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Article ; Online: NeoAgDT: Optimization of personal neoantigen vaccine composition by digital twin simulation of a cancer cell population.

Mösch, Anja / Grazioli, Filippo / Machart, Pierre / Malone, Brandon

2024

Abstract: Motivation: Neoantigen vaccines make use of tumor-specific mutations to enable the patient's immune system to recognize and eliminate cancer. Selecting vaccine elements, however, is a complex task which needs to take into account not only the underlying ...

Abstract	Motivation: Neoantigen vaccines make use of tumor-specific mutations to enable the patient's immune system to recognize and eliminate cancer. Selecting vaccine elements, however, is a complex task which needs to take into account not only the underlying antigen presentation pathway but also tumor heterogeneity. Results: Here, we present NeoAgDT, a two-step approach consisting of: (1) simulating individual cancer cells to create a digital twin of the patient's tumor cell population and (2) optimizing the vaccine composition by integer linear programming based on this digital twin. NeoAgDT shows improved selection of experimentally-validated neoantigens over ranking-based approaches in a study of seven patients. Availability: The NeoAgDT code is published on Github: https://github.com/nec-research/neoagdt. Supplementary information: Supplementary data are available at Bioinformatics online.
Language	English
Publishing date	2024-04-13
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btae205
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Article ; Online: Publisher Correction: Molnupiravir: coding for catastrophe.

Malone, Brandon / Campbell, Elizabeth A

Nature structural & molecular biology

2021 Volume 28, Issue 11, Page(s) 955

Language	English
Publishing date	2021-10-11
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/s41594-021-00683-6
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Zs.A 4101: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Molnupiravir: coding for catastrophe.

Malone, Brandon / Campbell, Elizabeth A

Nature structural & molecular biology

2021 Volume 28, Issue 9, Page(s) 706–708

MeSH term(s)	Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Base Pairing ; Cytidine/analogs & derivatives ; Cytidine/chemistry ; Cytidine/pharmacology ; Cytidine/therapeutic use ; DNA-Directed RNA Polymerases/metabolism ; Genes, Lethal ; Genome, Viral/drug effects ; Humans ; Hydroxylamines/chemistry ; Hydroxylamines/pharmacology ; Hydroxylamines/therapeutic use ; Molecular Structure ; Mutagenesis ; Nucleic Acid Conformation ; RNA, Viral/biosynthesis ; RNA, Viral/chemistry ; RNA, Viral/drug effects ; RNA, Viral/genetics ; SARS-CoV-2/drug effects ; SARS-CoV-2/genetics ; Substrate Specificity ; Templates, Genetic ; Virus Replication/drug effects ; COVID-19 Drug Treatment
Chemical Substances	Antiviral Agents ; Hydroxylamines ; RNA, Viral ; Cytidine (5CSZ8459RP) ; DNA-Directed RNA Polymerases (EC 2.7.7.6) ; POLRMT protein, human (EC 2.7.7.6) ; molnupiravir (YA84KI1VEW)
Language	English
Publishing date	2021-09-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/s41594-021-00657-8
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Article ; Online: Corrigendum: Experimental validation of immunogenic SARS-CoV-2 T cell epitopes identified by artificial intelligence.

Federico, Lorenzo / Malone, Brandon / Tennøe, Simen / Chaban, Viktoriia / Osen, Julie Røkke / Gainullin, Murat / Smorodina, Eva / Kared, Hassen / Akbar, Rahmad / Greiff, Victor / Stratford, Richard / Clancy, Trevor / Munthe, Ludvig Andre

Frontiers in immunology

2024 Volume 15, Page(s) 1377041

Abstract: This corrects the article DOI: 10.3389/fimmu.2023.1265044.]. ...

Abstract	[This corrects the article DOI: 10.3389/fimmu.2023.1265044.].
Language	English
Publishing date	2024-02-21
Publishing country	Switzerland
Document type	Published Erratum
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2024.1377041
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Article: CoV-er all the bases: Structural perspectives of SARS-CoV-2 RNA synthesis.

Malone, Brandon / Campbell, Elizabeth A / Darst, Seth A

The Enzymes

2021 Volume 49, Page(s) 1–37

Abstract: The ongoing Covid-19 pandemic has spurred research in the biology of the nidovirus severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Much focus has been on the viral RNA synthesis machinery due to its fundamental role in viral propagation. ... ...

