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Blake ME, Kleinpeter AB, Jureka AS, Petit CM. Structural Investigations of Interactions between the Influenza a Virus NS1 and Host Cellular Proteins. Viruses 2023; 15:2063. [PMID: 37896840 PMCID: PMC10612106 DOI: 10.3390/v15102063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
The Influenza A virus is a continuous threat to public health that causes yearly epidemics with the ever-present threat of the virus becoming the next pandemic. Due to increasing levels of resistance, several of our previously used antivirals have been rendered useless. There is a strong need for new antivirals that are less likely to be susceptible to mutations. One strategy to achieve this goal is structure-based drug development. By understanding the minute details of protein structure, we can develop antivirals that target the most conserved, crucial regions to yield the highest chances of long-lasting success. One promising IAV target is the virulence protein non-structural protein 1 (NS1). NS1 contributes to pathogenicity through interactions with numerous host proteins, and many of the resulting complexes have been shown to be crucial for virulence. In this review, we cover the NS1-host protein complexes that have been structurally characterized to date. By bringing these structures together in one place, we aim to highlight the strength of this field for drug discovery along with the gaps that remain to be filled.
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Affiliation(s)
| | | | | | - Chad M. Petit
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.E.B.)
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2
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D2I and F9Y Mutations in the NS1 Protein of Influenza A Virus Affect Viral Replication via Regulating Host Innate Immune Responses. Viruses 2022; 14:v14061206. [PMID: 35746676 PMCID: PMC9228823 DOI: 10.3390/v14061206] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 12/04/2022] Open
Abstract
Influenza A viruses (IAV) modulate host antiviral responses to promote viral growth and pathogenicity. The non-structural (NS1) protein of influenza A virus has played an indispensable role in the inhibition of host immune responses, especially in limiting interferon (IFN) production. In this study, random site mutations were introduced into the NS1 gene of A/WSN/1933 (WSN, H1N1) via an error prone PCR to construct a random mutant plasmid library. The NS1 random mutant virus library was generated by reverse genetics. To screen out the unidentified NS1 functional mutants, the library viruses were lung-to-lung passaged in mice and individual plaques were picked from the fourth passage in mice lungs. Sanger sequencing revealed that eight different kinds of mutations in the NS1 gene were obtained from the passaged library virus. We found that the NS1 F9Y mutation significantly enhanced viral growth in vitro (MDCK and A549 cells) and in vivo (BALB/c mice) as well as increased virulence in mice. The NS1 D2I mutation attenuated the viral replication and pathogenicity in both in vitro and in vivo models. Further studies demonstrated that the NS1 F9Y mutant virus exhibited systematic and selective inhibition of cytokine responses as well as inhibited the expression of IFN. In addition, the expression levels of innate immunity-related cytokines were significantly up-regulated after the rNS1 D2I virus infected A549 cells. Collectively, our results revealed that the two mutations in the N-terminal of the NS1 protein could alter the viral properties of IAV and provide additional evidence that the NS1 protein is a critical virulence factor. The two characterized NS1 mutations may serve as potential targets for antiviral drugs as well as attenuated vaccine development.
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Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. Viruses 2021; 13:v13050905. [PMID: 34068322 PMCID: PMC8153306 DOI: 10.3390/v13050905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 01/23/2023] Open
Abstract
Influenza A viruses (IAV) modulate host antiviral responses to promote growth and pathogenicity. Here, we examined the multifunctional IAV nonstructural protein 1 (NS1) of influenza A virus to better understand factors that contribute to viral replication efficiency or pathogenicity. In 2009, a pandemic H1N1 IAV (A/California/07/2009 pH1N1) emerged in the human population from swine. Seasonal variants of this virus are still circulating in humans. Here, we compared the sequence of a seasonal variant of this H1N1 influenza virus (A/Urumqi/XJ49/2018(H1N1), first isolated in 2018) with the pandemic strain A/California/07/2009. The 2018 virus harbored amino acid mutations (I123V and N205S) in important functional sites; however, 108R and 189G were highly conserved between A/California/07/2009 and the 2018 variant. To better understand interactions between influenza viruses and the human innate immune system, we generated and rescued seasonal 2009 H1N1 IAV mutants expressing an NS1 protein harboring a dual mutation (R108K/G189D) at these conserved residues and then analyzed its biological characteristics. We found that the mutated NS1 protein exhibited systematic and selective inhibition of cytokine responses via a mechanism that may not involve binding to cleavage and polyadenylation specificity factor 30 (CPSF30). These results highlight the complexity underlying host–influenza NS1 protein interactions.
