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Crees ZD, Rettig MP, Jayasinghe RG, Stockerl-Goldstein K, Larson SM, Arpad I, Milone GA, Martino M, Stiff P, Sborov D, Pereira D, Micallef I, Moreno-Jiménez G, Mikala G, Coronel MLP, Holtick U, Hiemenz J, Qazilbash MH, Hardy N, Latif T, García-Cadenas I, Vainstein-Haras A, Sorani E, Gliko-Kabir I, Goldstein I, Ickowicz D, Shemesh-Darvish L, Kadosh S, Gao F, Schroeder MA, Vij R, DiPersio JF. Motixafortide and G-CSF to mobilize hematopoietic stem cells for autologous transplantation in multiple myeloma: a randomized phase 3 trial. Nat Med 2023; 29:869-879. [PMID: 37069359 PMCID: PMC10115633 DOI: 10.1038/s41591-023-02273-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 02/22/2023] [Indexed: 04/19/2023]
Abstract
Autologous hematopoietic stem cell transplantation (ASCT) improves survival in multiple myeloma (MM). However, many individuals are unable to collect optimal CD34+ hematopoietic stem and progenitor cell (HSPC) numbers with granulocyte colony-stimulating factor (G-CSF) mobilization. Motixafortide is a novel cyclic-peptide CXCR4 inhibitor with extended in vivo activity. The GENESIS trial was a prospective, phase 3, double-blind, placebo-controlled, multicenter study with the objective of assessing the superiority of motixafortide + G-CSF over placebo + G-CSF to mobilize HSPCs for ASCT in MM. The primary endpoint was the proportion of patients collecting ≥6 × 106 CD34+ cells kg-1 within two apheresis procedures; the secondary endpoint was to achieve this goal in one apheresis. A total of 122 adult patients with MM undergoing ASCT were enrolled at 18 sites across five countries and randomized (2:1) to motixafortide + G-CSF or placebo + G-CSF for HSPC mobilization. Motixafortide + G-CSF enabled 92.5% to successfully meet the primary endpoint versus 26.2% with placebo + G-CSF (odds ratio (OR) 53.3, 95% confidence interval (CI) 14.12-201.33, P < 0.0001). Motixafortide + G-CSF also enabled 88.8% to meet the secondary endpoint versus 9.5% with placebo + G-CSF (OR 118.0, 95% CI 25.36-549.35, P < 0.0001). Motixafortide + G-CSF was safe and well tolerated, with the most common treatment-emergent adverse events observed being transient, grade 1/2 injection site reactions (pain, 50%; erythema, 27.5%; pruritis, 21.3%). In conclusion, motixafortide + G-CSF mobilized significantly greater CD34+ HSPC numbers within two apheresis procedures versus placebo + G-CSF while preferentially mobilizing increased numbers of immunophenotypically and transcriptionally primitive HSPCs. Trial Registration: ClinicalTrials.gov , NCT03246529.
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Affiliation(s)
- Zachary D Crees
- Division of Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
| | - Michael P Rettig
- Division of Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Reyka G Jayasinghe
- Division of Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | - Sarah M Larson
- Division of Hematology-Oncology, UCLA School of Medicine, Los Angeles, CA, USA
| | - Illes Arpad
- Division of Hematology, Department of Internal Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Giulio A Milone
- Unità di Trapianto Emopoietico, Azienda Ospedaliero Universitaria 'Policlinico-San Marco', Catania, Italy
| | - Massimo Martino
- Unit of Stem Cell Transplantation and Cellular Therapies, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, Reggio Calabria, Italy
| | | | - Douglas Sborov
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Denise Pereira
- Sylvester Comprehensive Cancer Center, University of Miami Health System, Miami, FL, USA
| | | | | | - Gabor Mikala
- Center Hospital of Southern Pest, National Institute of Hematology and Infectious Diseases, Budapest, Hungary
| | | | - Udo Holtick
- Department I of Internal Medicine, Medical Faculty and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - John Hiemenz
- Division of Hematology-Oncology, University of Florida, Gainesville, FL, USA
| | - Muzaffar H Qazilbash
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nancy Hardy
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Tahir Latif
- Division of Hematology-Oncology, University of Cincinnati, Cincinnati, OH, USA
| | - Irene García-Cadenas
- Department of Hematology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | | | | | | | | | | | | | | | - Feng Gao
- Division of Public Health Sciences, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Mark A Schroeder
- Division of Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Ravi Vij
- Division of Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - John F DiPersio
- Division of Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
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2
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Külp M, Siemund AL, Larghero P, Dietz A, Alten J, Cario G, Eckert C, Caye-Eude A, Cavé H, Bardini M, Cazzaniga G, De Lorenzo P, Valsecchi MG, Diehl L, Bonig H, Meyer C, Marschalek R. The immune checkpoint ICOSLG is a relapse-predicting biomarker and therapeutic target in infant t(4;11) acute lymphoblastic leukemia. iScience 2022; 25:104613. [PMID: 35800767 PMCID: PMC9253708 DOI: 10.1016/j.isci.2022.104613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/14/2022] [Accepted: 06/01/2022] [Indexed: 11/23/2022] Open
Abstract
The most frequent genetic aberration leading to infant ALL (iALL) is the chromosomal translocation t(4;11), generating the fusion oncogenes KMT2A:AFF1 and AFF1:KMT2A, respectively. KMT2A-r iALL displays a dismal prognosis through high relapse rates and relapse-associated mortality. Relapse occurs frequently despite ongoing chemotherapy and without the accumulation of secondary mutations. A rational explanation for the observed chemo-resistance and satisfactory treatment options remain to be elucidated. We found that elevated ICOSLG expression level at diagnosis was associated with inferior event free survival (EFS) in a cohort of 43 patients with t(4;-11) iALL and that a cohort of 18 patients with iALL at relapse displayed strongly increased ICOSLG expression. Furthermore, co-culturing t(4;11) ALL cells (ICOSLGhi) with primary T-cells resulted in the development of Tregs. This was impaired through treatment with a neutralizing ICOSLG antibody. These findings imply ICOSLG (1) as a relapse-predicting biomarker, and (2) as a therapeutic target involved in a potential immune evasion relapse-mechanism of infant t(4;11) ALL. Early growth response 3 (EGR3) is a direct transactivator of the immune checkpoint gene ICOSLG high ICOSLG expression at diagnosis is predictive for ALL relapse EGR3 and ICOSLG expressions are relapse-associated expression of ICOSLG on t(4;11) ALL cells leads to the rapid expansion of Tregs
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3
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Bhandari N, Khare S, Walambe R, Kotecha K. Comparison of machine learning and deep learning techniques in promoter prediction across diverse species. PeerJ Comput Sci 2021; 7:e365. [PMID: 33817015 PMCID: PMC7959599 DOI: 10.7717/peerj-cs.365] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
Gene promoters are the key DNA regulatory elements positioned around the transcription start sites and are responsible for regulating gene transcription process. Various alignment-based, signal-based and content-based approaches are reported for the prediction of promoters. However, since all promoter sequences do not show explicit features, the prediction performance of these techniques is poor. Therefore, many machine learning and deep learning models have been proposed for promoter prediction. In this work, we studied methods for vector encoding and promoter classification using genome sequences of three distinct higher eukaryotes viz. yeast (Saccharomyces cerevisiae), A. thaliana (plant) and human (Homo sapiens). We compared one-hot vector encoding method with frequency-based tokenization (FBT) for data pre-processing on 1-D Convolutional Neural Network (CNN) model. We found that FBT gives a shorter input dimension reducing the training time without affecting the sensitivity and specificity of classification. We employed the deep learning techniques, mainly CNN and recurrent neural network with Long Short Term Memory (LSTM) and random forest (RF) classifier for promoter classification at k-mer sizes of 2, 4 and 8. We found CNN to be superior in classification of promoters from non-promoter sequences (binary classification) as well as species-specific classification of promoter sequences (multiclass classification). In summary, the contribution of this work lies in the use of synthetic shuffled negative dataset and frequency-based tokenization for pre-processing. This study provides a comprehensive and generic framework for classification tasks in genomic applications and can be extended to various classification problems.
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Affiliation(s)
- Nikita Bhandari
- Computer Science, Symbiosis Institute of Technology, Symbiosis International (Deemed University), Pune, MH, India
| | - Satyajeet Khare
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, MH, India
| | - Rahee Walambe
- Symbiosis Centre for Applied Artificial Intelligence, Symbiosis International (Deemed University), Pune, Maharashtra, India
- Electronics and Telecommunication Dept, Symbiosis Institute of Technology, Pune, Maharashtra, India
| | - Ketan Kotecha
- Computer Science, Symbiosis Institute of Technology, Symbiosis International (Deemed University), Pune, MH, India
- Symbiosis Centre for Applied Artificial Intelligence, Symbiosis International (Deemed University), Pune, Maharashtra, India
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Hoffmann H, Thiede C, Glauche I, Bornhaeuser M, Roeder I. Differential response to cytotoxic therapy explains treatment dynamics of acute myeloid leukaemia patients: insights from a mathematical modelling approach. J R Soc Interface 2020; 17:20200091. [PMID: 32900301 DOI: 10.1098/rsif.2020.0091] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Disease response and durability of remission are very heterogeneous in patients with acute myeloid leukaemia (AML). There is increasing evidence that the individual risk of early relapse can be predicted based on the initial treatment response. However, it is unclear how such a correlation is linked to functional aspects of AML progression and treatment. We suggest a mathematical model in which leukaemia-initiating cells and normal/healthy haematopoietic stem and progenitor cells reversibly change between an active state characterized by proliferation and chemosensitivity and a quiescent state, in which the cells do not divide, but are also insensitive to chemotherapy. Applying this model to 275 molecular time courses of nucleophosmin 1-mutated patients, we conclude that the differential chemosensitivity of the leukaemia-initiating cells together with the cells' intrinsic proliferative capacity is sufficient to reproduce both, early relapse as well as long-lasting remission. We can, furthermore, show that the model parameters associated with individual chemosensitivity and proliferative advantage of the leukaemic cells are closely linked to the patients' time to relapse, while a reliable prediction based on early response only is not possible based on the currently available data. Although we demonstrate with our approach, that the complete response data is sufficient to quantify the aggressiveness of the disease, further investigations are necessary to study how an intensive early sampling strategy may prospectively improve risk assessment and help to optimize individual treatments.
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Affiliation(s)
- H Hoffmann
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany
| | - C Thiede
- Medical Clinic and Polyclinic I, University Hospital Dresden Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - I Glauche
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany
| | - M Bornhaeuser
- Medical Clinic and Polyclinic I, University Hospital Dresden Carl Gustav Carus, TU Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
| | - I Roeder
- Institute for Medical Informatics and Biometry, Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
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Guo Z, Zhu H, Xu W, Wang X, Liu H, Wu Y, Wang M, Chu H, Zhang Z. Alternative splicing related genetic variants contribute to bladder cancer risk. Mol Carcinog 2020; 59:923-929. [PMID: 32339354 DOI: 10.1002/mc.23207] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/01/2020] [Accepted: 04/19/2020] [Indexed: 01/20/2023]
Abstract
Emerging evidence has shown that aberrant alternative splicing (AS) events are involved in the carcinogenesis. The association between genetic variants in AS and bladder cancer susceptibility remains to be fully elucidated. We searched for single nucleotide polymorphisms (SNPs) which are located in splicing quantitative trait loci (sQTLs) in bladder cancer through CancerSplicingQTL database and the 1000 Genomes Project. A case-control study including 580 cases and 1,101 controls was conducted to assess the association between the functional genetic variants and bladder cancer risk. Next, we used GTEx, TCGA, and GEO databases conducting sQTL analysis and gene expression differences analysis to evaluate the potential biological function of the candidate SNPs and related genes. We found that SNP rs4383 C>G was remarkably related with the reduced risk of bladder cancer (odds ratio = 0.68, 95% confidence interval = 0.59-0.79, P = 3.91 × 10-7 ). Similar results were obtained in codominant, dominant and recessive model. Stratified analyses revealed that the effect of SNP rs4383 C>G on bladder cancer was more significant in the older subjects (age > 65), female and nonsmokers. sQTL analysis showed that SNP rs4383 was associated with the AS events of its downstream gene MAFF with a splicing event of alternative 5' splice site. The messenger RNA expression of MAFF in bladder tumor tissues was lowered compared with normal tissues. Patients with high expression of MAFF had higher survival rates. These findings indicated that SNP rs4383 related with the AS events of MAFF was associated with bladder cancer risk and could represent a possible biomarker for bladder cancer susceptibility.
