Latent space search based multimodal optimization with personalized edge-network biomarker for multi-purpose early disease prediction.

Considering that cancer is resulting from the comutation of several essential genes of individual patients, researchers have begun to focus on identifying personalized edge-network biomarkers (PEBs) using personalized edge-network analysis for clinical practice. However, most of existing methods ignored the optimization of PEBs when multimodal biomarkers exist in multi-purpose early disease prediction (MPEDP). To solve this problem, this study proposes a novel model (MMPDENB-RBM) that combines personalized dynamic edge-network biomarkers (PDENB) theory, multimodal optimization strategy and latent space search scheme to identify biomarkers with different configurations of PDENB modules (i.e. to effectively identify multimodal PDENBs). The application to the three largest cancer omics datasets from The Cancer Genome Atlas database (i.e. breast invasive carcinoma, lung squamous cell carcinoma and lung adenocarcinoma) showed that the MMPDENB-RBM model could more effectively predict critical cancer state compared with other advanced methods. And, our model had better convergence, diversity and multimodal property as well as effective optimization ability compared with the other state-of-art methods. Particularly, multimodal PDENBs identified were more enriched with different functional biomarkers simultaneously, such as tissue-specific synthetic lethality edge-biomarkers including cancer driver genes and disease marker genes. Importantly, as our aim, these multimodal biomarkers can perform diverse biological and biomedical significances for drug target screen, survival risk assessment and novel biomedical sight as the expected multi-purpose of personalized early disease prediction. In summary, the present study provides multimodal property of PDENBs, especially the therapeutic biomarkers with more biological significances, which can help with MPEDP of individual cancer patients.

Multi-modal optimization to identify personalized biomarkers for disease prediction of individual patients with cancer.

Finding personalized biomarkers for disease prediction of patients with cancer remains a massive challenge in precision medicine. Most methods focus on one subnetwork or module as a network biomarker; however, this ignores the early warning capabilities of other modules with different configurations of biomarkers (i.e. multi-modal personalized biomarkers). Identifying such modules would not only predict disease but also provide effective therapeutic drug target information for individual patients. To solve this problem, we developed a novel model (denoted multi-modal personalized dynamic network biomarkers (MMPDNB)) based on a multi-modal optimization mechanism and personalized dynamic network biomarker (PDNB) theory, which can provide multiple modules of personalized biomarkers and unveil their multi-modal properties. Using the genomics data of patients with breast or lung cancer from The Cancer Genome Atlas database, we validated the effectiveness of the MMPDNB model. The experimental results showed that compared with other advanced methods, MMPDNB can more effectively predict the critical state with the highest early warning signal score during cancer development. Furthermore, MMPDNB more significantly identified PDNBs containing driver and biomarker genes specific to cancer tissues. More importantly, we validated the biological significance of multi-modal PDNBs, which could provide effective drug targets of individual patients as well as markers for predicting early warning signals of the critical disease state. In conclusion, multi-modal optimization is an effective method to identify PDNBs and offers a new perspective for understanding tumor heterogeneity in cancer precision medicine.

Comparison of machine learning-based CT fractional flow reserve with cardiac MR perfusion mapping for ischemia diagnosis in stable coronary artery disease.

OBJECTIVES: To compare the diagnostic performance of machine learning (ML)-based computed tomography-derived fractional flow reserve (CT-FFR) and cardiac magnetic resonance (MR) perfusion mapping for functional assessment of coronary stenosis. METHODS: Between October 2020 and March 2022, consecutive participants with stable coronary artery disease (CAD) were prospectively enrolled and underwent coronary CTA, cardiac MR, and invasive fractional flow reserve (FFR) within 2 weeks. Cardiac MR perfusion analysis was quantified by stress myocardial blood flow (MBF) and myocardial perfusion reserve (MPR). Hemodynamically significant stenosis was defined as FFR ≤ 0.8 or > 90% stenosis on invasive coronary angiography (ICA). The diagnostic performance of CT-FFR, MBF, and MPR was compared, using invasive FFR as a reference. RESULTS: The study protocol was completed in 110 participants (mean age, 62 years ± 8; 73 men), and hemodynamically significant stenosis was detected in 36 (33%). Among the quantitative perfusion indices, MPR had the largest area under receiver operating characteristic curve (AUC) (0.90) for identifying hemodynamically significant stenosis, which is in comparison with ML-based CT-FFR on the vessel level (AUC 0.89, p = 0.71), with comparable sensitivity (89% vs 79%, p = 0.20), specificity (87% vs 84%, p = 0.48), and accuracy (88% vs 83%, p = 0.24). However, MPR outperformed ML-based CT-FFR on the patient level (AUC 0.96 vs 0.86, p = 0.03), with improved specificity (95% vs 82%, p = 0.01) and accuracy (95% vs 81%, p < 0.01). CONCLUSION: ML-based CT-FFR and quantitative cardiac MR showed comparable diagnostic performance in detecting vessel-specific hemodynamically significant stenosis, whereas quantitative perfusion mapping had a favorable performance in per-patient analysis. CLINICAL RELEVANCE STATEMENT: ML-based CT-FFR and MPR derived from cardiac MR performed well in diagnosing vessel-specific hemodynamically significant stenosis, both of which showed no statistical discrepancy with each other. KEY POINTS: • Both machine learning (ML)-based computed tomography-derived fractional flow reserve (CT-FFR) and quantitative perfusion cardiac MR performed well in the detection of hemodynamically significant stenosis. • Compared with stress myocardial blood flow (MBF) from quantitative perfusion cardiac MR, myocardial perfusion reserve (MPR) provided higher diagnostic performance for detecting hemodynamically significant coronary artery stenosis. • ML-based CT-FFR and MPR from quantitative cardiac MR perfusion yielded similar diagnostic performance in assessing vessel-specific hemodynamically significant stenosis, whereas MPR had a favorable performance in per-patient analysis.

qPTMplants: an integrative database of quantitative post-translational modifications in plants.

As a crucial molecular mechanism, post-translational modifications (PTMs) play critical roles in a wide range of biological processes in plants. Recent advances in mass spectrometry-based proteomic technologies have greatly accelerated the profiling and quantification of plant PTM events. Although several databases have been constructed to store plant PTM data, a resource including more plant species and more PTM types with quantitative dynamics still remains to be developed. In this paper, we present an integrative database of quantitative PTMs in plants named qPTMplants (http://qptmplants.omicsbio.info), which hosts 1 242 365 experimentally identified PTM events for 429 821 nonredundant sites on 123 551 proteins under 583 conditions for 23 PTM types in 43 plant species from 293 published studies, with 620 509 quantification events for 136 700 PTM sites on 55 361 proteins under 354 conditions. Moreover, the experimental details, such as conditions, samples, instruments and methods, were manually curated, while a variety of annotations, including the sequence and structural characteristics, were integrated into qPTMplants. Then, various search and browse functions were implemented to access the qPTMplants data in a user-friendly manner. Overall, we anticipate that the qPTMplants database will be a valuable resource for further research on PTMs in plants.

Fully automated pixel-wise quantitative CMR-myocardial perfusion with CMR-coronary angiography to detect hemodynamically significant coronary artery disease.

OBJECTIVES: We applied a fully automated pixel-wise post-processing framework to evaluate fully quantitative cardiovascular magnetic resonance myocardial perfusion imaging (CMR-MPI). In addition, we aimed to evaluate the additive value of coronary magnetic resonance angiography (CMRA) to the diagnostic performance of fully automated pixel-wise quantitative CMR-MPI for detecting hemodynamically significant coronary artery disease (CAD). METHODS: A total of 109 patients with suspected CAD were prospectively enrolled and underwent stress and rest CMR-MPI, CMRA, invasive coronary angiography (ICA), and fractional flow reserve (FFR). CMRA was acquired between stress and rest CMR-MPI acquisition, without any additional contrast agent. Finally, CMR-MPI quantification was analyzed by a fully automated pixel-wise post-processing framework. RESULTS: Of the 109 patients, 42 patients had hemodynamically significant CAD (FFR ≤ 0.80 or luminal stenosis ≥ 90% on ICA) and 67 patients had hemodynamically non-significant CAD (FFR ˃ 0.80 or luminal stenosis < 30% on ICA) were enrolled. On the per-territory analysis, patients with hemodynamically significant CAD had higher myocardial blood flow (MBF) at rest, lower MBF under stress, and lower myocardial perfusion reserve (MPR) than patients with hemodynamically non-significant CAD (p < 0.001). The area under the receiver operating characteristic curve of MPR (0.93) was significantly larger than those of stress and rest MBF, visual assessment of CMR-MPI, and CMRA (p < 0.05), but similar to that of the integration of CMR-MPI with CMRA (0.90). CONCLUSIONS: Fully automated pixel-wise quantitative CMR-MPI can accurately detect hemodynamically significant CAD, but the integration of CMRA obtained between stress and rest CMR-MPI acquisition did not provide significantly additive value. KEY POINTS: • Full quantification of stress and rest cardiovascular magnetic resonance myocardial perfusion imaging can be postprocessed fully automatically, generating pixel-wise myocardial blood flow (MBF) and myocardial perfusion reserve (MPR) maps. • Fully quantitative MPR provided higher diagnostic performance for detecting hemodynamically significant coronary artery disease, compared with stress and rest MBF, qualitative assessment, and coronary magnetic resonance angiography (CMRA). • The integration of CMRA and MPR did not significantly improve the diagnostic performance of MPR alone.

Effect of Gushen shetuo decoction in improving motor and non-motor symptoms and the expression of PERK, ATF4 and CHOP in patients with Parkinson's disease.

This study aims to observe the therapeutic effect of Gushen Shetuo decoction on Parkinson's disease (PD), so as to provide reference for clinical practice. In order to demonstrate the clinical value of Gushen Shetuo Decoction, we selected 80 patients with PD for the study. Among them, 38 patients received the Gushen Shetuo decoction (research group), and 42 patients received Levodopa and Benserazide Hydrochloride Tablets (control group). There was no difference in Non-Motor Symptoms Scale (NMSS) scores between the research group and the control group (P>0. 05). However, the scores of motor complications in Movement Disorder Society-sponsored revision of the Parkinson's Disease Rating Scale (MDS-UPDRS) and those of Drooling Severity and Frequency Scale (DSFS) in the research group were lower than those in the control group (P<0. 05). Subsequently, we established PD model rats, and after Gushen Shetuo Decoction gavage treatment, we found that rats in the intervention group had increased mobility (P<0. 05), as well as notably improved pathological damage of substantia nigra and striatum. Also, the expression of PERK, ATF4 and CHOP in the brain tissues of rats in the intervention group was lower than those in the control group (P<0. 05). These results confirm that Gushen Shetuo decoction effectively improved the drooling of patients with PD and showed high safety.

Efficient genome editing in cotton using the virus-mediated CRISPR/Cas9 and grafting system.

KEY MESSAGE: The extensive application of CRISPR in cotton was limited due to the labor-intensive transformation process. Thus, we here established a convenient method of CRISPR in cotton by CLCrV-mediated sgRNA delivery.

Network controllability-based algorithm to target personalized driver genes for discovering combinatorial drugs of individual patients.

Multiple driver genes in individual patient samples may cause resistance to individual drugs in precision medicine. However, current computational methods have not studied how to fill the gap between personalized driver gene identification and combinatorial drug discovery for individual patients. Here, we developed a novel structural network controllability-based personalized driver genes and combinatorial drug identification algorithm (CPGD), aiming to identify combinatorial drugs for an individual patient by targeting personalized driver genes from network controllability perspective. On two benchmark disease datasets (i.e. breast cancer and lung cancer datasets), performance of CPGD is superior to that of other state-of-the-art driver gene-focus methods in terms of discovery rate among prior-known clinical efficacious combinatorial drugs. Especially on breast cancer dataset, CPGD evaluated synergistic effect of pairwise drug combinations by measuring synergistic effect of their corresponding personalized driver gene modules, which are affected by a given targeting personalized driver gene set of drugs. The results showed that CPGD performs better than existing synergistic combinatorial strategies in identifying clinical efficacious paired combinatorial drugs. Furthermore, CPGD enhanced cancer subtyping by computationally providing personalized side effect signatures for individual patients. In addition, CPGD identified 90 drug combinations candidates from SARS-COV2 dataset as potential drug repurposing candidates for recently spreading COVID-19.

PLAGL2 promotes the stemness and is upregulated by transcription factor E2F1 in human lung cancer.

This study mainly focuses on revealing the role of PLAGL2 in lung cancer stemness. In vitro and in vivo experiments were performed to evaluate the effects of PLAGL2 on lung cancer cell stemness. Mechanistic analysis using luciferase reporter and ChIP assays were implemented to reveal the underlying mechanisms. The transcriptional factor E2F1 transcriptionally activated PLAGL2 expression via directly binding to PLAGL2 promoter in lung cancer cells. Moreover, PLAGL2 promoted the stemness of lung cancer cells dependent on E2F1-mediated transcriptional activation. This study provides a potential target for lung cancer progression.

Prioritization of cancer driver gene with prize-collecting steiner tree by introducing an edge weighted strategy in the personalized gene interaction network.

BACKGROUND: Cancer is a heterogeneous disease in which tumor genes cooperate as well as adapt and evolve to the changing conditions for individual patients. It is a meaningful task to discover the personalized cancer driver genes that can provide diagnosis and target drug for individual patients. However, most of existing methods mainly ranks potential personalized cancer driver genes by considering the patient-specific nodes information on the gene/protein interaction network. These methods ignore the personalized edge weight information in gene interaction network, leading to false positive results. RESULTS: In this work, we presented a novel algorithm (called PDGPCS) to predict the Personalized cancer Driver Genes based on the Prize-Collecting Steiner tree model by considering the personalized edge weight information. PDGPCS first constructs the personalized weighted gene interaction network by integrating the personalized gene expression data and prior known gene/protein interaction network knowledge. Then the gene mutation data and pathway data are integrated to quantify the impact of each mutant gene on every dysregulated pathway with the prize-collecting Steiner tree model. Finally, according to the mutant gene's aggregated impact score on all dysregulated pathways, the mutant genes are ranked for prioritizing the personalized cancer driver genes. Experimental results on four TCGA cancer datasets show that PDGPCS has better performance than other personalized driver gene prediction methods. In addition, we verified that the personalized edge weight of gene interaction network can improve the prediction performance. CONCLUSIONS: PDGPCS can more accurately identify the personalized driver genes and takes a step further toward personalized medicine and treatment. The source code of PDGPCS can be freely downloaded from https://github.com/NWPU-903PR/PDGPCS .

Network control principles for identifying personalized driver genes in cancer.

To understand tumor heterogeneity in cancer, personalized driver genes (PDGs) need to be identified for unraveling the genotype-phenotype associations corresponding to particular patients. However, most of the existing driver-focus methods mainly pay attention on the cohort information rather than on individual information. Recent developing computational approaches based on network control principles are opening a new way to discover driver genes in cancer, particularly at an individual level. To provide comprehensive perspectives of network control methods on this timely topic, we first considered the cancer progression as a network control problem, in which the expected PDGs are altered genes by oncogene activation signals that can change the individual molecular network from one health state to the other disease state. Then, we reviewed the network reconstruction methods on single samples and introduced novel network control methods on single-sample networks to identify PDGs in cancer. Particularly, we gave a performance assessment of the network structure control-based PDGs identification methods on multiple cancer datasets from TCGA, for which the data and evaluation package also are publicly available. Finally, we discussed future directions for the application of network control methods to identify PDGs in cancer and diverse biological processes.

Performance assessment of sample-specific network control methods for bulk and single-cell biological data analysis.

In the past few years, a wealth of sample-specific network construction methods and structural network control methods has been proposed to identify sample-specific driver nodes for supporting the Sample-Specific network Control (SSC) analysis of biological networked systems. However, there is no comprehensive evaluation for these state-of-the-art methods. Here, we conducted a performance assessment for 16 SSC analysis workflows by using the combination of 4 sample-specific network reconstruction methods and 4 representative structural control methods. This study includes simulation evaluation of representative biological networks, personalized driver genes prioritization on multiple cancer bulk expression datasets with matched patient samples from TCGA, and cell marker genes and key time point identification related to cell differentiation on single-cell RNA-seq datasets. By widely comparing analysis of existing SSC analysis workflows, we provided the following recommendations and banchmarking workflows. (i) The performance of a network control method is strongly dependent on the up-stream sample-specific network method, and Cell-Specific Network construction (CSN) method and Single-Sample Network (SSN) method are the preferred sample-specific network construction methods. (ii) After constructing the sample-specific networks, the undirected network-based control methods are more effective than the directed network-based control methods. In addition, these data and evaluation pipeline are freely available on https://github.com/WilfongGuo/Benchmark_control.

Weighted minimum feedback vertex sets and implementation in human cancer genes detection.

BACKGROUND: Recently, many computational methods have been proposed to predict cancer genes. One typical kind of method is to find the differentially expressed genes between tumour and normal samples. However, there are also some genes, for example, 'dark' genes, that play important roles at the network level but are difficult to find by traditional differential gene expression analysis. In addition, network controllability methods, such as the minimum feedback vertex set (MFVS) method, have been used frequently in cancer gene prediction. However, the weights of vertices (or genes) are ignored in the traditional MFVS methods, leading to difficulty in finding the optimal solution because of the existence of many possible MFVSs. RESULTS: Here, we introduce a novel method, called weighted MFVS (WMFVS), which integrates the gene differential expression value with MFVS to select the maximum-weighted MFVS from all possible MFVSs in a protein interaction network. Our experimental results show that WMFVS achieves better performance than using traditional bio-data or network-data analyses alone. CONCLUSION: This method balances the advantage of differential gene expression analyses and network analyses, improves the low accuracy of differential gene expression analyses and decreases the instability of pure network analyses. Furthermore, WMFVS can be easily applied to various kinds of networks, providing a useful framework for data analysis and prediction.

Silencing of a LIM gene in cotton exhibits enhanced resistance against Apolygus lucorum.

Plant bugs (Miridae species) have become major agricultural pests that cause increasing and severe economic damage. Plant-mediated RNA interference (RNAi) is emerging as an eco-friendly, efficient, and reliable strategy for pest management. In this study, we isolated and characterized a lethal gene of Apolygus lucorum and named it Apolygus lucorum LIM (AlLIM), which produced A. lucorum mortality rates ranging from 38% to 81%. Downregulation of the AlLIM gene expression in A. lucorum by injection of a double-stranded RNA (dsRNA) led to muscle structural disorganization that resulted in metamorphosis deficiency and increased mortality. Then we constructed a plant expression vector that enabled transgenic cotton to highly and stably express dsRNA of AlLIM (dsAlLIM) by Agrobacterium-mediated genetic transformation. In the field bioassay, dsAlLIM transgenic cotton was protected from A. lucorum damage with high efficiency, with almost no detectable yield loss. Therefore, our study successfully provides a promising genetically modified strategy to overpower A. lucorum attack.

Prospective comparison of integrated on-site CT-fractional flow reserve and static CT perfusion with coronary CT angiography for detection of flow-limiting coronary stenosis.

OBJECTIVES: To compare the diagnostic power of separately integrating on-site computed tomography (CT)-derived fractional flow reserve (CT-FFR) and static CT stress myocardial perfusion (CTP) with coronary computed tomography angiography (CCTA) in detecting patients with flow-limiting CAD. The flow-limiting stenosis was defined as obstructive (≥ 50%) stenosis by invasive coronary angiography (ICA) with a corresponding perfusion deficit on stress single photon emission computed tomography (SPECT/MPI). METHODS: Forty-eight patients (74 vessels) were enrolled who underwent research-indicated combined CTA-CTP (320-row CT scanner, temporal resolution 137 ms) and SPECT/MPI prior to conventional coronary angiography. CT-FFR was computed on-site using resting CCTA data with dedicated workstation-based software. All five imaging modalities were analyzed in blinded independent core laboratories. Logistic regression and the integrated discrimination improvement (IDI) index were used to evaluate incremental differences in CT-FFR or CTP compared with CCTA alone. RESULTS: The prevalence of obstructive CAD defined by combined ICA-SPECT/MPI was 40%. Per-vessel sensitivity and specificity were 95 and 42% for CCTA, 76 and 89% for CCTA + CTP, and 81 and 96% for CCTA + CT-FFR, respectively. The diagnostic performance of CCTA (AUC = 0.82) was improved by combining it with CT-FFR (AUC = 0.92, p = 0.01; IDI = 0.27, p < 0.001) or CTP (AUC = 0.90, p = 0.02; IDI = 0.18, p = 0.003). CONCLUSION: On-site CT-FFR combined with CCTA provides an incremental diagnostic improvement over CCTA alone in identifying patients with flow-limiting CAD defined by ICA + SPECT/MPI, with a comparable diagnostic accuracy for integrated CTP and CCTA. KEY POINTS: • Both on-site CT-FFR and CTP perform well with high diagnostic accuracy in the detection of flow-limiting stenosis. • Comparable diagnostic accuracy between CCTA + CT-FFR and CCTA + CTP is demonstrated to detect flow-limiting stenosis. • Integrated CT-FFR and CCTA derived from a single widened CCTA data acquisition can accurately and conveniently evaluate both coronary anatomy and physiology in the future management of patients with suspected CAD, without the need for additional vasodilator administration and contrast and radiation exposure.

A novel network control model for identifying personalized driver genes in cancer.

Although existing computational models have identified many common driver genes, it remains challenging to identify the personalized driver genes by using samples of an individual patient. Recently, the methods of exploiting the structure-based control principles of complex networks provide new clues for identifying minimum number of driver nodes to drive the state transition of large-scale complex networks from an initial state to the desired state. However, the structure-based network control methods cannot be directly applied to identify the personalized driver genes due to the unknown network dynamics of the personalized system. Here we proposed the personalized network control model (PNC) to identify the personalized driver genes by employing the structure-based network control principle on genetic data of individual patients. In PNC model, we firstly presented a paired single sample network construction method to construct the personalized state transition network for capturing the phenotype transitions between healthy and disease states. Then, we designed a novel structure-based network control method from the Feedback Vertex Sets-based control perspective to identify the personalized driver genes. The wide experimental results on 13 cancer datasets from The Cancer Genome Atlas firstly showed that PNC model outperforms current state-of-the-art methods, in terms of F-measures for identifying cancer driver genes enriched in the gold-standard cancer driver gene lists. Furthermore, these results showed that personalized driver genes can be explored by their network characteristics even when they are hidden factors in transcription and mutation profiles. Our PNC gives novel insights and useful tools into understanding the tumor heterogeneity in cancer. The PNC package and data resources used in this work can be freely downloaded from https://github.com/NWPU-903PR/PNC.

Discovering personalized driver mutation profiles of single samples in cancer by network control strategy.

Motivation: It is a challenging task to discover personalized driver genes that provide crucial information on disease risk and drug sensitivity for individual patients. However, few methods have been proposed to identify the personalized-sample driver genes from the cancer omics data due to the lack of samples for each individual. To circumvent this problem, here we present a novel single-sample controller strategy (SCS) to identify personalized driver mutation profiles from network controllability perspective. Results: SCS integrates mutation data and expression data into a reference molecular network for each patient to obtain the driver mutation profiles in a personalized-sample manner. This is the first such a computational framework, to bridge the personalized driver mutation discovery problem and the structural network controllability problem. The key idea of SCS is to detect those mutated genes which can achieve the transition from the normal state to the disease state based on each individual omics data from network controllability perspective. We widely validate the driver mutation profiles of our SCS from three aspects: (i) the improved precision for the predicted driver genes in the population compared with other driver-focus methods; (ii) the effectiveness for discovering the personalized driver genes and (iii) the application to the risk assessment through the integration of the driver mutation signature and expression data, respectively, across the five distinct benchmarks from The Cancer Genome Atlas. In conclusion, our SCS makes efficient and robust personalized driver mutation profiles predictions, opening new avenues in personalized medicine and targeted cancer therapy. Availability and implementation: The MATLAB-package for our SCS is freely available from http://sysbio.sibcb.ac.cn/cb/chenlab/software.htm. Contact: zhangsw@nwpu.edu.cn or zengtao@sibs.ac.cn or lnchen@sibs.ac.cn. Supplementary information: Supplementary data are available at Bioinformatics online.

A novel algorithm for finding optimal driver nodes to target control complex networks and its applications for drug targets identification.

BACKGROUND: The advances in target control of complex networks not only can offer new insights into the general control dynamics of complex systems, but also be useful for the practical application in systems biology, such as discovering new therapeutic targets for disease intervention. In many cases, e.g. drug target identification in biological networks, we usually require a target control on a subset of nodes (i.e., disease-associated genes) with minimum cost, and we further expect that more driver nodes consistent with a certain well-selected network nodes (i.e., prior-known drug-target genes). RESULTS: Therefore, motivated by this fact, we pose and address a new and practical problem called as target control problem with objectives-guided optimization (TCO): how could we control the interested variables (or targets) of a system with the optional driver nodes by minimizing the total quantity of drivers and meantime maximizing the quantity of constrained nodes among those drivers. Here, we design an efficient algorithm (TCOA) to find the optional driver nodes for controlling targets in complex networks. We apply our TCOA to several real-world networks, and the results support that our TCOA can identify more precise driver nodes than the existing control-fucus approaches. Furthermore, we have applied TCOA to two bimolecular expert-curate networks. Source code for our TCOA is freely available from http://sysbio.sibcb.ac.cn/cb/chenlab/software.htm or https://github.com/WilfongGuo/guoweifeng . CONCLUSIONS: In the previous theoretical research for the full control, there exists an observation and conclusion that the driver nodes tend to be low-degree nodes. However, for target control the biological networks, we find interestingly that the driver nodes tend to be high-degree nodes, which is more consistent with the biological experimental observations. Furthermore, our results supply the novel insights into how we can efficiently target control a complex system, and especially many evidences on the practical strategic utility of TCOA to incorporate prior drug information into potential drug-target forecasts. Thus applicably, our method paves a novel and efficient way to identify the drug targets for leading the phenotype transitions of underlying biological networks.

Catalytic Asymmetric [4+2] Cycloaddition of in Situ Generated o-Quinone Methide Imines with o-Hydroxystyrenes: Diastereo- and Enantioselective Construction of Tetrahydroquinoline Frameworks.

A catalytic asymmetric [4+2] cycloaddition of ortho-quinone methide imines in situ generated from o-aminobenzyl alcohols with o-hydroxystyrenes has been established under the catalysis of chiral phosphoramide, which afforded chiral tetrahydroquinolines in moderate to good yields, good enantioselectivities, and excellent diastereoselectivities (up to 82% yield, 93:7 er, all >95:5 dr). In this catalytic asymmetric [4+2] cycloaddition, the hydrogen-bonding interaction between chiral phosphoramide and two substrates was proposed to play a crucial role in controlling the enantioselectivity. This reaction not only provides a useful approach for constructing chiral tetrahydroquinoline frameworks, but also demonstrates the great practicability of ortho-quinone methide imines in catalytic asymmetric cycloadditions.

Local network component analysis for quantifying transcription factor activities.

Transcription factors (TFs) could regulate physiological transitions or determine stable phenotypic diversity. The accurate estimation on TF regulatory signals or functional activities is of great significance to guide biological experiments or elucidate molecular mechanisms, but still remains challenging. Traditional methods identify TF regulatory signals at the population level, which masks heterogeneous regulation mechanisms in individuals or subgroups, thus resulting in inaccurate analyses. Here, we propose a novel computational framework, namely local network component analysis (LNCA), to exploit data heterogeneity and automatically quantify accurate transcription factor activity (TFA) in practical terms, through integrating the partitioned expression sets (i.e., local information) and prior TF-gene regulatory knowledge. Specifically, LNCA adopts an adaptive optimization strategy, which evaluates the local similarities of regulation controls and corrects biases during data integration, to construct the TFA landscape. In particular, we first numerically demonstrate the effectiveness of LNCA for the simulated data sets, compared with traditional methods, such as FastNCA, ROBNCA and NINCA. Then, we apply our model to two real data sets with implicit temporal or spatial regulation variations. The results show that LNCA not only recognizes the periodic mode along the S. cerevisiae cell cycle process, but also substantially outperforms over other methods in terms of accuracy and consistency. In addition, the cross-validation study for glioblastomas multiforme (GBM) indicates that the TFAs, identified by LNCA, can better distinguish clinically distinct tumor groups than the expression values of the corresponding TFs, thus opening a new way to classify tumor subtypes and also providing a novel insight into cancer heterogeneity. AVAILABILITY: LNCA was implemented as a Matlab package, which is available at http://sysbio.sibcb.ac.cn/cb/chenlab/software.htm/LNCApackage_0.1.rar.