Abstract	The ongoing Covid-19 pandemic has spurred research in the biology of the nidovirus severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Much focus has been on the viral RNA synthesis machinery due to its fundamental role in viral propagation. The central and essential enzyme of the RNA synthesis process, the RNA-dependent RNA polymerase (RdRp), functions in conjunction with a coterie of viral-encoded enzymes that mediate crucial nucleic acid transactions. Some of these enzymes share common features with other RNA viruses, while others play roles unique to nidoviruses or CoVs. The RdRps are proven targets for viral pathogens, and many of the other nucleic acid processing enzymes are promising targets. The purpose of this review is to summarize recent advances in our understanding of the mechanisms of RNA synthesis in CoVs. By reflecting on these studies, we hope to emphasize the remaining gaps in our knowledge. The recent onslaught of structural information related to SARS-CoV-2 RNA synthesis, in combination with previous structural, genetic and biochemical studies, have vastly improved our understanding of how CoVs replicate and process their genomic RNA. Structural biology not only provides a blueprint for understanding the function of the enzymes and cofactors in molecular detail, but also provides a basis for drug design and optimization. The concerted efforts of researchers around the world, in combination with the renewed urgency toward understanding this deadly family of viruses, may eventually yield new and improved antivirals that provide relief to the current global devastation.
MeSH term(s)	RNA, Viral/biosynthesis ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase/genetics ; SARS-CoV-2/genetics
Chemical Substances	RNA, Viral ; RNA-Dependent RNA Polymerase (EC 2.7.7.48)
Language	English
Publishing date	2021-08-23
Publishing country	United States
Document type	Journal Article ; Review
ISSN	0423-2607
ISSN	0423-2607
DOI	10.1016/bs.enz.2021.06.004
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Article ; Online: BERTMHC: improved MHC-peptide class II interaction prediction with transformer and multiple instance learning.

Cheng, Jun / Bendjama, Kaïdre / Rittner, Karola / Malone, Brandon

Bioinformatics (Oxford, England)

2021 Volume 37, Issue 22, Page(s) 4172–4179

Abstract: Motivation: Increasingly comprehensive characterization of cancer-associated genetic alterations has paved the way for the development of highly specific therapeutic vaccines. Predicting precisely the binding and presentation of peptides to major ... ...

Abstract	Motivation: Increasingly comprehensive characterization of cancer-associated genetic alterations has paved the way for the development of highly specific therapeutic vaccines. Predicting precisely the binding and presentation of peptides to major histocompatibility complex (MHC) alleles is an important step toward such therapies. Recent data suggest that presentation of both class I and II epitopes are critical for the induction of a sustained effective immune response. However, the prediction performance for MHC class II has been limited compared to class I. Results: We present a transformer neural network model which leverages self-supervised pretraining from a large corpus of protein sequences. We also propose a multiple instance learning (MIL) framework to deconvolve mass spectrometry data where multiple potential MHC alleles may have presented each peptide. We show that pretraining boosted the performance for these tasks. Combining pretraining and the novel MIL approach, our model outperforms state-of-the-art models based on peptide and MHC sequence only for both binding and cell surface presentation predictions. Availability and implementation: Our source code is available at https://github.com/s6juncheng/BERTMHC under a noncommercial license. A webserver is available at https://bertmhc.privacy.nlehd.de/. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Protein Binding ; Histocompatibility Antigens Class II/metabolism ; Peptides/chemistry ; Amino Acid Sequence
Chemical Substances	Histocompatibility Antigens Class II ; Peptides
Language	English
Publishing date	2021-06-05
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btab422
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Article ; Online: Choice effects associated with banning the word “meat” on alternative protein labels

DeMuth, Benjamin / Malone, Trey / McFadden, Brandon R. / Wolf, Christopher A.

Applied Economic Perspectives and Policy. 2023 Mar., v. 45, no. 1 p.128-144

2023

Abstract: There is debate about whether meat labeling regulations might prevent consumer confusion or simply reduce the substitution between competing products. Using a between‐subjects experiment with a sample of 1504 U.S. households, we tested whether U.S. ... ...

Abstract	There is debate about whether meat labeling regulations might prevent consumer confusion or simply reduce the substitution between competing products. Using a between‐subjects experiment with a sample of 1504 U.S. households, we tested whether U.S. consumers could accurately identify the nutrition content and ingredients in traditional and nontraditional meat. We then conducted a discrete choice experiment to test for likely changes in choices between traditional and nontraditional meat products. Results suggest that more than 30% of consumers cannot accurately distinguish between the two. We find that labeling restrictions do not decrease consumer confusion and are unlikely to substantially affect how consumers substitute between traditional and nontraditional meat.
Keywords	issues and policy ; meat ; nutrition
Language	English
Dates of publication	2023-03
Size	p. 128-144.
Publishing place	Wiley Periodicals, Inc.
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2518384-9
ISSN	2040-5790
ISSN	2040-5790
DOI	10.1002/aepp.13319
Database	NAL-Catalogue (AGRICOLA)

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Article: Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.

Saecker, Ruth M / Mueller, Andreas U / Malone, Brandon / Chen, James / Budell, William C / Dandey, Venkata P / Maruthi, Kashyap / Mendez, Joshua H / Molina, Nina / Eng, Edward T / Yen, Laura Y / Potter, Clinton S / Carragher, Bridget / Darst, Seth A

bioRxiv : the preprint server for biology

2024

Abstract: During formation of the transcription-competent open complex (RPo) by bacterial RNA polymerases (RNAP), transient intermediates pile up before overcoming a rate-limiting step. Structural descriptions of these interconversions in real time are unavailable. ...

