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ORCIDGenomics, Proteomics & Bioinformatics, Volume 20
Volume 20, Number 1, February 2022
- Weihua Pan
, Jue Ruan:
En Route to Completion: What Is An Ideal Reference Genome? 1-3
- Bo Wang, Xiaofei Yang, Yanyan Jia, Yu Xu, Peng Jia, Ningxin Dang, Songbo Wang, Tun Xu, Xixi Zhao, Shenghan Gao, Quanbin Dong, Kai Ye:
High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads. 4-13 - Ruicai Long, Fan Zhang, Zhiwu Zhang, Mingna Li, Lin Chen, Xue Wang, Wenwen Liu, Tiejun Zhang, Long-Xi Yu, Fei He, Xueqian Jiang, Xijiang Yang, Changfu Yang, Zhen Wang, Junmei Kang, Qingchuan Yang:
Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits. 14-28 - Chunming Yang, Jun Yan, Shuqin Jiang, Xia Li, Haowei Min, Xiangfeng Wang, Dongyun Hao:
Resequencing 250 Soybean Accessions: New Insights into Genes Associated with Agronomic Traits and Genetic Networks. 29-41 - Jianjun Lu, Cheng Pan, Wei Fan, Wanfei Liu, Huayan Zhao, Donghai Li, Sen Wang, Lianlian Hu, Bing He, Kun Qian, Rui Qin, Jue Ruan, Qiang Lin, Shiyou Lü, Peng Cui:
A Chromosome-level Genome Assembly of Wild Castor Provides New Insights into its Adaptive Evolution in Tropical Desert. 42-59 - Wentai Ma, Jing Yang, Haoyi Fu, Chao Su, Caixia Yu, Qihui Wang, Ana Tereza Ribeiro de Vasconcelos, Georgii A. Bazykin, Yiming Bao, Mingkun Li:
Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant. 60-69 - Chen Zhang, Xueshuai Han, Jingkun Liu, Lei Chen, Ying Lei, Kunying Chen, Jia Si, Tian-yi Wang, Hui Zhou, Xiaoyun Zhao, Xiaohui Zhang, Yihua An, Yueying Li, Qian-Fei Wang:
Single-cell Transcriptomic Analysis Reveals the Cellular Heterogeneity of Mesenchymal Stem Cells. 70-86 - Xinran Li, Jiaqi Zhou, Wenjuan Zhao, Qing Wen, Weijie Wang, Huipai Peng, Yuan Gao, Kelly J. Bouchonville, Steven M. Offer, Kuiming Chan, Zhiquan Wang, Nan Li, Haiyun Gan:
Defining Proximity Proteome of Histone Modifications by Antibody-mediated Protein A-APEX2 Labeling. 87-100 - Xin Liu, Qiu Sun, Qi Wang, Chuansheng Hu, Xuecheng Chen, Hua Li, Daniel M. Czajkowsky, Zhifeng Shao:
Epithelial Cells in 2D and 3D Cultures Exhibit Large Differences in Higher-order Genomic Interactions. 101-109 - Sue Yu, Jia Li, Guanxu Ji, Zhen Long Ng, Jiamin Siew, Wan Ning Lo, Ying Ye, Yuan Yuan Chew, Yun Chau Long, Wensheng Zhang, Ernesto Guccione, Yuin Han Loh, Zhi-Hong Jiang, Henry Yang, Qiang Wu:
Npac Is A Co-factor of Histone H3K36me3 and Regulates Transcriptional Elongation in Mouse Embryonic Stem Cells. 110-128 - Jes-Niels Boeckel, Maximilian Möbius-Winkler, Marion Müller, Sabine Rebs, Nicole Eger, Laura Schoppe, Rewati Tappu, Karoline E. Kokot, Jasmin M. Kneuer, Susanne Gaul, Diana M. Bordalo, Alan Lai, Jan Haas, Mahsa Ghanbari, Philipp Drewe-Boss, Martin Liss, Hugo A. Katus, Uwe Ohler, Michael Gotthardt, Ulrich Laufs, Katrin Streckfuss-Bömeke, Benjamin Meder:
SLM2 Is A Novel Cardiac Splicing Factor Involved in Heart Failure due to Dilated Cardiomyopathy. 129-146 - Yikai Luo, Han Liang:
