novo protein design in creating multi-state protein systems with new functions.
Article
Biology
Carol Moraga, Evelyn Sanchez, Mariana Galvao Ferrarini, Rodrigo A. Gutierrez, Elena A. Vidal, Marie-France Sagot
Summary: In this study, we developed an algorithm called BrumiR, which can directly and exclusively discover miRNAs from sRNA-seq data. BrumiR showed high performance in identifying miRNAs in animal and plant species, with faster speed and higher efficiency compared to existing tools. BrumiR also provided additional information and a mapping tool, and improved prediction through a machine learning classifier.
Review
Spectroscopy
Kenneth Verheggen, Helge Raeder, Frode S. Berven, Lennart Martens, Harald Barsnes, Marc Vaudel
MASS SPECTROMETRY REVIEWS
(2020)
Article
Biochemical Research Methods
Pierre-Alain Binz, Jim Shofstahl, Juan Antonio Vizcaino, Harald Barsnes, Robert J. Chalkley, Gerben Menschaert, Emanuele Alpi, Karl Clauser, Jimmy K. Eng, Lydie Lane, Sean L. Seymour, Luis Francisco Hernandez Sanchez, Gerhard Mayer, Martin Eisenacher, Yasset Perez-Riverol, Eugene A. Kapp, Luis Mendoza, Peter R. Baker, Andrew Collins, Tim Van den Bossche, Eric W. Deutsch
JOURNAL OF PROTEOME RESEARCH
(2019)
Article
Genetics & Heredity
Nicole M. Warrington, Robin N. Beaumont, Momoko Horikoshi, Felix R. Day, Oyvind Helgeland, Charles Laurin, Jonas Bacelis, Shouneng Peng, Ke Hao, Bjarke Feenstra, Andrew R. Wood, Anubha Mahajan, Jessica Tyrrell, Neil R. Robertson, N. William Rayner, Zhen Qiao, Gunn-Helen Moen, Marc Vaudel, Carmen J. Marsit, Jia Chen, Michael Nodzenski, Theresia M. Schnurr, Mohammad H. Zafarmand, Jonathan P. Bradfield, Niels Grarup, Marjolein N. Kooijman, Ruifang Li-Gao, Frank Geller, Tarunveer S. Ahluwalia, Lavinia Paternoster, Rico Rueedi, Ville Huikari, Jouke-Jan Hottenga, Leo-Pekka Lyytikainen, Alana Cavadino, Sarah Metrustry, Diana L. Cousminer, Ying Wu, Elisabeth Thiering, Carol A. Wang, Christian T. Have, Natalia Vilor-Tejedor, Peter K. Joshi, Jodie N. Painter, Ioanna Ntalla, Ronny Myhre, Niina Pitkanen, Elisabeth M. van Leeuwen, Raimo Joro, Vasiliki Lagou, Rebecca C. Richmond, Ana Espinosa, Sheila J. Barton, Hazel M. Inskip, John W. Holloway, Loreto Santa-Marina, Xavier Estivill, Wei Ang, Julie A. Marsh, Christoph Reichetzeder, Letizia Marullo, Berthold Hocher, Kathryn L. Lunetta, Joanne M. Murabito, Caroline L. Relton, Manolis Kogevinas, Leda Chatzi, Catherine Allard, Luigi Bouchard, Marie-France Hivert, Ge Zhang, Louis J. Muglia, Jani Heikkinen, Camilla S. Morgen, Antoine H. C. van Kampen, Barbera D. C. van Schaik, Frank D. Mentch, Claudia Langenberg, Jian'an Luan, Robert A. Scott, Jing Hua Zhao, Gibran Hemani, Susan M. Ring, Amanda J. Bennett, Kyle J. Gaulton, Juan Fernandez-Tajes, Natalie R. van Zuydam, Carolina Medina-Gomez, Hugoline G. de Haan, Frits R. Rosendaal, Zoltan Kutalik, Pedro Marques-Vidal, Shikta Das, Gonneke Willemsen, Hamdi Mbarek, Martina Mueller-Nurasyid, Marie Standl, Emil V. R. Appel, Cilius E. Fonvig, Caecilie Trier, Catharina E. M. van Beijsterveldt, Mario Murcia, Mariona Bustamante, Silvia Bonas-Guarch, David M. Hougaard, Josep M. Mercader, Allan Linneberg, Katharina E. Schraut, Penelope A. Lind, Sarah E. Medland, Beverley M. Shields, Bridget A. Knight, Jin-Fang Chai, Kalliope Panoutsopoulou, Meike Bartels, Friman Sanchez, Jakob Stokholm, David Torrents, Rebecca K. Vinding, Sara M. Willems, Mustafa Atalay, Bo L. Chawes, Peter Kovacs, Inga Prokopenko, Marcus A. Tuke, Hanieh Yaghootkar, Katherine S. Ruth, Samuel E. Jones, Po-Ru Loh, Anna Murray, Michael N. Weedon, Anke Toenjes, Michael Stumvoll, Kim F. Michaelsen, Aino-Maija Eloranta, Timo A. Lakka, Cornelia M. van Duijn, Wieland Kiess, Antje Koerner, Harri Niinikoski, Katja Pahkala, Olli T. Raitakari, Bo Jacobsson, Eleftheria Zeggini, George V. Dedoussis, Yik-Ying Teo, Seang-Mei Saw, Grant W. Montgomery, Harry Campbell, James F. Wilson, Tanja G. M. Vrijkotte, Martine Vrijheid, Eco J. C. N. de Geus, M. Geoffrey Hayes, Haja N. Kadarmideen, Jens-Christian Holm, Lawrence J. Beilin, Craig E. Pennell, Joachim Heinrich, Linda S. Adair, Judith B. Borja, Karen L. Mohlke, Johan G. Eriksson, Elisabeth E. Widen, Andrew T. Hattersley, Tim D. Spector, Mika Kaehoenen, Jorma S. Viikari, Terho Lehtimaeki, Dorret I. Boomsma, Sylvain Sebert, Peter Vollenweider, Thorkild I. A. Sorensen, Hans Bisgaard, Klaus Bonnelykke, Jeffrey C. Murray, Mads Melbye, Ellen A. Nohr, Dennis O. Mook-Kanamori, Fernando Rivadeneira, Albert Hofman, Janine F. Felix, Vincent W. V. Jaddoe, Torben Hansen, Charlotta Pisinger, Allan A. Vaag, Oluf Pedersen, Andre G. Uitterlinden, Marjo-Riitta Jarvelin, Christine Power, Elina Hypponen, Denise M. Scholtens, William L. Lowe, George Davey Smith, Nicholas J. Timpson, Andrew P. Morris, Nicholas J. Wareham, Hakon Hakonarson, Struan F. A. Grant, Timothy M. Frayling, Debbie A. Lawlor, Pal R. Njolstad, Stefan Johansson, Ken K. Ong, Mark I. McCarthy, John R. B. Perry, David M. Evans, Rachel M. Freathy
Review
Biology
Bjoern A. Gruening, Samuel Lampa, Marc Vaudel, Daniel Blankenberg
Article
Physics, Atomic, Molecular & Chemical
Bram Burger, Ragnhild Reehorst Lereim, Frode S. Berven, Harald Barsnes
EUROPEAN JOURNAL OF MASS SPECTROMETRY
(2019)
Article
Biochemistry & Molecular Biology
Jonathan P. Bradfield, Suzanne Vogelezang, Janine F. Felix, Alessandra Chesi, Oyvind Helgeland, Momoko Horikoshi, Ville Karhunen, Estelle Lowry, Diana L. Cousminer, Tarunveer S. Ahluwalia, Elisabeth Thiering, Eileen Tai-Hui Boh, Mohammad H. Zafarmand, Natalia Vilor-Tejedor, Carol A. Wang, Raimo Joro, Zhanghua Chen, William J. Gauderman, Niina Pitkanen, Esteban J. Parra, Lindsay Fernandez-Rhodes, Akram Alyass, Claire Monnereau, John A. Curtin, Christian T. Have, Shana E. McCormack, Mette Hollensted, Christine Frithioff-Bojsoe, Adan Valladares-Salgado, Jesus Peralta-Romero, Yik-Ying Teo, Marie Standl, Jaakko T. Leinonen, Jens-Christian Holm, Triinu Peters, Jesus Vioque, Martine Vrijheid, Angela Simpson, Adnan Custovic, Marc Vaudel, Mickael Canouil, Virpi Lindi, Mustafa Atalay, Mika Kahonen, Olli T. Raitakari, Barbera D. C. van Schaik, Robert Berkowitz, Shelley A. Cole, V. Saroja Voruganti, Yujie Wang, Heather M. Highland, Anthony G. Comuzzie, Nancy F. Butte, Anne E. Justice, Sheila Gahagan, Estela Blanco, Terho Lehtimaki, Timo A. Lakka, Johannes Hebebrand, Amelie Bonnefond, Niels Grarup, Philippe Froguel, Leo-Pekka Lyytikainen, Miguel Cruz, Sayuko Kobes, Robert L. Hanson, Babette S. Zemel, Anke Hinney, Koon K. Teo, David Meyre, Kari E. North, Frank D. Gilliland, Hans Bisgaard, Mariona Bustamante, Klaus Bonnelykke, Craig E. Pennell, Fernando Rivadeneira, Andre G. Uitterlinden, Leslie J. Baier, Tanja G. M. Vrijkotte, Joachim Heinrich, Thorkild I. A. Sorensen, Seang-Mei Saw, Oluf Pedersen, Torben Hansen, Johan Eriksson, Elisabeth Widen, Mark McCarthy, Pal R. Njolstad, Christine Power, Elina Hypponen, Sylvain Sebert, Christopher D. Brown, Marjo-Riitta Jarvelin, Nicholas J. Timpson, Stefan Johansson, Hakon Hakonarson, Vincent W. V. Jaddoe, Struan F. A. Grant
HUMAN MOLECULAR GENETICS
(2019)
Article
Biology
Luis Francisco Hernandez Sanchez, Bram Burger, Carlos Horro, Antonio Fabregate, Stefan Johansson, Pal Rasmus Njolstad, Harald Barsnese, Henning Hermjakob, Marc Vaudel
Article
Behavioral Sciences
Zhen Qiao, Jie Zheng, Oyvind Helgeland, Marc Vaudel, Stefan Johansson, Pal R. Njolstad, George Davey Smith, Nicole M. Warrington, David M. Evans
Article
Biochemical Research Methods
Niels Hulstaert, Jim Shofstahl, Timo Sachsenberg, Mathias Walzer, Harald Barsnes, Lennart Martens, Yasset Perez-Riverol
JOURNAL OF PROTEOME RESEARCH
(2020)
Article
Cell & Tissue Engineering
Larry Sai Weng Loo, Heidrun Vethe, Andreas Alvin Purnomo Soetedjo, Joao A. Paulo, Joanita Jasmen, Nicholas Jackson, Yngvild Bjorlykke, Ivan A. Valdez, Marc Vaudel, Harald Barsnes, Steven P. Gygi, Helge Raeder, Adrian Kee Keong Teo, Rohit N. Kulkarni
Article
Biochemical Research Methods
Tim Van den Bossche, Pieter Verschaffelt, Kay Schallert, Harald Barsnes, Peter Dawyndt, Dirk Benndorf, Bernhard Y. Renard, Bart Mesuere, Lennart Martens, Thilo Muth
JOURNAL OF PROTEOME RESEARCH
(2020)
Article
Biochemical Research Methods
Bram Burger, Marc Vaudel, Harald Barsnes
Summary: Randomization is an effective tool in experimental design for reducing unanticipated confounders, but complete randomization can result in imbalanced designs. Block randomization serves as a method to prevent severe imbalances in sample allocation, addressing both known and unknown confounders. This provides insight into how to effectively organize samples during experimental design, particularly in the context of proteomics research.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Astrid Guldbrandsen, Ragnhild Reehorst Lereim, Mari Jacobsen, Hilde Garberg, Ann Cathrine Kroksveen, Harald Barsnes, Frode S. Berven
CLINICAL PROTEOMICS
(2020)
Article
Multidisciplinary Sciences
Eystein Oveland, Intakhar Ahmad, Ragnhild Reehorst Lereim, Ann Cathrine Kroksveen, Harald Barsnes, Astrid Guldbrandsen, Kjell-Morten Myhr, Lars Bo, Frode S. Berven, Stig Wergeland
Summary: By analyzing two different experimental models of multiple sclerosis using quantitative proteomics in the frontal cortex, new protein alterations were discovered as potential diagnostic, prognostic, or treatment targets. While there were some overlapping proteins between the two models, significant differences were also observed, such as the upregulation of legumain in multiple sclerosis patients, which may be associated with lesion activity.
SCIENTIFIC REPORTS
(2021)
Article
Cell & Tissue Engineering
Manoj K. Gupta, Heidrun Vethe, Samir Softic, Tata Nageswara Rao, Vilas Wagh, Jun Shirakawa, Harald Barsnes, Marc Vaudel, Tomozumi Takatani, Sevim Kahraman, Masaji Sakaguchi, Rachael Martinez, Jiang Hu, Yngvild Bjorlykke, Helge Raeder, Rohit N. Kulkarni
