Article
Biochemical Research Methods
Ramin Shirali Hossein Zade, Aysun Urhan, Alvaro Assis de Souza, Akash Singh, Thomas Abeel
Summary: This study introduces a new tool called HAT for haplotype assembly, which utilizes short and long reads along with a reference genome to obtain higher-quality continuous haplotypes.
Article
Biochemical Research Methods
Dehan Cai, Yanni Sun
Summary: In this study, a new tool called RVHaplo was developed for reconstructing haplotypes for known viruses from long reads. The results demonstrated that RVHaplo outperforms other tools for viral haplotype reconstruction from long reads.
Article
Biology
Damian G. Hernandez, Catalina Rivera, Jessica Cande, Baohua Zhou, David L. Stern, Gordon J. Berman
Summary: The study introduces a new framework for simultaneously studying the evolution of multiple behaviors. By measuring the behavioral repertoire of fruit flies and estimating intra- and inter-species behavioral covariances, the research found similarities in the covariance structure of intra-specific behavioral variation and proposed a method to identify groups of behaviors that appear to have evolved in a correlated manner.
Article
Immunology
Brian M. Petersen, Sophia A. Ulmer, Emily R. Rhodes, Matias F. Gutierrez-Gonzalez, Brandon J. Dekosky, Kayla G. Sprenger, Timothy A. Whitehead
Summary: Monoclonal antibodies are key therapeutics for cancer, inflammation, and infectious diseases. Natural human antibody repertoire-based scoring matrices can accurately predict mutations in therapeutic antibodies. High frequency mutations in natural human antibody repertoires have the potential to improve existing therapeutic antibodies and reduce immunogenicity.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Sheila M. Keating, Rena A. Mizrahi, Matthew S. Adams, Michael A. Asensio, Emily Benzie, Kyle P. Carter, Yao Chiang, Robert C. Edgar, Bishal K. Gautam, Ashley Gras, Jackson Leong, Renee Leong, Yoong Wearn Lim, Vishal A. Manickam, Angelica Medina-Cucurella, Ariel R. Niedecken, Jasmeen Saini, Jan Fredrik Simons, Matthew J. Spindler, Kacy Stadtmiller, Brendan Tinsley, Ellen K. Wagner, Nicholas Wayham, LaRee Tracy, Carina Vingsbo Lundberg, Dirk Buscher, Jose Vicente Terencio, Lucy Roalfe, Emma Pearce, Hayley Richardson, David Goldblatt, Anushka T. Ramjag, Christine V. F. Carrington, Graham Simmons, Marcus O. Muench, Steven M. Chamow, Bryan Monroe, Charles Olson, Thomas H. Oguin, Heather Lynch, Robert Jeanfreau, Rachel A. Mosher, Matthew J. Walch, Christopher R. Bartley, Carl A. Ross, Everett H. Meyer, Adam S. Adler, David S. Johnson
Summary: This method utilizes diverse mammalian antibody repertoires to create recombinant antibody mixtures enriched for specificity and activity against therapeutic targets, allowing for the generation of hyperimmune globulins against various diseases. Additionally, a recombinant human version was developed to address limitations of existing antibody therapeutics, such as rabbit-derived anti-thymocyte globulin.
NATURE BIOTECHNOLOGY
(2021)
Article
Biochemical Research Methods
E. Sacristan-Horcajada, S. Gonzalez-de la Fuente, R. Peiro-Pastor, F. Carrasco-Ramiro, R. Amils, J. M. Requena, J. Berenguer, B. Aguado
Summary: Researchers have developed a NGS long-reads indels correction pipeline called ARAMIS, which combines multiple correction software in one step using accurate short reads to address insertions and deletions errors in long-read sequencing. The study found systematic sequencing errors in PacBio sequences affecting homopolymeric regions, and that the type of indel errors introduced during PacBio sequencing are related to the GC content of the organism.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Environmental Sciences
Mengyang Xu, Lidong Guo, Yanwei Qi, Chengcheng Shi, Xiaochuan Liu, Jianwei Chen, Jinglin Han, Li Deng, Xin Liu, Guangyi Fan
Summary: We present a reference-free approach, Symbiont-Screener, to identify high-confidence host's long reads from symbionts and contaminants and overcome the low sequencing accuracy. It maintains higher precision and recall rates compared to other tools, enabling high-quality reconstruction of the host genome and associated metagenomes. Application of this method on a real host-microbe system demonstrates improved host assembly and symbiotic microbiome profiling, providing a novel perspective on symbiotic research.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Biology
Spyridon Megremis, Thomas D. J. Walker, Xiaotong He, James O'Sullivan, William E. R. Ollier, Hector Chinoy, Neil Pendleton, Antony Payton, Lynne Hampson, Ian Hampson, Janine A. Lamb
Summary: The study reveals a wider array of microbial antigens and human protein antibodies in adult-onset dermatomyositis patients, as well as evidence of non-random targeting of specific signaling pathways. Molecular mimicry and epitope spreading events may play a role in dermatomyositis pathogenesis.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Daniel Neumeier, Alexander Yermanos, Andreas Agrafiotis, Lucia Csepregi, Tasnia Chowdhury, Roy A. Ehling, Raphael Kuhn, Tudor-Stefan Cotet, Rapha El Brisset-Di Roberto, Mariangela Di Tacchio, Renan Antonialli, Dale Starkie, Daniel J. Lightwood, Annette Oxenius, Sai T. Reddy
Summary: The capacity of humoral B cell-mediated immunity to effectively respond to and protect against pathogenic infections relies on the presence of diverse polyclonal antibodies in the serum. Recent studies have investigated the balance between deterministic mechanisms and stochasticity of antibody repertoires on a genotypic level. It has been found that clonal expansion drives antigen specificity of the most expanded clones, while the antigen specificity among the rest of the clonal repertoire is stochastic, with implications for effective vaccine assessment.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Immunology
Xaquin Castro Dopico, Marco Mandolesi, Gunilla B. Karlsson Hedestam
Summary: Immunoglobulin (IG) genes encoding B cell receptors (BCRs) are crucial for the immune system in recognizing diverse antigens and generating antibody responses. Understanding the impact of IG genetic diversity on host traits, disease susceptibility, and antibody recall responses is of great interest. Studying IG genetics can help decipher preferences for IG gene or allele usage and improve our understanding of antibody responses at the population level.
IMMUNOLOGY LETTERS
(2023)
Article
Immunology
Doaa Waly, Aradana Muthupandian, Chia-Wei Fan, Harrison Anzinger, Brad G. G. Magor
Summary: This study reveals the existence of Aicda(+) cell clusters in fish that functionally resemble germinal centers in mammals. These clusters undergo B-cell clonal expansion and VDJ somatic hypermutation to achieve antibody affinity maturation. The study also provides evidence for positive selection for replacement mutations in regions encoding the antigen contact loops, leading to functional antibody modification. Additionally, melano-macrophages in the clusters trap antigens used for post-mutation B-cell selection, serving a role similar to follicular dendritic cells in mammalian germinal centers.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Peter Blazso, Krisztian Csomos, Christopher M. Tipton, Boglarka Ujhazi, Jolan E. Walter
Summary: The computational approach ImmChainTracer allows for the extraction and visualization of clonal relationships in B-cell lineages by collecting IgH sequences related to polyreactive B-cells. This method was successfully applied to IgH repertoires of patients with monogenic hypomorphic RAG1 and 2 deficiency or polygenic systemic lupus erythematosus autoimmune diseases. Signs of clonal expansion, affinity maturation, and class-switching events were revealed in both polyreactive and non-polyreactive B-cell lineages.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Immunology
Haripriya Vaidehi Narayanan, Alexander Hoffmann
Summary: Antibody-mediated adaptive immunity must provide long-term protection against rapidly mutating pathogens in a diverse human population. Understanding the multiscale germinal center (GC) reaction, which is responsible for the evolution of high-affinity antigen-specific antibodies, is crucial. This article advocates for a mechanistic understanding of B-cell dynamics at organism, tissue/cellular, and molecular scales, and emphasizes the importance of quantitative multi-scale mathematical models in predicting B-cell and GC reaction dynamics for practical applications such as vaccine design.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemical Research Methods
Xuan Zhang, Yuansheng Liu, Zuguo Yu, Michael Blumenstein, Gyorgy Hutvagner, Jinyan Li
Summary: The study introduces an instance-based error correction strategy focusing on specific disease-associated genes, utilizing local sequence features and statistics related to these genes. Extensive experiments show superior performance in comparison to current methods, especially in precision, recall, and sequence assembly results for lung cancer associated genes. This approach showcases high precision error correction and accurate gene sequence assembly, particularly beneficial for SNP studies and investigations on disease-causing mutations.
BMC BIOINFORMATICS
(2021)
Article
Computer Science, Information Systems
Johan Chrisnata, Han Mao Kiah, Eitan Yaakobi
Summary: This article introduces the sequence reconstruction problem proposed by Levenshtein in 2001, which examines a communication scenario where the sender transmits a codeword and the receiver obtains noisy reads. The researchers have developed a reconstruction code that can reconstruct codewords from noisy reads, and have demonstrated its optimality. Additionally, the article discusses the application of this reconstruction code in deletion channels.
IEEE TRANSACTIONS ON INFORMATION THEORY
(2022)
Article
Biochemistry & Molecular Biology
Alex L. Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R. Crusoe, Varsha Kale, Simon C. Potter, Lorna J. Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyayskaya, Alla Lapidus, Robert D. Finn
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemical Research Methods
Tatiana Dvorkina, Andrey Bzikadze, Pavel A. Pevzner
Article
Multidisciplinary Sciences
Karen H. Miga, Sergey Koren, Arang Rhie, Mitchell R. Vollger, Ariel Gershman, Andrey Bzikadze, Shelise Brooks, Edmund Howe, David Porubsky, Glennis A. Logsdon, Valerie A. Schneider, Tamara Potapova, Jonathan Wood, William Chow, Joel Armstrong, Jeanne Fredrickson, Evgenia Pak, Kristof Tigyi, Milinn Kremitzki, Christopher Markovic, Valerie Maduro, Amalia Dutra, Gerard G. Bouffard, Alexander M. Chang, Nancy F. Hansen, Amy B. Wilfert, Francoise Thibaud-Nissen, Anthony D. Schmitt, Jon-Matthew Belton, Siddarth Selvaraj, Megan Y. Dennis, Daniela C. Soto, Ruta Sahasrabudhe, Gulhan Kaya, Josh Quick, Nicholas J. Loman, Nadine Holmes, Matthew Loose, Urvashi Surti, Rosa Ana Risques, Tina A. Graves Lindsay, Robert Fulton, Ira Hall, Benedict Paten, Kerstin Howe, Winston Timp, Alice Young, James C. Mullikin, Pavel A. Pevzner, Jennifer L. Gerton, Beth A. Sullivan, Evan E. Eichler, Adam M. Phillippy
Article
Biotechnology & Applied Microbiology
Andrey Bzikadze, Pavel A. Pevzner
NATURE BIOTECHNOLOGY
(2020)
Article
Multidisciplinary Sciences
Glennis A. Logsdon, Mitchell R. Vollger, PingHsun Hsieh, Yafei Mao, Mikhail A. Liskovykh, Sergey Koren, Sergey Nurk, Ludovica Mercuri, Philip C. Dishuck, Arang Rhie, Leonardo G. de Lima, Tatiana Dvorkina, David Porubsky, William T. Harvey, Alla Mikheenko, Andrey Bzikadze, Milinn Kremitzki, Tina A. Graves-Lindsay, Chirag Jain, Kendra Hoekzema, Shwetha C. Murali, Katherine M. Munson, Carl Baker, Melanie Sorensen, Alexandra M. Lewis, Urvashi Surti, Jennifer L. Gerton, Vladimir Larionov, Mario Ventura, Karen H. Miga, Adam M. Phillippy, Evan E. Eichler
Summary: The study completed the linear assembly of human chromosome 8 using long-read sequencing technologies, resolving five long-standing gaps, including regions important for disease risk. The research revealed that the centromeric alpha-satellite sequence is generally methylated, and conducted comparative analysis of centromeres in chimpanzee, orangutan and macaque. The study estimates that the mutation rate of centromeric satellite DNA is accelerated compared to unique portions of the genome.
Editorial Material
Biochemical Research Methods
Kerui Peng, Yana Safonova, Mikhail Shugay, Alice B. Popejoy, Oscar L. Rodriguez, Felix Breden, Petter Brodin, Amanda M. Burkhardt, Carlos Bustamante, Van-Mai Cao-Lormeau, Martin M. Corcoran, Darragh Duffy, Macarena Fuentes-Guajardo, Ricardo Fujita, Victor Greiff, Vanessa D. Jonsson, Xiao Liu, Lluis Quintana-Murci, Maura Rossetti, Jianming Xie, Gur Yaari, Wei Zhang, Malak S. Abedalthagafi, Khalid O. Adekoya, Rahaman A. Ahmed, Wei-Chiao Chang, Clive Gray, Yusuke Nakamura, William D. Lees, Purvesh Khatri, Houda Alachkar, Cathrine Scheepers, Corey T. Watson, Gunilla B. Karlsson Hedestam, Serghei Mangul
Summary: Including a greater diversity of individuals in immunogenomics studies will enhance our understanding of human immunology by identifying variations in adaptive immune responses across populations.
Article
Computer Science, Information Systems
Vinnu Bhardwaj, Pavel A. Pevzner, Cyrus Rashtchian, Yana Safonova
Summary: The problem of trace reconstruction, introduced by Vladimir Levenshtein two decades ago, has seen considerable theoretical work but only recently practical solutions have started to emerge in immunogenomics and DNA data storage. This paper introduces new trace generation models and open questions, surveys theoretical results, and discusses the applicability and shortcomings of known solutions in computational biology, highlighting connections to immunogenomics and DNA data storage.
IEEE TRANSACTIONS ON INFORMATION THEORY
(2021)
Article
Multidisciplinary Sciences
Alex Shlemov, Theodore Alexandrov, Nina Golyandina, David Holloway, Stefan Baumgartner, Alexander V. Spirov
Summary: The Bicoid protein is a key determinant of early anterior-posterior axis specification in Drosophila embryogenesis. Analyzing the dynamic distribution of bcd mRNA can reveal important factors in the formation and maintenance of the Bcd protein gradient. The early developmental dynamics of bcd and Stau proteins appear to be coordinated and are crucial for understanding morphogenetic processes.
Article
Immunology
Jeong Hyun Lee, Laura Toy, Justin T. Kos, Yana Safonova, William R. Schief, Colin Havenar-Daughton, Corey T. Watson, Shane Crotty
Summary: The study demonstrates that a successful HIV vaccine must activate naive precursor B cells encoding broadly neutralizing antibodies, and the use of germline-targeting immunogens and high-throughput single-cell BCR sequencing can efficiently screen large numbers of BCR sequences to elucidate precursor frequencies. Furthermore, analysis of IGHV1-2 allelic usage across different cohorts reveals common alleles previously thought incompatible with VRC01-class responses, and germline variation within IGHV1-2 associates with gene usage frequencies in the naive BCR repertoire.
Article
Biochemistry & Molecular Biology
Vikram Sirupurapu, Yana Safonova, Pavel A. Pevzner
Summary: The IGDetective algorithm was developed to predict IG genes and it generated a large collection of IG genes across multiple species. Evolutionary analysis revealed highly conserved V genes in distant species and a new family of V genes with noncanonical cysteines in bats.
Article
Biochemistry & Molecular Biology
Yana Safonova, Sung Bong Shin, Luke Kramer, James Reecy, Corey T. Watson, Timothy P. L. Smith, Pavel A. Pevzner
Summary: An important challenge in vaccine development is understanding why vaccines work differently in different individuals. A study of 204 calves vaccinated against bovine respiratory disease found that variations in immunoglobulin genes and somatic hypermutations can impact vaccine response efficacy. This study represents the largest personalized immunogenomics study to date and has implications for selecting cattle for breeding programs.
Article
Immunology
Wan-ting He, Rami Musharrafieh, Ge Song, Katharina Dueker, Longping V. Tse, David R. Martinez, Alexandra Schafer, Sean Callaghan, Peter Yong, Nathan Beutler, Jonathan L. Torres, Reid M. Volk, Panpan Zhou, Meng Yuan, Hejun Liu, Fabio Anzanello, Tazio Capozzola, Mara Parren, Elijah Garcia, Stephen A. Rawlings, Davey M. Smith, Ian A. Wilson, Yana Safonova, Andrew B. Ward, Thomas F. Rogers, Ralph S. Baric, Lisa E. Gralinski, Dennis R. Burton, Raiees Andrabi
Summary: This study isolated and characterized a large panel of sarbecovirus broadly neutralizing antibodies (bnAbs) that were able to neutralize all SARS-CoV-2 variants of concern (VOCs), including Omicron. These antibodies also demonstrated prophylaxis in mice infected with diverse sarbecoviruses, suggesting their potential use in next-generation antibody-based prophylactic and therapeutic applications.
Article
Cell Biology
Wan-Ting He, Meng Yuan, Sean Callaghan, Rami Musharrafieh, Ge Song, Murillo Silva, Nathan Beutler, Wen-Hsin Lee, Peter Yong, Jonathan L. Torres, Mariane Melo, Panpan Zhou, Fangzhu Zhao, Xueyong Zhu, Linghang Peng, Deli Huang, Fabio Anzanello, James Ricketts, Mara Parren, Elijah Garcia, Melissa Ferguson, William Rinaldi, Stephen A. Rawlings, David Nemazee, Davey M. Smith, Bryan Briney, Yana Safonova, Thomas F. Rogers, Jennifer M. Dan, Zeli Zhang, Daniela Weiskopf, Alessandro Sette, Shane Crotty, Darrell J. Irvine, Andrew B. Ward, Ian A. Wilson, Dennis R. Burton, Raiees Andrabi
Summary: Immunization of macaques with SARS-CoV-2 spike protein generated potent cross-neutralizing antibody responses, effective against both SARS-CoV-2 and SARS-CoV-1, as well as most SARS-CoV-2 variants.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Multidisciplinary Sciences
Mikhail Lebedin, Mathilde Foglierini, Svetlana Khorkova, Clara Vazquez Garcia, Christoph Ratswohl, Alexey N. Davydov, Maria A. Turchaninova, Claudia Daubenberger, Dmitriy M. Chudakov, Antonio Lanzavecchia, Kathrin de la Rosa
Summary: Recombination of antibody genes in B cells can lead to the formation of hybrid antibodies with broad reactivity for Plasmodium falciparum. This study introduces a technique to analyze non-VDJ elements from distant genes in antibody transcripts. Non-VDJ inserts were found in 80% of individuals, and were mainly detected in heavy chain transcripts. The inserts were classified into four types based on their origin and destination. Fragile site inserts were exclusively found in memory and activated B cells. This study reveals a mechanism of antibody diversification layered on top of classical V(D)J and switch recombination.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Oscar L. Rodriguez, Yana Safonova, Catherine A. Silver, Kaitlyn Shields, William S. Gibson, Justin T. Kos, David Tieri, Hanzhong Ke, Katherine J. L. Jackson, Scott D. Boyd, Melissa L. Smith, Wayne A. Marasco, Corey T. Watson
Summary: Variation in the antibody response is linked to disease outcomes, vaccine and therapeutic responsiveness. Polymorphisms within the immunoglobulin heavy chain locus have an impact on the antibody repertoire, indicating genetic predisposition. Understanding IGH genetics can help comprehend the regulation, function, and dynamics of the antibody response.
NATURE COMMUNICATIONS
(2023)