Abstract	During formation of the transcription-competent open complex (RPo) by bacterial RNA polymerases (RNAP), transient intermediates pile up before overcoming a rate-limiting step. Structural descriptions of these interconversions in real time are unavailable. To address this gap, time-resolved cryo-electron microscopy (cryo-EM) was used to capture four intermediates populated 120 or 500 milliseconds (ms) after mixing
Language	English
Publishing date	2024-03-14
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.03.13.584744
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Article ; Online: Structures and functions of coronavirus replication-transcription complexes and their relevance for SARS-CoV-2 drug design.

Malone, Brandon / Urakova, Nadya / Snijder, Eric J / Campbell, Elizabeth A

Nature reviews. Molecular cell biology

2021 Volume 23, Issue 1, Page(s) 21–39

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed millions of people and continues to cause massive global upheaval. Coronaviruses are positive-strand RNA viruses with an unusually large genome of ~30 kb. They express an RNA- ... ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed millions of people and continues to cause massive global upheaval. Coronaviruses are positive-strand RNA viruses with an unusually large genome of ~30 kb. They express an RNA-dependent RNA polymerase and a cohort of other replication enzymes and supporting factors to transcribe and replicate their genomes. The proteins performing these essential processes are prime antiviral drug targets, but drug discovery is hindered by our incomplete understanding of coronavirus RNA synthesis and processing. In infected cells, the RNA-dependent RNA polymerase must coordinate with other viral and host factors to produce both viral mRNAs and new genomes. Recent research aiming to decipher and contextualize the structures, functions and interplay of the subunits of the SARS-CoV-2 replication and transcription complex proteins has burgeoned. In this Review, we discuss recent advancements in our understanding of the molecular basis and complexity of the coronavirus RNA-synthesizing machinery. Specifically, we outline the mechanisms and regulation of RNA translation, replication and transcription. We also discuss the composition of the replication and transcription complexes and their suitability as targets for antiviral therapy.
MeSH term(s)	Animals ; Antiviral Agents/pharmacology ; Drug Design ; Humans ; RNA, Viral/metabolism ; SARS-CoV-2/genetics ; SARS-CoV-2/physiology ; Transcription, Genetic/drug effects ; Virus Replication/drug effects ; Virus Replication/physiology
Chemical Substances	Antiviral Agents ; RNA, Viral
Language	English
Publishing date	2021-11-25
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2031313-5
ISSN	1471-0080 ; 1471-0072
ISSN (online)	1471-0080
ISSN	1471-0072
DOI	10.1038/s41580-021-00432-z
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Article ; Online: Beverage milk consumption patterns in the United States: Who is substituting from dairy to plant-based beverages?

Wolf, Christopher A / Malone, Trey / McFadden, Brandon R

Journal of dairy science

2020 Volume 103, Issue 12, Page(s) 11209–11217

Abstract: This research used a survey of 995 US households to explore how dairy milk and plant-based beverage substitutes were consumed. Long-term trends of declining beverage milk consumption have been exacerbated in recent years by increasing consumption of ... ...

Abstract	This research used a survey of 995 US households to explore how dairy milk and plant-based beverage substitutes were consumed. Long-term trends of declining beverage milk consumption have been exacerbated in recent years by increasing consumption of plant-based beverages. Although beverage milk consumption has been declining, total dairy consumption in the United States continues to increase, driven by growth in sales of cheese, butter, and yogurt. Using k-means cluster analysis, 3 consumption clusters for US households were identified. The largest cluster, consisting of 61.6% of households, consumed dairy milk with some regularity and consumed little or no plant-based beverages. A second cluster, flexitarian households, consisting of 15.6% of respondent households, frequently consumed both dairy milk and plant-based beverages. The third cluster, plant-based consumers, consisting of 22.8% of households, consumed almost exclusively plant-based beverages. Examining differences in demographics between clusters, flexitarian households were larger, more likely to include young children, more likely to include a vegetarian or vegan, and more liberal than traditional dairy-consuming households. Plant-based households had many similarities to flexitarian households. The flexitarian and plant-based clusters were willing to substitute plant-based beverages for dairy milk for almost all consumption uses.
MeSH term(s)	Adult ; Animals ; Beverages/economics ; Commerce ; Consumer Behavior ; Diet, Vegetarian ; Energy Intake ; Family Characteristics ; Female ; Humans ; Male ; Milk/economics ; Nutrition Surveys ; United States
Language	English
Publishing date	2020-10-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	242499-x
ISSN	1525-3198 ; 0022-0302
ISSN (online)	1525-3198
ISSN	0022-0302
DOI	10.3168/jds.2020-18741
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