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NeoHunter:Flexible software for systematically detecting neoantigens from sequencing data

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Quantitative Biology 2024年第1期12卷 70-84页

作者： Tianxing Ma Zetong Zhao Haochen Li Lei Wei Xuegong Zhang MOE Key Lab of bioinformatics Bioinformatics Division of BNRIST and Department of AutomationTsinghua UniversityBeijingChina School of Medicine Tsinghua UniversityBeijingChina School of Life Sciences Tsinghua UniversityBeijingChina

Complicated molecular alterations in tumors generate various mutant *** of these mutant peptides can be presented to the cell surface and then elicit immune responses,and such mutant peptides are called *** detection of neoantigens could help to design personalized cancer *** some computational frameworks for neoantigen detection have been proposed,most of them can only detect SNV-and indel-derived *** addition,current frameworks adopt oversimplified neoantigen prioritization *** factors hinder the comprehensive and effective detection of *** developed NeoHunter,flexible software to systematically detect and prioritize neoantigens from sequencing data in different *** can detect not only SNV-and indel-derived neoantigens but also gene fusion-and aberrant splicing-derived *** supports both direct and indirect immunogenicity evaluation strategies to prioritize candidate *** strategies utilize binding characteristics,existing biological big data,and T-cell receptor specificity to ensure accurate detection and *** applied NeoHunter to the TESLA dataset,cohorts of melanoma and non-small cell lung cancer *** achieved high performance across the TESLA cancer patients and detected 79%(27 out of 34)of validated neoantigens in ***-and indel-derived neoantigens accounted for 90%of the top 100 candidate neoantigens while neoantigens from aberrant splicing accounted for 9%.Gene fusion-derived neoantigens were detected in one *** is a powerful tool to‘catch all’neoantigens and is available for free academic use on Github(XuegongLab/NeoHunter).

关键词： cancer vaccine molecular alteration neoantigen neoantigen prioritization

Recurrent evolution of seaweed body plan complexity among photosynthetic eukaryotes

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Molecular Plant 2024年第7期17卷 999-1001页

作者： Elisa S.Goldbecker Iker Irisarri Jan de Vries Department of applied bioinformatics Institute for Microbiology and GeneticsUniversity of GottingenGoldschmidtstr.137077 GottingenGermany Section Phylogenomics Center for Molecular Biodiversity ResearchLeibniz Institute for the Analysis of Biodiversity Change(LIB)Museum of Nature HamburgMartin-Luther-King-Platz 320146 HamburgGermany Department of applied bioinformatics Campus Institute Data Science(CIDAS)University of GottingenGoldschmidtstr.137077 GottingenGermany Department of applied bioinformatics Gottingen Center for Molecular Biosciences(GZMB)University of GottingenGoldschmidtstr.137077 GottingenGermany

The evolutionary origin of multicellularity is an age-old question in biological *** studies have delved into the evolutionary processes that led to the evolution of multicellular life forms from unicellular *** beauty and the challenge about this topic are that evolution has brought forth various forms of multicellular life,multiple times independently,scattered across the evolutionary tree of *** to the challenge,multicellular organisms exist in a diversity of forms and complexities,and the mechanisms by which multicellularity emerged are also likely different between animals,algae,or fungi(Niklas and Newman,2020).Recently,Nelson et al.(2024)presented a large-scale comparative genomics study focused on particularly intricate multicellular organisms:macroalgae(seaweeds),which emerged independently in three distinct eukaryotic lineages-green algae(Chlorophyta),red algae(Rhodophyta),and brown algae(Phaeophyceae).

关键词： algae seaweed evolution

A simple method for pulse contrast enhancement via self-focusing

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High Power Laser Science and Engineering 2024年第2期12卷 51-61页

作者： Zaharit Refaeli Gilad Marcus Yariv Shamir applied Physics division Soreq NRCYavneIsrael applied Physics Institute The Hebrew UniversityThe Edmond J.Safra Campus-Givat RamJerusalemIsrael

Here we report on a simple-to-implement and cost-effective approach for laser pulse contrast enhancement,based on the χ(3)nonlinear self-focusing *** intentionally induced and gently controlled self-focusing in a thin glass transforms the time-dependent intensity into variation in beam *** by a spatial discriminating filter,only the strongly focused fraction traverses the setup,at the expense of efficiency.A numerical model,accounting for the pulse and material parameters via a Gaussian ABCD matrix,provides an estimate for the instantaneous beam waist and transmission efficiency,which enables us to evaluate the resulting contrast *** estimated contrast enhancement spans between 0.5 and 2.5 orders of magnitude,in conjunction with approximately 25%–90%estimated efficiency,depending on the pulse *** a preliminary experiment we demonstrated the effect with 10s-μJ sub GW regime with approximately 40%efficiency and a contrast improvement of more than or equal to 20 dB.

关键词： nonlinear optics pulse contrast self-focusing ultrafast laser

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scEpiTools: a database to comprehensively interrogate analytic tools for single-cell epigenomic data

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Journal of Genetics and Genomics 2024年第4期51卷 462-465页

作者： Zijing Gao Xiaoyang Chen Zhen Li Xuejian Cui Qun Jiang Keyi Li Shengquan Chen Rui Jiang Ministry of Education Key Laboratory of bioinformatics Bioinformatics Division at the Beijing National Research Center for Information Science and TechnologyCenter for Synthetic and Systems BiologyDepartment of AutomationTsinghua UniversityBeijing 100084China School of Mathematical Sciences and LPMC Nankai UniversityTianjin 300071China

Recent advances in single-cell sequencing technologies provide significant implications for understanding cellular heterogeneity,developmental biology,and disease *** fully exploit the potential of these data,numerous tools have been proposed for upstream and downstream *** the the single-cell RNA sequencing(scRNA-seq)community,scRNA-tools(Zappia et al.,2018)was proposed to help researchers navigate the plethora of tools by *** its inception,scRNA-tools has been widely used and its updated version further reveals trends in the field with over 1000 collected tools(Zappia and Theis,2021),providing a valuable guidance in selecting tools for analyses.

关键词： analytic selecting Tools

Lax-Oleinik-Type Formulas and Efficient Algorithms for Certain High-Dimensional Optimal Control Problems

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Communications on applied Mathematics and Computation 2024年第2期6卷 1428-1471页

作者： Paula Chen Jerome Darbon Tingwei Meng division of applied Mathematics Brown UniversityProvidenceRIUSA Department of Mathematics UCLALos AngelesCAUSA

Two of the main challenges in optimal control are solving problems with state-dependent running costs and developing efficient numerical solvers that are computationally tractable in high *** this paper,we provide analytical solutions to certain optimal control problems whose running cost depends on the state variable and with constraints on the *** also provide Lax-Oleinik-type representation formulas for the corresponding Hamilton-Jacobi partial differential equations with state-dependent ***,we present an efficient,grid-free numerical solver based on our representation formulas,which is shown to scale linearly with the state dimension,and thus,to overcome the curse of *** existing optimization methods and the min-plus technique,we extend our numerical solvers to address more general classes of convex and nonconvex initial *** demonstrate the capabilities of our numerical solvers using implementations on a central processing unit(CPU)and a field-programmable gate array(FPGA).In several cases,our FPGA implementation obtains over a 10 times speedup compared to the CPU,which demonstrates the promising performance boosts FPGAs can *** numerical results show that our solvers have the potential to serve as a building block for solving broader classes of high-dimensional optimal control problems in real-time.

关键词： Optimal control Hamilton-Jacobi partial differential equations Grid-free numerical methods High dimensions Field-programmable gate arrays(FPGAs)

SCREEN:predicting single-cell gene expression perturbation responses via optimal transport

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Frontiers of Computer Science 2024年第3期18卷 255-257页

作者： Haixin WANG Yunhan WANG Qun JIANG Yan ZHANG Shengquan CHEN Cadre Medical Department The 1st Clinical CenterChinese PLA General HospitalBeijing 100853China School of Statistics Renmin University of ChinaBeijing 100872China Ministry of Education Key Laboratory of bioinformatics Bioinformatics Division of BNRISTDepartment of AutomationTsinghua UniversityBeijing 100084China School of Mathematical Sciences and LPMC Nankai UniversityTianjin 300071China

1 Introduction Recent advances in single-cell RNA sequencing(scRNA-seq)have enabled the study of how individual cells respond to various external perturbations such as drug stimulation at gene expression level[1].Precisely inferring perturbation responses allows us to explore how and why individual tumor cells evade cancer treatment,greatly advancing personalized medicine research and deepening our understanding of biological mechanisms[2].However,considering the high costs of sequencing and the complexity of obtaining perturbed samples,utilizing computational methods to predict cellular responses to perturbations holds great potential[2].

关键词： stimulation perturbation deepening

Lithiophilic CoF2@C hollow spheres towards spatial lithium deposition for stable lithium metal batteries

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Journal of Energy Chemistry 2024年第10期97卷 55-67页

作者： Jianxing Wang Shuhao Yao Runming Tao Xiaolang Liu Jiazhi Geng Chang Hong Huiying Li Guiyun Yu Haifeng Li Xiao-Guang Sun Jianlin Li Jiyuan Liang School of Optoelectronic Materials & Technology Jianghan University Institute for Advanced Materials and Manufacturing University of Tennessee applied Materials division Argonne National Laboratory School of Chemistry & Chemical Engineering Yancheng Institute of Technology Chemical Sciences division Oak Ridge National Laboratory

Lithium metal（LM） is a promising anode for next-generation batteries due to its high theoretical capacity and low electrode ***,side reactions,volume change,and unwanted lithium dendrite growth seriously limit the practical application of ***,with the aid of a hard template approach,a novel lithiophilic CoF2-carbon hollow sphere（CoF2@C-HS） composite material is successfully prepared via a facile in-situ fluorination and etching *** lithiophilic CoF2acts as nucleation sites to reduce nucleation overpotential as well as induces the spatial Li deposition and the formation of LiFrich solid electrolyte interphase（SEI）,and the hollow carbon matrix can enhance the electrical conductivity and offer free space for LM *** simulations reveal that the synergistic effect of lithiophilic CoF2and hollow carbon matrix homogenizes the electric field distribution and Li+*** from these advantages,the CoF2@C-HS-modified copper substrate electrode delivers an enhanced Coulombic efficiency（CE） of 93.7% for 280 cycles at 1 mA cm-2and 1 mA h *** symmetrical cell using CoF2@C-HS can stably cycle more than 1800 h with a low voltage hysteresis of 11 mV at a current density of 0.5 MA cm-2and an areal capacity of 0.5 mA h ***,the Li@CoF2@C-HS composite anode enables more than 300 stable cycles at 1 C with a capacity retention of 95% in LiFePO4-based full cell and 110 stable cycles at 1 C in LiNi0.8Co0.1Mn0.1O2（NCM811）-based highvoltage full *** work might shed a new light on designing lithiophilic hosts to spatially confine LM deposition,realizing dendrite-free LM anodes and the practical applications of LM batteries.

关键词： Lithiophilic CoF2 Lithium metal anode Nanocomposite Spatial deposition, Stability

Genome-resolved metagenomics of Venice Lagoon surface sediment bacteria reveals high biosynthetic potential and metabolic plasticity as successful strategies in an impacted environment

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Marine Life Science & Technology 2024年第1期6卷 126-142页

作者： Elisa Banchi Erwan Corre Paola Del Negro Mauro Celussi Francesca Malfatti National Institute of Oceanography and applied Geophysics OGS TriesteItaly FR2424 Station Biologique de RoscoffPlateforme ABiMS(Analysis and Bioinformatics for Marine Science)Sorbonne Universite CNRS29680 RoscoffFrance Department of Life Sciences University of TriesteTriesteItaly

Bacteria living in sediments play essential roles in marine ecosystems and deeper insights into the ecology and biogeochemistry of these largely unexplored organisms can be obtained from‘omics’***,we characterized metagenome-assembled-genomes(MAGs)from the surface sediment microbes of the Venice Lagoon(northern Adriatic Sea)in distinct sub-basins exposed to various natural and anthropogenic *** were explored for biodiversity,major marine metabolic processes,anthropogenic activity-related functions,adaptations at the microscale,and biosynthetic gene *** from 126 MAGs,a non-redundant dataset of 58 was compiled,the majority of which(35)belonged to(Alpha-and Gamma-)*** the broad microbial metabolic repertoire(including C,N,and S metabolisms)the potential to live without oxygen emerged as one of the most important *** was also found as a successful *** analysis showed that different MAGs encoded the same metabolic patterns(e.g.,C fixation,sulfate oxidation)thus suggesting metabolic *** and toxic compounds resistance genes were coupled,a condition that could promote the spreading of these genetic *** showed a high biosynthetic potential related to antimicrobial and biotechnological classes and to organism defense and interactions as well as adaptive strategies for micronutrient uptake and cellular *** results highlighted that bacteria living in an impacted environment,such as the surface sediments of the Venice Lagoon,may benefit from metabolic plasticity as well as from the synthesis of a wide array of secondary metabolites,promoting ecosystem resilience and stability toward environmental pressures.

关键词： Antibiotic resistance PAHs Biosynthetic gene clusters Microscale Mobilome Resistome

Recent progress and prospects of electrolytes for electrocatalytic nitrogen reduction toward ammonia

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Chinese Chemical Letters 2024年第4期35卷 3-16页

作者： Sajid Mahmood Haiyan Wang Fang Chen Yijun Zhong Yong Hu Key Laboratory of the Ministry of Education for Advanced Catalysis Materials Department of ChemistryZhejiang Normal UniversityJinhua 321004China The Center for applied Mathematics and bioinformatics(CAMB) Gulf University for Science and TechnologyMishref 32093Kuwait Hangzhou Institute of Advanced Studies Zhejiang Normal UniversityHangzhou 311231China

Electrochemical nitrogen reduction reaction(ENRR) provides a promising strategy to achieve sustainable synthesis of ammonia. However, despite great efforts devoted to this research field, the problems such as low energy efficiency and weak selectivity still impede its practical implementation. Most of the research to date has been concentrated on creating sophisticated electrocatalysts, and adequate knowledge of electrolytes is still lacking. Herein, the recent progress in electrolytes for ENRR, including alkaline, neutral,acidic, water-in-salt, organic, ionic liquid, and mixed water-organic electrolytes, is thoroughly reviewed to obtain an in-depth understanding of their effects on electrocatalytic performance. Recently developed representative electrocatalysts in various types of electrolytes are also introduced, and future research priorities of different electrolytes are proposed to develop new and efficient ENRR systems.

关键词： Electrocatalytic nitrogen reduction Ammonia Electrolytes Production rate Faradaic efficiency