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Affiliation(s)
- Zheng Guo
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Huanhuan Zhu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Weidong Xu
- Department of Urology, Yizheng Hospital, Drum Tower Hospital Group of Nanjing, Yizheng, China
| | - Xi Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hanting Liu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yanling Wu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Haiyan Chu
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
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6
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Uras IZ, Sexl V, Kollmann K. CDK6 Inhibition: A Novel Approach in AML Management. Int J Mol Sci 2020; 21:ijms21072528. [PMID: 32260549 PMCID: PMC7178035 DOI: 10.3390/ijms21072528] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 03/29/2020] [Accepted: 04/02/2020] [Indexed: 02/01/2023] Open
Abstract
Acute myeloid leukemia (AML) is a complex disease with an aggressive clinical course and high mortality rate. The standard of care for patients has only changed minimally over the past 40 years. However, potentially useful agents have moved from bench to bedside with the potential to revolutionize therapeutic strategies. As such, cell-cycle inhibitors have been discussed as alternative treatment options for AML. In this review, we focus on cyclin-dependent kinase 6 (CDK6) emerging as a key molecule with distinct functions in different subsets of AML. CDK6 exerts its effects in a kinase-dependent and -independent manner which is of clinical significance as current inhibitors only target the enzymatic activity.
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Affiliation(s)
- Iris Z. Uras
- Department of Pharmacology, Center of Physiology and Pharmacology & Comprehensive Cancer Center (CCC), Medical University of Vienna, 1090 Vienna, Austria;
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - Karoline Kollmann
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, 1210 Vienna, Austria;
- Correspondence: ; Tel.: + 43-1-25077-2917
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7
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CDK6 coordinates JAK2 V617F mutant MPN via NF-κB and apoptotic networks. Blood 2019; 133:1677-1690. [PMID: 30635286 DOI: 10.1182/blood-2018-08-872648] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/07/2019] [Indexed: 01/27/2023] Open
Abstract
Over 80% of patients with myeloproliferative neoplasms (MPNs) harbor the acquired somatic JAK2 V617F mutation. JAK inhibition is not curative and fails to induce a persistent response in most patients, illustrating the need for the development of novel therapeutic approaches. We describe a critical role for CDK6 in MPN evolution. The absence of Cdk6 ameliorates clinical symptoms and prolongs survival. The CDK6 protein interferes with 3 hallmarks of disease: besides regulating malignant stem cell quiescence, it promotes nuclear factor κB (NF-κB) signaling and contributes to cytokine production while inhibiting apoptosis. The effects are not mirrored by palbociclib, showing that the functions of CDK6 in MPN pathogenesis are largely kinase independent. Our findings thus provide a rationale for targeting CDK6 in MPN.
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Zheng WJ, Ruan J, Xu H, Zhao Z, Liu Z. The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work. BMC SYSTEMS BIOLOGY 2017; 11:88. [PMID: 28984194 PMCID: PMC5629615 DOI: 10.1186/s12918-017-0461-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Between December 8–10, 2016, the International Conference on Intelligent Biology and Medicine (ICIBM 2016) was held in Houston, Texas, USA. The conference included eight scientific sessions, four tutorials, one poster session, four highlighted talks and four keynotes that covered topics in 3D genome structure analysis and visualization, next generation sequencing analysis, computational drug discovery, medical informatics, cancer genomics and systems biology. Systems biology has been a main theme in ICIBM 2016, with exciting advances were presented in many areas of systems biology. Here, we selected seven high quality papers to be published in BMC Systems Biology.
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Affiliation(s)
- W Jim Zheng
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Jianhua Ruan
- Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Hua Xu
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Zhangdong Liu
- The Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX, 77030, USA
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