Convergent Usage of Amino Acids in Human Cancers as A Reversed Process of Tissue Development. 147-162 - Feiyang Ji, Menghao Zhou, Huihui Zhu, Zhengyi Jiang, Qirui Li, Xiaoxi Ouyang, Yiming Lv, Sainan Zhang, Tian Wu, Lanjuan Li:
Integrative Proteomic Analysis of Multiple Posttranslational Modifications in Inflammatory Response. 163-176 - Yaqiang Hong, Dake Zhang, Xiangtian Zhou, Aili Chen, Amir Abliz, Jian Bai, Liang Wang, Qingtao Hu, Kenan Gong, Xiaonan Guan, Mengfei Liu, Xinchang Zheng, Shujuan Lai, Hongzhu Qu, Fuxin Zhao, Shuang Hao, Zhen Wu, Hong Cai, Shaoyan Hu, Yue Ma, Junting Zhang, Yang Ke, Qian-Fei Wang, Wei Chen, Changqing Zeng:
Common Postzygotic Mutational Signatures in Healthy Adult Tissues Related to Embryonic Hypoxia. 177-191 - Xiao Du, Lili Li, Fan Liang, Sanyang Liu, Wenxin Zhang, Shuai Sun, Yuhui Sun, Fei Fan, Linying Wang, Xinming Liang, Weijin Qiu, Guangyi Fan, Ou Wang, Weifei Yang, Jiezhong Zhang, Yuhui Xiao, Yang Wang, Depeng Wang, Shoufang Qu, Fang Chen, Jie Huang:
Robust Benchmark Structural Variant Calls of An Asian Using State-of-the-art Long-read Sequencing Technologies. 192-204
- Jiadong Lin, Xiaofei Yang, Walter A. Kosters, Tun Xu, Yanyan Jia, Songbo Wang, Qihui Zhu, Mallory Ryan, Li Guo, Chengsheng Zhang:
Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants. 205-218
Volume 20, Number 2, April 2022
- Rui Wang, Xixi Liu, Li Li, Ming Yang, Jun Yong, Fan Zhai, Lu Wen, Liying Yan, Jie Qiao, Fuchou Tang:
Dissecting Human Gonadal Cell Lineage Specification and Sex Determination Using A Single-cell RNA-seq Approach. 223-245 - Jie Zhu, Liu Tian, Peishan Chen, Mo Han, Liju Song, Xin Tong, Xiaohuan Sun, Fangming Yang, Zhipeng Lin, Xing Liu, Chuan Liu, Xiaohan Wang, Yuxiang Lin, Kaiye Cai, Yong Hou, Xun Xu, Huanming Yang, Jian Wang, Karsten Kristiansen, Liang Xiao, Tao Zhang, Huijue Jia, Zhuye Jie:
Over 50, 000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa. 246-259 - Zhenwei Liu, Tao Zhang, Keke Wu, Zhongshan Li, Xiaomin Chen, Shan Jiang, Lifeng Du, Saisai Lu, Chongxiang Lin, Jinyu Wu, Xiaobing Wang:
Metagenomic Analysis Reveals A Possible Association Between Respiratory Infection and Periodontitis. 260-273 - Anouck Becker, Georges Pierre Schmartz, Laura Gröger, Nadja Liddy Grammes, Valentina Galata, Hannah Philippeit, Jacqueline Weiland, Nicole Ludwig, Eckart Meese, Sascha Tierling, Jörn Walter, Andreas Schwiertz, Jörg Spiegel, Gudrun Wagenpfeil, Klaus Faßbender, Andreas Keller, Marcus M. Unger:
Effects of Resistant Starch on Symptoms, Fecal Markers, and Gut Microbiota in Parkinson's Disease - The RESISTA-PD Trial. 274-287 - Mingyue Li, Weina Guo, Yalan Dong, Wenzhu Wang, Chunxia Tian, Zili Zhang, Ting Yu, Haifeng Zhou, Yang Gui, Kaming Xue, Junyi Li, Feng Jiang, Alexey Sarapultsev, Huafang Wang, Ge Zhang, Shanshan Luo, Heng Fan, Desheng Hu:
Beneficial Effects of Celastrol on Immune Balance by Modulating Gut Microbiota in Experimental Ulcerative Colitis Mice. 288-303 - Zhuye Jie, Chen Chen, Lilan Hao, Fei Li, Liju Song, Xiaowei Zhang, Jie Zhu, Liu Tian, Xin Tong, Kaiye Cai, Zhe Zhang, Yanmei Ju, Xinlei Yu, Ying Li, Hongcheng Zhou, Haorong Lu, Xuemei Qiu, Qiang Li, Yunli Liao, Dongsheng Zhou, Heng Lian, Yong Zuo, Xiaomin Chen, Weiqiao Rao, Yan Ren, Yuan Wang, Jin Zi, Rong Wang, Na Liu, Jinghua Wu, Wei Zhang, Xiao Liu, Yang Zong, Weibin Liu, Liang Xiao, Yong Hou, Xun Xu, Huanming Yang, Jian Wang, Karsten Kristiansen, Huijue Jia:
Life History Recorded in the Vagino-cervical Microbiome Along with Multi-omes. 304-321 - Xiaoai Zhang, Qingzhi Zhai, Jinfeng Wang, Xiuling Ma, Bo Xing, Hang Fan, Zhiying Gao, Fangqing Zhao, Wei Liu:
Variation of the Vaginal Microbiome During and After Pregnancy in Chinese Women. 322-333 - Hao Li, Jan P. Meier-Kolthoff, Canxin Hu, Zhongjie Wang, Jun Zhu, Wei Zheng, Yun Tian, Feng Guo:
Panoramic Insights into Microevolution and Macroevolution of A Prevotella copri-containing Lineage in Primate Guts. 334-349 - Zhi-Yuan Wei, Jun-Hua Rao, Ming-Tian Tang, Guo-An Zhao, Qi-Chun Li, Li-Ming Wu, Shao-Qiang Liu, Bi-Hai Li, Bai-Quan Xiao, Xingyin Liu, Jian-Huan Chen:
Characterization of Changes and Driver Microbes in Gut Microbiota During Healthy Aging Using A Captive Monkey Model. 350-365 - Yue Xie, Sen Wang, Shuangyang Wu, Shenghan Gao, Qingshu Meng, Chengdong Wang, Jingchao Lan, Li Luo, Xuan Zhou, Jing Xu, Xiaobin Gu, Ran He, Zijiang Yang, Xuerong Peng, Songnian Hu, Guangyou Yang:
Genome of the Giant Panda Roundworm Illuminates Its Host Shift and Parasitic Adaptation. 366-381 - Yanze Li, Wenming Cao, Na L. Gao, Xing-Ming Zhao, Wei-Hua Chen:
Consistent Alterations of Human Fecal Microbes After Transplantation into Germ-free Mice. 382-393 - Yanxue Yu, Qi Wang, Ping Zhou, Na Lv, Wei Li, Fangqing Zhao, Shuifang Zhu, Di Liu:
First Glimpse of Gut Microbiota of Quarantine Insects in China. 394-404 - Jacqueline Rehner, Georges Pierre Schmartz, Laura Groeger, Jan Dastbaz, Nicole Ludwig, Matthias Hannig, Stefan Rupf, Berthold Seitz, Elias Flockerzi, Tim Berger, Matthias Christian Reichert, Marcin Krawczyk, Eckart Meese, Christian Herr, Robert Bals, Sören L. Becker, Andreas Keller, Rolf Müller:
Systematic Cross-biospecimen Evaluation of DNA Extraction Kits for Long- and Short-read Multi-metagenomic Sequencing Studies. 405-417 - Jing Fu, Ju Zhang, Li Yang, Nan Ding, Liya Yue, Xiangli Zhang, Dandan Lu, Xinmiao Jia, Cuidan Li, Chongye Guo, Zhe Yin, Xiaoyuan Jiang, Yongliang Zhao, Fei Chen, Dongsheng Zhou:
Precision Methylome and In Vivo Methylation Kinetics Characterization of Klebsiella pneumoniae. 418-434
Volume 20, Number 3, June 2022
- Chunyan Fan, Xiujuan Lei, Jiaojiao Tie, Yuchen Zhang, Fang-Xiang Wu, Yi Pan:
CircR2Disease v2.0: An Updated Web Server for Experimentally Validated circRNA-disease Associations and Its Application. 435-445 - Feng Xu, Yifan Wang, Yunchao Ling, Chenfen Zhou, Haizhou Wang, Andrew E. Teschendorff, Yi Zhao, Haitao Zhao, Yungang He, Guoqing Zhang, Zhen Yang:
dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms. 446-454 - Jianing Gao, Huan Zhang, Xiaohua Jiang, Asim Ali, Daren Zhao, Jianqiang Bao, Long Jiang, Furhan Iqbal, Qinghua Shi, Yuanwei Zhang:
FertilityOnline: A Straightforward Pipeline for Functional Gene Annotation and Disease Mutation Discovery. 455-465
- Kyubin Lee, Doyeong Yu, Daejin Hyung, Soo Young Cho, Charny Park:
ASpediaFI: Functional Interaction Analysis of Alternative Splicing Events. 466-482 - Zhongxiao Li, Yisheng Li, Bin Zhang, Yu Li, Yongkang Long, Juexiao Zhou, Xudong Zou, Min Zhang, Yuhui Hu, Wei Chen, Xin Gao:
DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning. 483-495 - Qiao Liu, Kui Hua, Xuegong Zhang, Wing Hung Wong, Rui Jiang:
DeepCAGE: Incorporating Transcription Factors in Genome-wide Prediction of Chromatin Accessibility. 496-507 - Fengxia Zhou, Rui Gan, Fan Zhang, Chunyan Ren, Ling Yu, Yu Si, Zhiwei Huang:
PHISDetector: A Tool to Detect Diverse In Silico Phage-host Interaction Signals for Virome Studies. 508-523 - Qichao Lian, Yamao Chen, Fang Chang, Ying Fu, Ji Qi:
inGAP-family: Accurate Detection of Meiotic Recombination Loci and Causal Mutations by Filtering Out Artificial Variants due to Genome Complexities. 524-535
- Zhang Zhang:
KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences. 536-540 - Tongwu Zhang, Alyssa Klein, Jian Sang, Jiyeon Choi, Kevin M. Brown:
ezQTL: A Web Platform for Interactive Visualization and Colocalization of QTLs and GWAS Loci. 541-548 - Zelin Liu, Huiru Ding, Jianqi She, Chunhua Chen, Weiguang Zhang, Ence Yang:
DEBKS: A Tool to Detect Differentially Expressed Circular RNAs. 549-556 - Ting Zhang, Jingjing Zhai, Xiaorong Zhang, Lei Ling, Menghan Li, Shang Xie, Minggui Song, Chuang Ma:
Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA. 557-567 - Arsenij Ustjanzew, Jens Preussner, Mette Bentsen, Carsten Kuenne, Mario Looso:
i2dash: Creation of Flexible, Interactive, and Web-based Dashboards for Visualization of Omics Data. 568-577 - Mikaela Koutrouli, Evangelos Karatzas, Katerina Papanikolopoulou, Georgios A. Pavlopoulos:
NORMA: The Network Makeup Artist - A Web Tool for Network Annotation Visualization. 578-586 - Shuyu Zheng, Wenyu Wang, Jehad Aldahdooh, Alina Malyutina, Tolou Shadbahr, ZiaurRehman Tanoli, Alberto Pessia, Jing Tang:
SynergyFinder Plus: Toward Better Interpretation and Annotation of Drug Combination Screening Datasets. 587-596
Volume 20, Number 4, August 2022
- Yuejing Jiang, Xiaoji Cong, Shangwen Jiang, Ying Dong, Lei Zhao, Yi Zang, Minjia Tan, Jia Li:
Phosphoproteomics Reveals the AMPK Substrate Network in Response to DNA Damage and Histone Acetylation. 597-613 - Zhengguang Guo, Chen Shao, Yang Zhang, Wenying Qiu, Wenting Li, Weimin Zhu, Qian Yang, Yin Huang, Lili Pan, Yuepan Dong, Haidan Sun, Xiaoping Xiao, Wei Sun, Chao Ma, Liwei Zhang:
A Global Multiregional Proteomic Map of the Human Cerebral Cortex. 614-632 - Xiuxiu Jin, Jingyang Liu, Weiping Wang, Jiangfeng Li, Guangming Liu, Ruiqi Qiu, Mingzhu Yang, Meng Liu, Lin Yang, Xiaofeng Du, Bo Lei:
Identification of Age-associated Proteins and Functional Alterations in Human Retinal Pigment Epithelium. 633-647 - Qiushi Chen, Yuanliang Zhang, Keren Zhang, Jie Liu, Huozhen Pan, Xinran Wang, Siqi Li, Dandan Hu, Zhilong Lin, Yun Zhao, Guixue Hou, