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1. Optimal weak estimates for Riesz potentials

Author

Huang, Liang and Tang, Hanli

Subjects
Riesz potentials, sharp constant, optimal estimate, Mathematics, QA1-939
Abstract

In this note we prove a sharp reverse weak estimate for Riesz potentials \[ \Vert I_{s}(f)\Vert _{L^{\frac{n}{n-s},\infty }}\ge \gamma _sv_{n}^{\frac{n-s}{n}}\Vert f\Vert _{L^1}~\text{for}~0

Published
2023
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5. List of contributors

Author

Aizawa, Shin-Ichi, primary, Alberdi, Pilar, additional, Alexander, David C., additional, Alía, Alberto, additional, Allison, D.G., additional, Amyes, Sebastian G.B., additional, An, Haoran, additional, Andrade, María J., additional, Antelmann, Haike, additional, Arias, Cesar A., additional, Asensio, Miguel A., additional, Axell-House, Dierdre B., additional, Bae, Hee-Won, additional, Baena, Laura Muñoz, additional, Baig, Abdul Mannan, additional, Bailey, Spenser O., additional, Baize, Sylvain, additional, Baldi, Pablo C., additional, Barbosa, Angela Silva, additional, Barbuddhe, Sukhadeo B., additional, Bard, Emilie, additional, Barry, Eileen M., additional, Basarab, Gregory S., additional, Beloborodova, N.V, additional, Bermúdez, Elena, additional, Bidmos, Fadil A., additional, Bisgaard, Magne, additional, Blakely, Garry W., additional, Bloch, Evan, additional, Boesen, Thias Oberg, additional, Bose, Dipayan, additional, Botero, Javier Enrique, additional, Bouabe, Hicham, additional, Bouchard, Michael J., additional, Bozue, Joel A., additional, Bradbury, Richard S., additional, Brett Moreau, G., additional, Cabezas-Cruz, Alejandro, additional, Cai, Rong-Jun, additional, Calderón, Enrique J., additional, Cao, Boyang, additional, Carmena, David, additional, Carvalho, Eneas, additional, Caulfield, Amanda D., additional, Cen, Shan, additional, Chai, Jong-Yil, additional, Chamberland, Robin R., additional, Champredon, David, additional, Chan, Edward D., additional, Charbon, Godefroid, additional, Chato, Connor, additional, Chelomina, G.N., additional, Chen, Jingyu, additional, Chen, Min, additional, Chen, Shuyu, additional, Chen, Suilin, additional, Chen, Yanfei, additional, Chen, Zhaoyuan, additional, Cheng, Aimin, additional, Cheng, Keding, additional, Chiu, Charles Y., additional, Cho, You-Hee, additional, Christensen, Henrik, additional, Chrtdernevskaya, E.A., additional, Contreras, Adolfo, additional, Contreras, Marinela, additional, Córdoba, Juan J., additional, Córdoba, María G., additional, Costa, Rita, additional, Cote, Christopher K., additional, Cui, Xiangling, additional, Cui, Yujun, additional, Dacal, Elena, additional, Dammann, Allison N., additional, Das, Shubhagata, additional, Dashti, Alejandro, additional, de la Fuente, José, additional, de la Garza, Mireya, additional, Delgado, Josué, additional, Delgado-Cuesta, Juan, additional, Deng, Haiteng, additional, Deng, Li, additional, Dey, Debajit, additional, Dhama, Kuldeep, additional, Diego, Juan García-Bernalt, additional, Ding, Hao, additional, Doern, Christopher D., additional, Dorman, Charles J., additional, Du, Zongmin, additional, Dunbar, Sherry A., additional, Duthie, Malcolm, additional, Dybvig, Kevin F., additional, Eakin, Ann E., additional, Eallonardo, Samuel J., additional, Eberly, Allison R., additional, Echeverry, Adriana Jaramillo, additional, Egland, Paul G., additional, El Zowalaty, Mohamed E., additional, Endsley, Janice Jones, additional, Eom, Keeseon S., additional, Evans, Benjamin A., additional, Falkinham, Joseph O., additional, Feng, Siwei, additional, Feng, Yaoyu, additional, Feng, Zongdi, additional, Fernández-Soto, Pedro, additional, Ferreira, Roux-Cil, additional, Flores-Huerta, Nadia, additional, Foster, Timothy J., additional, Fox-Moon, Sandra M., additional, Fraga, Tatiana Rodrigues, additional, Fredricks, David N., additional, Freitag, Nancy E., additional, Frimodt-Møller, Jakob, additional, Fuller, Risa, additional, Ganesh, Balasubramanian, additional, Gao, Ning, additional, García-Carnero, Laura C., additional, Garzetti, Debora, additional, Geoghegan, Joan A., additional, Ghenim, Raed, additional, Giambartolomei, Guillermo H., additional, Gilbert, Nicole M., additional, Gillis, Thomas Phillip, additional, Gladstone, Camilla A., additional, Gómez-Gaviria, Manuela, additional, Gómez-Marín, Jorge E., additional, Gong, Tengfang, additional, González, Ramón A., additional, Gray-Owen, Scott D., additional, Gu, Bing, additional, Guzmán-Téllez, Paula, additional, Hajal, Caroline, additional, Han, Yanping, additional, Hao, Yi, additional, Harrington, Amanda T., additional, Harris, Jason B., additional, Harvill, Eric T., additional, Hasan, S. Saif, additional, He, Guang-Jun, additional, He, Yongqun, additional, Heffron, Jared D., additional, Hidalgo, Paloma, additional, Hindiyeh, Musa Y., additional, Hreha, Teri N., additional, Hu, Xiaoyu, additional, Huang, Guanghua, additional, Huang, Jiangqing, additional, Huang, Liang, additional, Huang, Shifeng, additional, Huang, Xingxu, additional, Huang, Xueting, additional, Huang, Yilun, additional, Huffman, Anthony, additional, Humphreys, Tricia L., additional, Hunstad, David A., additional, Inglis, Timothy J.J., additional, Isaac, Lourdes, additional, Jacobs, Samantha E., additional, Janowicz, Diane M., additional, Jeon, Hyeong-Kyu, additional, Ji, Quanjiang, additional, Jia, Qi, additional, Jia, Wei, additional, Jin, Shouguang, additional, Jneidi, Lama, additional, Jose, Shinsmon, additional, Jung, Bong-Kwang, additional, Kattan, Randa, additional, Kaushik, Rahul, additional, Khare, Reeti, additional, Kim, Eun Sook, additional, Kirn, Thomas J., additional, Koo, Hyun, additional, Köster, Pamela C., additional, Krause, Peter J., additional, Kumar, Sanjai, additional, Kupz, Andreas, additional, Lambert, P.A., additional, Lamont, Richard J., additional, Langford, Paul R., additional, Lebeaux, David, additional, Legname, Giuseppe, additional, Li, Bin, additional, Li, Chunhao, additional, Li, Fen, additional, Li, Jun, additional, Li, Lanjuan, additional, Li, Ruofan, additional, Li, Ruoyu, additional, Li, Ting, additional, Li, Yang-Yang, additional, Li, Yanhua, additional, Li, Zhuorong, additional, Liang, Xiaomeng, additional, Liao, Guojian, additional, Lin, Ping, additional, Ling, Yun, additional, Liu, Bo, additional, Liu, Dongyou, additional, Liu, Guohua, additional, Liu, Huidi, additional, Liu, Jiafeng, additional, Liu, Jintao, additional, Liu, Qi, additional, Liu, Shu-Lin, additional, Liu, Taiping, additional, Liu, Tongbao, additional, Liu, Wei, additional, Liu, Yan, additional, Liu, Yanni, additional, Liu, Yisong, additional, Liu, Yuan, additional, Løbner-Olesen, Anders, additional, Loeffelholz, Michael, additional, Lu, Hongzhou, additional, Luna, Brian, additional, Ma, Bingting, additional, Ma, Chengying, additional, Ma, Shuang, additional, Ma, TianLi, additional, Madan, Rajat, additional, Mahle, Rachael E., additional, Mahlen, Steven D., additional, Malik, Satya Veer Singh, additional, Malik, Yashpal Singh, additional, Malvy, Denis, additional, Mann, Barbara J., additional, Marasini, Daya, additional, Maris, Alexander S., additional, Marjomäki, Varpu, additional, Marjuki, Henju, additional, Martín, Alberto, additional, Martín, Irene, additional, Martínez-Castillo, Moisés, additional, Martínez-Pabón, María Cecilia, additional, Mathison, Blaine A., additional, Ma’ayeh, Showgy, additional, McDowell, Andrew, additional, McLaughlin, Stephanie E., additional, McSheffrey, Gordon G., additional, Medrano, Francisco J., additional, Meehan, Conor J., additional, Mehta, Dhwani, additional, Mejía-Oquendo, Manuela, additional, Melo-Cristino, José, additional, Mendoza-Barberá, Elena, additional, Meng, Xinan, additional, Merino, Susana, additional, Merritt, Adam J., additional, Miller, Steve, additional, Miller, William R., additional, Minamino, Tohru, additional, Mirzaei, Mohammadali Khan, additional, Mora-Montes, Héctor M., additional, Mortensen, Joel, additional, Mostafa, Heba H., additional, Muhsen, Khitam, additional, Mujahed, Ahlam, additional, Muro, Antonio, additional, Murphy, Olwen C., additional, Newton, Hayley J., additional, Nguyen, April H., additional, Nichols, Wright W., additional, Niu, Siqiang, additional, Núñez, Félix, additional, Obregon, Dasiel, additional, Okamoto, Akira, additional, Okutani, Akiko, additional, Olabode, Abayomi, additional, Omar, Muna, additional, Ong, Edison, additional, Ouyang, Zhiming, additional, Pacak, Christina A., additional, Pacheco-Yépez, Judith, additional, Palmer, John, additional, Pang, Xiaoli, additional, Paredes-Sabja, Daniel, additional, Peng, Zhong, additional, Peng, Zonggen, additional, Pérez-Nevado, Francisco, additional, Poon, Art, additional, Pospíšilová, Petra, additional, Potts, Caelin C., additional, Pu, Qinqin, additional, Pujic, Petar, additional, Qi, Rui, additional, Qian, Chenyun, additional, Qian, Liu, additional, Qin, Aiping, additional, Qu, Fen, additional, Rakin, Alexander, additional, Ramesh, Ashwin, additional, Ramirez, Mario, additional, Rao, Yu, additional, Ratner, Adam J., additional, Rawool, Deepak B., additional, Rehman, Asma, additional, Ren, Jie, additional, Ren, Ping, additional, Retchless, Adam C., additional, Robertson, Erle S., additional, Rodríguez, Alicia, additional, Rodriguez, Azucena, additional, Rodríguez-Medina, Carolina, additional, Rodriguez-Nava, Veronica, additional, Rohde, Manfred, additional, Romero-Rodríguez, Alba, additional, Rosales-Morgan, Gabriela, additional, Rosenkranz, Andrea L., additional, Ruiz-Moyano, Santiago, additional, Ruokolainen, Visa, additional, Sabateen, Ali, additional, Sahu, Radhakrishna, additional, Sails, Andrew, additional, Sang, Yu, additional, Santana, Clarissa H., additional, Santos, Jesus A., additional, Santos, Renato L., additional, Schmitz, Jonathan E., additional, Serrano-Luna, Jesús, additional, Shen, Jianzhong, additional, Shen, Zhangqi, additional, Shibayama, Mineko, additional, Shirtliff, Mark E., additional, Silva-Costa, Catarina, additional, Silva-Olivares, Angélica, additional, Singh, Niraj Kumar, additional, Šmajs, David, additional, Smith, Robert P., additional, Smith, Sophie, additional, Snyder, Lori A.S., additional, Song, Yinggai, additional, Soro, Aurea Simon, additional, Spearman, Paul, additional, Spellberg, Brad, additional, Sprague, Lisa D., additional, Stratton, Charles W., additional, Strenk, Susan M., additional, Strugnell, Richard A., additional, Sun, Keer, additional, Suo, Xun, additional, Suzuki-Hatano, Silveli, additional, Svärd, Staffan, additional, Talbot, Elizabeth A., additional, Tamez-Castrellón, Alma K., additional, Tan, Nie, additional, Tang, Cynthia Y., additional, Tang, Yi-Wei, additional, Tao, Jia, additional, Tao, Lili, additional, Terrero-Salcedo, David, additional, Tharmalingam, Jayaraman, additional, Thwe, Phyu M., additional, Tiamani, Kawtar, additional, Tomás, Juan M., additional, Topaz, Nadav, additional, Tsai, Ang-Chen, additional, Tsalik, Ephraim L., additional, Tuomanen, Elaine I., additional, Turenne, Christine Y., additional, Tyagi, Anuj, additional, Uprety, Priyanka, additional, Valour, Florent, additional, van Hensbergen, Vincent P., additional, Venkatesan, Arun, additional, Vergis, Jess, additional, Villar, Margarita, additional, Vollmer, Waldemar, additional, Waites, Ken B., additional, Wan, Xiu-Feng, additional, Wang, Guiqing, additional, Wang, Lijun, additional, Wang, Lin, additional, Wang, Linqi, additional, Wang, Xiangru, additional, Wang, Xin, additional, Wang, Xinjie, additional, Wang, Ya-Ting, additional, Wang, Yang, additional, Wang, Yating, additional, Weil, Ana A., additional, Welkos, Susan L., additional, Wengenack, Nancy L., additional, Westblade, Lars F., additional, Whitfield, Chris, additional, Wu, Hui, additional, Wu, Lijuan, additional, Wu, Min, additional, Wu, Yarong, additional, Wu, Zhaowei, additional, Xiang, Ye, additional, Xiao, Di, additional, Xiao, Li, additional, Xiao, Lihua, additional, Xu, Tao, additional, Xu, Wenyue, additional, Xu, Xinping, additional, Xue, Jinling, additional, Yadav, Jay Prakash, additional, Yan, Junxiang, additional, Yan, Yixin, additional, Yang, Changmei, additional, Yang, Ruifu, additional, Yang, Ying, additional, Yao, Kaihu, additional, Yao, Yu-Feng, additional, Yeakle, Kyle C., additional, Yu, Demin, additional, Yu, Hao, additional, Yu, Xue-Jie, additional, Yuan, Zhenghong, additional, Zai, Wenjing, additional, Zhang, Jianzhong, additional, Zhang, Jing-Ren, additional, Zhang, Lanyue, additional, Zhang, Lijie, additional, Zhang, Qiwei, additional, Zhang, Wenbao, additional, Zhang, Wenhong, additional, Zhang, Xinxin, additional, Zhao, Youbao, additional, Zhou, Chuanmin, additional, Zhu, Feng, additional, Zhu, Jingting, additional, and Zhu, Yongqun, additional

Published
2024
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7. Virus assembly

Author

Liu, Qi, primary, Huang, Liang, additional, Wang, Lin, additional, Jia, Qi, additional, Ma, Bingting, additional, Li, Ruofan, additional, and Xiang, Ye, additional

Published
2024
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13. Symmetry Hierarchy and Thermalization Frustration in Graphene Nanoresonators

Author

Wang, Yisen and Huang, Liang

Subjects
Condensed Matter - Statistical Mechanics
Abstract

As the essential cause of the intrinsic dissipation that limits the quality of graphene nanoresonators, intermodal energy transfer is also a key issue in thermalization dynamics. Typically systems with larger initial energy demand shorter time to be thermalized. However, we find quantitatively that instead of becoming shorter, the equipartition time of the graphene nanoresonator can increase abruptly by one order of magnitude. This thermalization frustration emerges due to the partition of the normal modes based on the hierarchical symmetry, and a sensitive on-off switching of the energy flow channels between symmetry classes controlled by Mathieu instabilities. The results uncover the decisive roles of symmetry in the thermalization at the nanoscale, and may also lead to strategies for improving the performance of graphene nanoresonators.

Published
2024

14. Exact periodic-orbit quantization of Klein tunneling: theory and experiment

Author

Peng, Xiao-Zhen, Zhang, Rui-Jie, Ni, Rui-Hua, Yang, Ri-Zhen, Hu, Yong-Yin, Xu, Hong-Ya, and Huang, Liang

Subjects
Quantum Physics
Abstract

Klein tunneling, a peculiar effect in relativistic quantum mechanics, poses an outstanding challenge to the quantum-classical correspondence. We establish, based on the scattering matrix framework, an exact periodic-orbit quantization of Klein tunneling for bounded Dirac systems with a step potential. It relies heavily on a family of distinct non-Newtonian orbits, the Klein orbits, to account for the non-decaying propagation inside the classically forbidden barrier. An explicit spectral counting function and a closed form of the Weyl formula with Klein tunneling based corrections are derived. The theoretical findings are supported by microwave analog experiments. The measured quantized levels and corresponding Klein tunneling states provide the first observation of Klein tunneling in bounded Dirac systems.

Published
2024

15. Scalable Identification of Minimum Undesignable RNA Motifs on Loop-Pair Graphs

Author

Zhou, Tianshuo, Tang, Wei Yu, Mathews, David H., and Huang, Liang

Subjects
Computer Science - Data Structures and Algorithms
Abstract

Motivation: RNA design aims to find at least one sequence that folds with the highest probability into a designated target structure, but some structures are undesignable in the sense that no sequence folds into them. Identifying undesignable structures is useful in delineating and understanding the limit of RNA designability, but has received little attention until recently. In addition, existing methods on undesignability are not scalable and not interpretable. Results: We introduce a novel graph representation and a new general algorithmic framework to efficiently identify undesignable motifs in a secondary structure. The proposed algorithm enumerates minimal motifs based on the loop-pair graph representation of a structure and establishes the undesignability of a motif by proposing rival substructure(s). Our work can also identify unique minimum undesignable motifs across different structures. Our implemented algorithms successfully identify 26 unique minimum undesignable motifs among 18 undesignable puzzles from the benchmark Eterna100. Additionally, our algorithm is so efficient that it scales to natural structures of 16S and 23S Ribosomal RNAs (about 1,500 and 3,000 nucleotides, resp.), and finds all of those structures in the widely used ArchiveII database to be undesignable, with 73 unique minimum undesignable motifs, under the standard Turner energy model in ViennaRNA.

Published
2024

16. Geometry-induced wavefunction collapse

Author

Ye, Li-Li, Han, Chen-Di, Huang, Liang, and Lai, Ying-Cheng

Subjects
Quantum Physics
Abstract

When a quantum particle moves in a curved space, a geometric potential can arise. In spite of a long history of extensive theoretical studies, to experimentally observe the geometric potential remains to be a challenge. What are the physically observable consequences of such a geometric potential? Solving the Schrodinger equation on a truncated conic surface, we uncover a class of quantum scattering states that bear a strong resemblance with the quasi-resonant states associated with atomic collapse about a Coulomb impurity, a remarkable quantum phenomenon in which an infinite number of quasi-resonant states emerge. A characteristic defining feature of such collapse states is the infinite oscillations of the local density of states (LDOS) about the zero energy point separating the scattering from the bound states. The emergence of such states in the curved (Riemannian) space requires neither a relativistic quantum mechanism nor any Coulomb impurity: they have zero angular momentum and their origin is purely geometrical - henceforth the term geometry-induced wavefunction collapse. We establish the collapsing nature of these states through a detailed comparative analysis of the behavior of the LDOS for both the zero and finite angular-momentum states as well as the corresponding classical picture. Potential experimental schemes to realize the geometry-induced collapse states are articulated. Not only has our study uncovered an intrinsic connection between the geometric potential and atomic collapse, it also provides a method to experimentally observe and characterize geometric potentials arising from different subfields of physics. For example, in nanoscience and nanotechnology, curved geometry has become increasingly common. Our finding suggests that wavefunction collapse should be an important factor of consideration in designing and developing nanodevices., Comment: 14 pages, 8 figures, journal

Published
2024
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17. Damping Separation of Finite Open Systems in Gravity-Related Experiments in the Free Molecular Flow Regime

Author

Teng, Hou-Qiang, Dong, Jia-Qi, Wang, Yisen, Huang, Liang, and Xu, Peng

Subjects
General Relativity and Quantum Cosmology, Physics - Instrumentation and Detectors
Abstract

The residual gas damping of the test mass (TM) in the free molecular flow regime is studied in the finite open systems for high-precision gravity-related experiments. Through strict derivation, we separate the damping coefficients for two finite open systems, i.e., the bi-plate system and the sensor core system, into base damping and diffusion damping. This elucidates the relationship between the free damping in the infinite gas volume and the proximity damping in the constrained volume, unifies them into one microscopic picture, and allows us to point out three pathways of energy dissipation in the bi-plate gap. We also provide the conditions that need to be met to achieve this separation. In applications, for space gravitational wave detection, our results for the residual gas damping coefficient for the 4TM torsion balance experiment is the closest one to the experimental and simulation data compared to previous models. For the LISA mission, our estimation for residual gas acceleration noise at the sensitive axis is consistent with the simulation result, within about $5\%$ difference. In addition, in the test of the gravitational inverse-square law, our results suggest that the constraint on the distance between TM and the conducting membrane can be reduced by about $28\%$.

Published
2024

18. Messenger RNA Design via Expected Partition Function and Continuous Optimization

Author

Dai, Ning, Tang, Wei Yu, Zhou, Tianshuo, Mathews, David H., and Huang, Liang

Subjects
Quantitative Biology - Biomolecules, Computer Science - Artificial Intelligence, Computer Science - Machine Learning
Abstract

The tasks of designing RNAs are discrete optimization problems, and several versions of these problems are NP-hard. As an alternative to commonly used local search methods, we formulate these problems as continuous optimization and develop a general framework for this optimization based on a generalization of classical partition function which we call "expected partition function". The basic idea is to start with a distribution over all possible candidate sequences, and extend the objective function from a sequence to a distribution. We then use gradient descent-based optimization methods to improve the extended objective function, and the distribution will gradually shrink towards a one-hot sequence (i.e., a single sequence). As a case study, we consider the important problem of mRNA design with wide applications in vaccines and therapeutics. While the recent work of LinearDesign can efficiently optimize mRNAs for minimum free energy (MFE), optimizing for ensemble free energy is much harder and likely intractable. Our approach can consistently improve over the LinearDesign solution in terms of ensemble free energy, with bigger improvements on longer sequences.

Published
2023

20. Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition

Author

Zhou, Tianshuo, Tang, Wei Yu, Mathews, David H., and Huang, Liang

Subjects
Quantitative Biology - Biomolecules
Abstract

RNA design is the search for a sequence or set of sequences that will fold into predefined structures, also known as the inverse problem of RNA folding. While numerous RNA design methods have been invented to find sequences capable of folding into a target structure, little attention has been given to the identification of undesignable structures according to the minimum free energy (MFE) criterion under the Turner model. In this paper, we address this gap by first introducing mathematical theorems outlining sufficient conditions for recognizing undesignable structures, then proposing efficient algorithms, guided by these theorems, to verify the undesignability of RNA structures. Through the application of these theorems and algorithms to the Eterna100 puzzles, we demonstrate the ability to efficiently establish that 15 of the puzzles indeed fall within the category of undesignable structures. In addition, we provide specific insights from the study of undesignability, in the hope that it will enable more understanding of RNA folding and RNA design.

Published
2023

21. Symmetry dictated universal helicity redistribution of Dirac fermions in transport

Author

Huang, Jun-Yin, Ni, Rui-Hua, Xu, Hong-Ya, and Huang, Liang

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

Helicity is a fundamental property of Dirac fermions. Yet, the general rule of how it changes in transport is still lacking. We uncover, theoretically, the universal spinor state transformation and consequently helicity redistribution rule in two cases of transport through potentials of electrostatic and mass types, respectively. The former is dictated by Lorentz boost and its complex counterpart in Klein tunneling regime, which establishes miraculously a unified yet latent connection between helicity, Klein tunneling, and Lorentz boost. The latter is governed by an abstract rotation group we construct, which reduces to SO(2) when acting on the plane of effective mass and momentum. They generate invariant submanifolds, i.e., leaves, that foliate the Hilbert space of Dirac spinors. Our results provide a basis for unified understanding of helicity transport, and may open a new window for exotic helicity-based physics and applications in mesoscopic systems., Comment: 6 pages, 4 figures

Published
2023

22. CoV-Seq, a New Tool for SARS-CoV-2 Genome Analysis and Visualization: Development and Usability Study

Author

Liu, Boxiang, Liu, Kaibo, Zhang, He, Zhang, Liang, Bian, Yuchen, and Huang, Liang

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Public aspects of medicine, RA1-1270
Abstract

BackgroundCOVID-19 became a global pandemic not long after its identification in late 2019. The genomes of SARS-CoV-2 are being rapidly sequenced and shared on public repositories. To keep up with these updates, scientists need to frequently refresh and reclean data sets, which is an ad hoc and labor-intensive process. Further, scientists with limited bioinformatics or programming knowledge may find it difficult to analyze SARS-CoV-2 genomes. ObjectiveTo address these challenges, we developed CoV-Seq, an integrated web server that enables simple and rapid analysis of SARS-CoV-2 genomes. MethodsCoV-Seq is implemented in Python and JavaScript. The web server and source code URLs are provided in this article. ResultsGiven a new sequence, CoV-Seq automatically predicts gene boundaries and identifies genetic variants, which are displayed in an interactive genome visualizer and are downloadable for further analysis. A command-line interface is available for high-throughput processing. In addition, we aggregated all publicly available SARS-CoV-2 sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID), National Center for Biotechnology Information (NCBI), European Nucleotide Archive (ENA), and China National GeneBank (CNGB), and extracted genetic variants from these sequences for download and downstream analysis. The CoV-Seq database is updated weekly. ConclusionsWe have developed CoV-Seq, an integrated web service for fast and easy analysis of custom SARS-CoV-2 sequences. The web server provides an interactive module for the analysis of custom sequences and a weekly updated database of genetic variants of all publicly accessible SARS-CoV-2 sequences. We believe CoV-Seq will help improve our understanding of the genetic underpinnings of COVID-19.

Published
2020
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41. Single-cell analysis of anti-BCMA CAR T cell therapy in patients with central nervous system autoimmunity

Author

Qin, Chuan, primary, Zhang, Min, additional, Mou, Da-Peng, additional, Zhou, Luo-Qi, additional, Dong, Ming-Hao, additional, Huang, Liang, additional, Wang, Wen, additional, Cai, Song-Bai, additional, You, Yun-Fan, additional, Shang, Ke, additional, Xiao, Jun, additional, Wang, Di, additional, Li, Chun-Rui, additional, Hao, Yi, additional, Heming, Michael, additional, Wu, Long-Jun, additional, Hörste, Gerd Meyer Zu, additional, Dong, Chen, additional, Bu, Bi-Tao, additional, Tian, Dai-Shi, additional, and Wang, Wei, additional

Published
2024
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46. Clinical significance of positive resection margin for patients with rectal neuroendocrine tumors within 20mm following initial endoscopic resection: A multi-center study

Author

duan, mengping, primary, wang, yunhua, additional, liu, Zhanzhen, additional, zhou, ziwei, additional, Wan, Taixuan, additional, xie, zhuowei, additional, wang, liwei, additional, zhou, yebohao, additional, sun, qiufeng, additional, Xie, hao, additional, lai, sicong, additional, Xiao, wei, additional, Zheng, Haoqi, additional, Zhou, Yihang, additional, Zhang, Zhihong, additional, Liu, Huashan, additional, Lei, Dongxu, additional, luo, shuanglin, additional, shi, Yunxing, additional, Ye, Fujin, additional, and Huang, Liang, additional

Published
2024
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