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Roles of the Non-Structural Proteins of Influenza A Virus. Pathogens 2020; 9:pathogens9100812. [PMID: 33023047 PMCID: PMC7600879 DOI: 10.3390/pathogens9100812] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 12/11/2022] Open
Abstract
Influenza A virus (IAV) is a segmented, negative single-stranded RNA virus that causes seasonal epidemics and has a potential for pandemics. Several viral proteins are not packed in the IAV viral particle and only expressed in the infected host cells. These proteins are named non-structural proteins (NSPs), including NS1, PB1-F2 and PA-X. They play a versatile role in the viral life cycle by modulating viral replication and transcription. More importantly, they also play a critical role in the evasion of the surveillance of host defense and viral pathogenicity by inducing apoptosis, perturbing innate immunity, and exacerbating inflammation. Here, we review the recent advances of these NSPs and how the new findings deepen our understanding of IAV–host interactions and viral pathogenesis.
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Feng Wang H, Xuan He H. Regulation of Yamanaka factors during H5N1 virus infection in A549 cells and HEK293T cells. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1541760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Hai Feng Wang
- School of Environmental Engineering, Central Plains Specialty Food Engineering & Technology Research Center, Yellow River Conservancy Technical Institute, Kaifeng, PR China
| | - Hong Xuan He
- National Research Center for Wildlife-Borne Diseases, Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, PR China
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Liu Y, Chia ZH, Liew JNMH, Or SM, Phua KKL. Modulation of mRNA Translation and Cell Viability by Influenza A Virus Derived Nonstructural Protein 1. Nucleic Acid Ther 2018; 28:200-208. [PMID: 29634401 DOI: 10.1089/nat.2017.0712] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Translation of in vitro transcribed messenger RNA (mRNA) is known to be compromised by cell's innate immune responses. Herein we show that when mRNA encoding nonstructural protein 1 (NS1), an immune evasion gene derived from influenza A virus, is co-delivered with mRNA encoding green fluorescent protein (GFP), higher GFP expression can be observed in four different interferon competent cell types within 6 h, indicating NS1's wide host range property and rapid counter response to the cells' innate immune response. Enhanced mRNA translation correlates with reduced interferon production in all tested cell types and substituting a small portion of luciferase mRNA with NS1 mRNA enhances luciferase production compared to the same dose composing of only luciferase mRNA although in a cell type specific manner. Toxicity caused by transfection of unmodified mRNA is mitigated with the delivery of NS1 mRNA and is observed only in NS1 without cleavage and polyadenylation specificity factor 30 kda (CPSF30) inhibition function. Conversely, delivery of mRNA encoding NS1 with CPSF30 inhibition function aggravated toxicity. Overall, we demonstrate that NS1 enhanced mRNA transfection through active evasion of innate immune responses and modulated cellular viability during mRNA transfection.
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Affiliation(s)
- Yi Liu
- Department of Chemical and Biomolecular Engineering, Faculty of Engineering, National University of Singapore , Singapore, Singapore
| | - Zhen Hua Chia
- Department of Chemical and Biomolecular Engineering, Faculty of Engineering, National University of Singapore , Singapore, Singapore
| | - Johannes Nathaniel Min Hui Liew
- Department of Chemical and Biomolecular Engineering, Faculty of Engineering, National University of Singapore , Singapore, Singapore
| | - Shi Min Or
- Department of Chemical and Biomolecular Engineering, Faculty of Engineering, National University of Singapore , Singapore, Singapore
| | - Kyle K L Phua
- Department of Chemical and Biomolecular Engineering, Faculty of Engineering, National University of Singapore , Singapore, Singapore
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Guo L, Liu Y. Crystal structure of the Kelch domain of human NS1-binding protein at 1.98 Å resolution. Acta Crystallogr F Struct Biol Commun 2018; 74:174-178. [PMID: 29497022 PMCID: PMC5947704 DOI: 10.1107/s2053230x18001577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 01/23/2018] [Indexed: 11/11/2022] Open
Abstract
NS1-binding protein (NS1-BP), which belongs to the Kelch protein superfamily, was first identified as a novel human 70 kDa protein that interacts with NS1 of Influenza A virus. It is involved in many cell functions, including pre-mRNA splicing, the ERK signalling pathway, the aryl hydrocarbon receptor (AHR) pathway, F-actin organization and protein ubiquitylation. However, the structure of NS1-BP is still unknown, which may impede functional studies. Here, the structure of the C-terminal Kelch domain of NS1-BP (NS1-BP-C; residues 330-642) was determined at 1.98 Å resolution. The Kelch domain adopts a highly symmetric six-bladed β-propeller fold structure. Each blade of the β-propeller is composed of four antiparallel β-strands. Comparison of the Kelch-domain structures of NS1-BP and its homologues showed that the Gly-Gly pair in β-strand B and the hydrophobic Trp residue in β-strand D are highly conserved, while the B-C loops in blades 2 and 6 are variable. This structure of the Kelch domain of NS1-BP extends the understanding of NS1-BP.
