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Sarygina EV, Kozlova AS, Ponomarenko EA, Ilgisonis EV. The human proteome size as a technological development function. BIOMEDITSINSKAIA KHIMIIA 2024; 70:364-373. [PMID: 39324201 DOI: 10.18097/pbmc20247005364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Changes in information on the number of human proteoforms, post-translational modification (PTM) events, alternative splicing (AS), single-amino acid polymorphisms (SAP) associated with protein-coding genes in the neXtProt database have been retrospectively analyzed. In 2016, our group proposed three mathematical models for predicting the number of different proteins (proteoforms) in the human proteome. Eight years later, we compared the original data of the information resources and their contribution to the prediction results, correlating the differences with new approaches to experimental and bioinformatic analysis of protein modifications. The aim of this work is to update information on the status of records in the databases of identified proteoforms since 2016, as well as to identify trends in changes in the quantities of these records. According to various information models, modern experimental methods may identify from 5 to 125 million different proteoforms: the proteins formed due to alternative splicing, the implementation of single nucleotide polymorphisms at the proteomic level, and post-translational modifications in various combinations. This result reflects an increase in the size of the human proteome by 20 or more times over the past 8 years.
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Affiliation(s)
- E V Sarygina
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A S Kozlova
- Institute of Biomedical Chemistry, Moscow, Russia
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Neagu AN, Whitham D, Seymour L, Haaker N, Pelkey I, Darie CC. Proteomics-Based Identification of Dysregulated Proteins and Biomarker Discovery in Invasive Ductal Carcinoma, the Most Common Breast Cancer Subtype. Proteomes 2023; 11:13. [PMID: 37092454 PMCID: PMC10123686 DOI: 10.3390/proteomes11020013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
Invasive ductal carcinoma (IDC) is the most common histological subtype of malignant breast cancer (BC), and accounts for 70-80% of all invasive BCs. IDC demonstrates great heterogeneity in clinical and histopathological characteristics, prognoses, treatment strategies, gene expressions, and proteomic profiles. Significant proteomic determinants of the progression from intraductal pre-invasive malignant lesions of the breast, which characterize a ductal carcinoma in situ (DCIS), to IDC, are still poorly identified, validated, and clinically applied. In the era of "6P" medicine, it remains a great challenge to determine which patients should be over-treated versus which need to be actively monitored without aggressive treatment. The major difficulties for designating DCIS to IDC progression may be solved by understanding the integrated genomic, transcriptomic, and proteomic bases of invasion. In this review, we showed that multiple proteomics-based techniques, such as LC-MS/MS, MALDI-ToF MS, SELDI-ToF-MS, MALDI-ToF/ToF MS, MALDI-MSI or MasSpec Pen, applied to in-tissue, off-tissue, BC cell lines and liquid biopsies, improve the diagnosis of IDC, as well as its prognosis and treatment monitoring. Classic proteomics strategies that allow the identification of dysregulated protein expressions, biological processes, and interrelated pathway analyses based on aberrant protein-protein interaction (PPI) networks have been improved to perform non-invasive/minimally invasive biomarker detection of early-stage IDC. Thus, in modern surgical oncology, highly sensitive, rapid, and accurate MS-based detection has been coupled with "proteome point sampling" methods that allow for proteomic profiling by in vivo "proteome point characterization", or by minimal tissue removal, for ex vivo accurate differentiation and delimitation of IDC. For the detection of low-molecular-weight proteins and protein fragments in bodily fluids, LC-MS/MS and MALDI-MS techniques may be coupled to enrich and capture methods which allow for the identification of early-stage IDC protein biomarkers that were previously invisible for MS-based techniques. Moreover, the detection and characterization of protein isoforms, including posttranslational modifications of proteins (PTMs), is also essential to emphasize specific molecular mechanisms, and to assure the early-stage detection of IDC of the breast.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of Iasi, Carol I bvd. No. 20A, 700505 Iasi, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Logan Seymour
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Norman Haaker
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Isabella Pelkey
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Costel C. Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
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Pan YJ, Liu BW, Pei DS. The Role of Alternative Splicing in Cancer: Regulatory Mechanism, Therapeutic Strategy, and Bioinformatics Application. DNA Cell Biol 2022; 41:790-809. [PMID: 35947859 DOI: 10.1089/dna.2022.0322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
[Formula: see text] Alternative splicing (AS) can generate distinct transcripts and subsequent isoforms that play differential functions from the same pre-mRNA. Recently, increasing numbers of studies have emerged, unmasking the association between AS and cancer. In this review, we arranged AS events that are closely related to cancer progression and presented promising treatments based on AS for cancer therapy. Obtaining proliferative capacity, acquiring invasive properties, gaining angiogenic features, shifting metabolic ability, and getting immune escape inclination are all splicing events involved in biological processes. Spliceosome-targeted and antisense oligonucleotide technologies are two novel strategies that are hopeful in tumor therapy. In addition, bioinformatics applications based on AS were summarized for better prediction and elucidation of regulatory routines mingled in. Together, we aimed to provide a better understanding of complicated AS events associated with cancer biology and reveal AS a promising target of cancer treatment in the future.
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Affiliation(s)
- Yao-Jie Pan
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
| | - Bo-Wen Liu
- Department of General Surgery, Xuzhou Medical University, Xuzhou, China
| | - Dong-Sheng Pei
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
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Meftahi GH, Bahari Z, Zarei Mahmoudabadi A, Iman M, Jangravi Z. Applications of western blot technique: From bench to bedside. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 49:509-517. [PMID: 33847452 DOI: 10.1002/bmb.21516] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
Western blot (WB) or immunoblot is a workhorse method. It is commonly used by biologists for study of different aspects of protein biomolecules. In addition, it has been widely used in disease diagnosis. Despite some limitations such as long time, different applications of WB have not been limited. In the present review, we have summarized scientific and clinical applications of WB. In addition, we described some new generation of WB techniques.
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Affiliation(s)
| | - Zahra Bahari
- Department of Physiology and Medical Physics, Faculty of Medicine, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Zarei Mahmoudabadi
- Department of Biochemistry, Faculty of Medicine, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Maryam Iman
- Department of Pharmaceutics, Faculty of Pharmacy, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Zohreh Jangravi
- Department of Biochemistry, Faculty of Medicine, Baqiyatallah University of Medical Sciences, Tehran, Iran
- Nanobiotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Jensen P, Patel B, Smith S, Sabnis R, Kaboord B. Improved Immunoprecipitation to Mass Spectrometry Method for the Enrichment of Low-Abundant Protein Targets. Methods Mol Biol 2021; 2261:229-246. [PMID: 33420993 DOI: 10.1007/978-1-0716-1186-9_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Immunoprecipitation (IP) is commonly used upstream of mass spectrometry (MS) as an enrichment tool for low-abundant protein targets. However, several aspects of the classical IP procedure such as nonspecific protein binding to the isolation matrix, detergents or high salt concentrations in wash and elution buffers, and antibody chain contamination in elution fractions render it incompatible with downstream mass spectrometry analysis. Here, we discuss an improved IP-MS workflow that is designed to minimize sample prep time and these contaminants. The method employs biotinylated antibodies to the targets of interest and streptavidin magnetic beads that exhibit low background binding. In addition, alterations in the elution protocol and subsequent MS sample prep were made to reduce time and antibody leaching in the eluent, minimizing potential ion suppression effects and thereby maximizing detection of multiple target antigens and interacting proteins.
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Affiliation(s)
| | | | | | - Renuka Sabnis
- Nisarga Biotech Pvt. Ltd., Satara, Maharashtra, India
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Guzman NA, Guzman DE. A Two-Dimensional Affinity Capture and Separation Mini-Platform for the Isolation, Enrichment, and Quantification of Biomarkers and Its Potential Use for Liquid Biopsy. Biomedicines 2020; 8:biomedicines8080255. [PMID: 32751506 PMCID: PMC7459796 DOI: 10.3390/biomedicines8080255] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023] Open
Abstract
Biomarker detection for disease diagnosis, prognosis, and therapeutic response is becoming increasingly reliable and accessible. Particularly, the identification of circulating cell-free chemical and biochemical substances, cellular and subcellular entities, and extracellular vesicles has demonstrated promising applications in understanding the physiologic and pathologic conditions of an individual. Traditionally, tissue biopsy has been the gold standard for the diagnosis of many diseases, especially cancer. More recently, liquid biopsy for biomarker detection has emerged as a non-invasive or minimally invasive and less costly method for diagnosis of both cancerous and non-cancerous diseases, while also offering information on the progression or improvement of disease. Unfortunately, the standardization of analytical methods to isolate and quantify circulating cells and extracellular vesicles, as well as their extracted biochemical constituents, is still cumbersome, time-consuming, and expensive. To address these limitations, we have developed a prototype of a portable, miniaturized instrument that uses immunoaffinity capillary electrophoresis (IACE) to isolate, concentrate, and analyze cell-free biomarkers and/or tissue or cell extracts present in biological fluids. Isolation and concentration of analytes is accomplished through binding to one or more biorecognition affinity ligands immobilized to a solid support, while separation and analysis are achieved by high-resolution capillary electrophoresis (CE) coupled to one or more detectors. When compared to other existing methods, the process of this affinity capture, enrichment, release, and separation of one or a panel of biomarkers can be carried out on-line with the advantages of being rapid, automated, and cost-effective. Additionally, it has the potential to demonstrate high analytical sensitivity, specificity, and selectivity. As the potential of liquid biopsy grows, so too does the demand for technical advances. In this review, we therefore discuss applications and limitations of liquid biopsy and hope to introduce the idea that our affinity capture-separation device could be used as a form of point-of-care (POC) diagnostic technology to isolate, concentrate, and analyze circulating cells, extracellular vesicles, and viruses.
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Affiliation(s)
- Norberto A. Guzman
- Princeton Biochemicals, Inc., Princeton, NJ 08816, USA
- Correspondence: ; Tel.: +1-908-510-5258
| | - Daniel E. Guzman
- Princeton Biochemicals, Inc., Princeton, NJ 08816, USA
- Department of Internal Medicine, University of California at San Francisco, San Francisco, CA 94143, USA; or
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Núñez C. Blood-based protein biomarkers in breast cancer. Clin Chim Acta 2018; 490:113-127. [PMID: 30597138 DOI: 10.1016/j.cca.2018.12.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/26/2018] [Accepted: 12/27/2018] [Indexed: 02/07/2023]
Abstract
Breast cancer (BCa) is a significant healthcare problem on women worldwide. Thus, early detection is very important to reduce mortality. Furthermore, better BCa prognosis could improve selection of patients eligible for adjuvant therapy. New markers for early diagnosis, accurate prognosis and prediction of response to treatment are necessary to improve BCa care. The present review summarizes important aspects of the potential usefulness of modern technologies, strategies, and scientific findings in proteomic research for discovery of breast cancer-associated blood-based protein biomarkers in the clinic.
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Affiliation(s)
- Cristina Núñez
- Research Unit, Hospital Universitario Lucus Augusti (HULA), Servizo Galego de Saúde (SERGAS), 27002 Lugo, Spain.
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Fesenko I, Khazigaleeva R, Kirov I, Kniazev A, Glushenko O, Babalyan K, Arapidi G, Shashkova T, Butenko I, Zgoda V, Anufrieva K, Seredina A, Filippova A, Govorun V. Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens. Sci Rep 2017; 7:2698. [PMID: 28578384 PMCID: PMC5457400 DOI: 10.1038/s41598-017-02970-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/20/2017] [Indexed: 12/13/2022] Open
Abstract
Alternative splicing (AS) can significantly impact the transcriptome and proteome of a eukaryotic cell. Here, using transcriptome and proteome profiling data, we analyzed AS in two life forms of the model moss Physcomitrella patens, namely protonemata and gametophores, as well as in protoplasts. We identified 12 043 genes subject to alternative splicing and analyzed the extent to which AS contributes to proteome diversity. We could distinguish a few examples that unambiguously indicated the presence of two or more splice isoforms from the same locus at the proteomic level. Our results indicate that alternative isoforms have a small effect on proteome diversity. We also revealed that mRNAs and pre-mRNAs have thousands of complementary binding sites for long non-coding RNAs (lncRNAs) that may lead to potential interactions in transcriptome. This finding points to an additional level of gene expression and AS regulation by non-coding transcripts in Physcomitrella patens. Among the differentially expressed and spliced genes we found serine/arginine-rich (SR) genes, which are known to regulate AS in cells. We found that treatment with abscisic (ABA) and methyl jasmonic acids (MeJA) led to an isoform-specific response and suggested that ABA in gametophores and MeJA in protoplasts regulate AS and the transcription of SR genes.
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Affiliation(s)
- Igor Fesenko
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
| | - Regina Khazigaleeva
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ilya Kirov
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - Andrey Kniazev
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Oksana Glushenko
- Laboratory of the Proteomic Analysis, Research Institute for Physico-Chemical Medicine, Moscow, Russia
| | - Konstantin Babalyan
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Georgij Arapidi
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatyana Shashkova
- Laboratory of the Proteomic Analysis, Research Institute for Physico-Chemical Medicine, Moscow, Russia
| | - Ivan Butenko
- Laboratory of the Proteomic Analysis, Research Institute for Physico-Chemical Medicine, Moscow, Russia
| | - Victor Zgoda
- Institute of Biomedical Chemistry, Moscow, Russian Federation
| | - Ksenia Anufrieva
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anna Seredina
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anna Filippova
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Vadim Govorun
- Laboratory of Proteomics, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Laboratory of the Proteomic Analysis, Research Institute for Physico-Chemical Medicine, Moscow, Russia
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Comparative Proteomics of Rubber Latex Revealed Multiple Protein Species of REF/SRPP Family Respond Diversely to Ethylene Stimulation among Different Rubber Tree Clones. Int J Mol Sci 2017; 18:ijms18050958. [PMID: 28468331 PMCID: PMC5454871 DOI: 10.3390/ijms18050958] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/03/2017] [Accepted: 04/21/2017] [Indexed: 01/26/2023] Open
Abstract
Rubber elongation factor (REF) and small rubber particle protein (SRPP) are two key factors for natural rubber biosynthesis. To further understand the roles of these proteins in rubber formation, six different genes for latex abundant REF or SRPP proteins, including REF138,175,258 and SRPP117,204,243, were characterized from Hevea brasiliensis Reyan (RY) 7-33-97. Sequence analysis showed that REFs have a variable and long N-terminal, whereas SRPPs have a variable and long C-terminal beyond the REF domain, and REF258 has a β subunit of ATPase in its N-terminal. Through two-dimensional electrophoresis (2-DE), each REF/SRPP protein was separated into multiple protein spots on 2-DE gels, indicating they have multiple protein species. The abundance of REF/SRPP proteins was compared between ethylene and control treatments or among rubber tree clones with different levels of latex productivity by analyzing 2-DE gels. The total abundance of each REF/SRPP protein decreased or changed a little upon ethylene stimulation, whereas the abundance of multiple protein species of the same REF/SRPP changed diversely. Among the three rubber tree clones, the abundance of the protein species also differed significantly. Especially, two protein species of REF175 or REF258 were ethylene-responsive only in the high latex productivity clone RY 8-79 instead of in RY 7-33-97 and PR 107. Some individual protein species were positively related to ethylene stimulation and latex productivity. These results suggested that the specific protein species could be more important than others for rubber production and post-translational modifications might play important roles in rubber biosynthesis.
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Huang K, Liu Y, Huang Y, Li L, Cooper L, Ruan J, Zhao Z. Intelligent biology and medicine in 2015: advancing interdisciplinary education, collaboration, and data science. BMC Genomics 2016; 17 Suppl 7:524. [PMID: 27556295 PMCID: PMC5001210 DOI: 10.1186/s12864-016-2893-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We summarize the 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) and the editorial report of the supplement to BMC Genomics. The supplement includes 20 research articles selected from the manuscripts submitted to ICIBM 2015. The conference was held on November 13-15, 2015 at Indianapolis, Indiana, USA. It included eight scientific sessions, three tutorials, four keynote presentations, three highlight talks, and a poster session that covered current research in bioinformatics, systems biology, computational biology, biotechnologies, and computational medicine.
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Affiliation(s)
- Kun Huang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210 USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Yufei Huang
- Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, TX 78249 USA
| | - Lang Li
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Lee Cooper
- Department of Biomedical Informatics, Emory University, Atlanta, GA 30322 USA
- Department of Biomedical Engineering, Emory University / Georgia Institute of Technology, Atlanta, GA 30322 USA
| | - Jianhua Ruan
- Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX 78249 USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
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