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Affiliation(s)
- Lu Guo
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Yingfang Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- Basic Medical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
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Zhao M, Wang L, Li S. Influenza A Virus-Host Protein Interactions Control Viral Pathogenesis. Int J Mol Sci 2017; 18:ijms18081673. [PMID: 28763020 PMCID: PMC5578063 DOI: 10.3390/ijms18081673] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 12/20/2022] Open
Abstract
The influenza A virus (IAV), a member of the Orthomyxoviridae family, is a highly transmissible respiratory pathogen and represents a continued threat to global health with considerable economic and social impact. IAV is a zoonotic virus that comprises a plethora of strains with different pathogenic profiles. The different outcomes of viral pathogenesis are dependent on the engagement between the virus and the host cellular protein interaction network. The interactions may facilitate virus hijacking of host molecular machinery to fulfill the viral life cycle or trigger host immune defense to eliminate the virus. In recent years, much effort has been made to discover the virus–host protein interactions and understand the underlying mechanisms. In this paper, we review the recent advances in our understanding of IAV–host interactions and how these interactions contribute to host defense and viral pathogenesis.
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Affiliation(s)
- Mengmeng Zhao
- 156 McElroy Hall, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Lingyan Wang
- 156 McElroy Hall, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Shitao Li
- 156 McElroy Hall, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078, USA.
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Sadewasser A, Paki K, Eichelbaum K, Bogdanow B, Saenger S, Budt M, Lesch M, Hinz KP, Herrmann A, Meyer TF, Karlas A, Selbach M, Wolff T. Quantitative Proteomic Approach Identifies Vpr Binding Protein as Novel Host Factor Supporting Influenza A Virus Infections in Human Cells. Mol Cell Proteomics 2017; 16:728-742. [PMID: 28289176 DOI: 10.1074/mcp.m116.065904] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/03/2017] [Indexed: 12/24/2022] Open
Abstract
Influenza A virus (IAV) infections are a major cause for respiratory disease in humans, which affects all age groups and contributes substantially to global morbidity and mortality. IAV have a large natural host reservoir in avian species. However, many avian IAV strains lack adaptation to other hosts and hardly propagate in humans. While seasonal or pandemic IAV strains replicate efficiently in permissive human cells, many avian IAV cause abortive nonproductive infections in these hosts despite successful cell entry. However, the precise reasons for these differential outcomes are poorly defined. We hypothesized that the distinct course of an IAV infection with a given virus strain is determined by the differential interplay between specific host and viral factors. By using Spike-in SILAC mass spectrometry-based quantitative proteomics we characterized sets of cellular factors whose abundance is specifically up- or downregulated in the course of permissive versus nonpermissive IAV infection, respectively. This approach allowed for the definition and quantitative comparison of about 3500 proteins in human lung epithelial cells in response to seasonal or low-pathogenic avian H3N2 IAV. Many identified proteins were similarly regulated by both virus strains, but also 16 candidates with distinct changes in permissive versus nonpermissive infection were found. RNAi-mediated knockdown of these differentially regulated host factors identified Vpr binding protein (VprBP) as proviral host factor because its downregulation inhibited efficient propagation of seasonal IAV whereas overexpression increased viral replication of both seasonal and avian IAV. These results not only show that there are similar differences in the overall changes during permissive and nonpermissive influenza virus infections, but also provide a basis to evaluate VprBP as novel anti-IAV drug target.
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Affiliation(s)
- Anne Sadewasser
- From the ‡Unit 17 Influenza and other Respiratory Viruses", Robert Koch Institut, Seestr. 10, 13353 Berlin, Germany
| | - Katharina Paki
- From the ‡Unit 17 Influenza and other Respiratory Viruses", Robert Koch Institut, Seestr. 10, 13353 Berlin, Germany
| | - Katrin Eichelbaum
- §Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Boris Bogdanow
- §Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Sandra Saenger
- From the ‡Unit 17 Influenza and other Respiratory Viruses", Robert Koch Institut, Seestr. 10, 13353 Berlin, Germany
| | - Matthias Budt
- From the ‡Unit 17 Influenza and other Respiratory Viruses", Robert Koch Institut, Seestr. 10, 13353 Berlin, Germany
| | - Markus Lesch
- ¶Max Planck Institute for Infection Biology, Charitéplatz, 110117 Berlin, Germany
| | - Klaus-Peter Hinz
- ‖Institute of Inorganic and Analytical Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Andreas Herrmann
- **Molecular Biophysics, Department of Biology, Humboldt-Universität zu Berlin, Invalidenstr. 43, 10115 Berlin, Germany
| | - Thomas F Meyer
- ¶Max Planck Institute for Infection Biology, Charitéplatz, 110117 Berlin, Germany
| | - Alexander Karlas
- ¶Max Planck Institute for Infection Biology, Charitéplatz, 110117 Berlin, Germany
| | - Matthias Selbach
- §Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Thorsten Wolff
- From the ‡Unit 17 Influenza and other Respiratory Viruses", Robert Koch Institut, Seestr. 10, 13353 Berlin, Germany;
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Ylösmäki L, Schmotz C, Ylösmäki E, Saksela K. Reorganization of the host cell Crk(L)-PI3 kinase signaling complex by the influenza A virus NS1 protein. Virology 2015; 484:146-152. [PMID: 26099693 DOI: 10.1016/j.virol.2015.06.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 06/04/2015] [Accepted: 06/05/2015] [Indexed: 11/26/2022]
Abstract
The non-structural protein-1 (NS1) of influenza A virus binds the p85β subunit of phosphoinositide 3-kinase (PI3K) to induce PI3K activity in the infected cells. Some virus strains encode NS1 containing a motif that binds tightly to the SH3 domain of the cellular adapter proteins Crk and CrkL to potentiate NS1-induced PI3K activation. Here we show that this potentiation involves reorganization of the natural CrkL-p85β complex into a novel trimeric complex where NS1 serves as a bridging factor. Of note, NS1 proteins that lack the SH3 binding capacity can also associate with CrkL, but in a less stable trimeric complex mediated by p85β. The data presented here establish Crk proteins as general host cell cofactors of NS1, and show that the enhanced PI3K activation by SH3 binding-competent NS1 variants is mediated by a more efficient tethering of Crk proteins to the NS1-PI3K complex.
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Affiliation(s)
- Leena Ylösmäki
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Constanze Schmotz
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Erkko Ylösmäki
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kalle Saksela
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
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Jain S, Gitter A, Bar-Joseph Z. Multitask learning of signaling and regulatory networks with application to studying human response to flu. PLoS Comput Biol 2014; 10:e1003943. [PMID: 25522349 PMCID: PMC4270428 DOI: 10.1371/journal.pcbi.1003943] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 09/28/2014] [Indexed: 01/04/2023] Open
Abstract
Reconstructing regulatory and signaling response networks is one of the major goals of systems biology. While several successful methods have been suggested for this task, some integrating large and diverse datasets, these methods have so far been applied to reconstruct a single response network at a time, even when studying and modeling related conditions. To improve network reconstruction we developed MT-SDREM, a multi-task learning method which jointly models networks for several related conditions. In MT-SDREM, parameters are jointly constrained across the networks while still allowing for condition-specific pathways and regulation. We formulate the multi-task learning problem and discuss methods for optimizing the joint target function. We applied MT-SDREM to reconstruct dynamic human response networks for three flu strains: H1N1, H5N1 and H3N2. Our multi-task learning method was able to identify known and novel factors and genes, improving upon prior methods that model each condition independently. The MT-SDREM networks were also better at identifying proteins whose removal affects viral load indicating that joint learning can still lead to accurate, condition-specific, networks. Supporting website with MT-SDREM implementation: http://sb.cs.cmu.edu/mtsdrem To understand why some flu strains are more virulent than others, researchers attempt to profile and model the molecular human response to these strains and identify similarities and differences between the resulting models. So far, the modeling and analysis part has been done independently for each strain and the results contrasted in a post-processing step. Here we present a new method, termed MT-SDREM, that simultaneously models the response to all strains allowing us to identify both, the core response elements that are shared among the strains, and factors that are uniquely activated or repressed by individual strains. We applied this method to study the human response to three flu strains: H1N1, H3N2 and H5N1. As we show, the method was able to correctly identify several common and known factors regulating immune response to such strains and also identified unique factors for each of the strains. The models reconstructed by the simultaneous analysis method improved upon those generated by methods that model each strain response separately. Our joint models can be used to identify strain specific treatments as well as treatments that are likely to be effective against all three strains.
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Affiliation(s)
- Siddhartha Jain
- Computer Science Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Anthony Gitter
- Microsoft Research, Cambridge, Massachusetts, United States of America
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Ziv Bar-Joseph
- Lane Center for Computational Biology and Machine Learning Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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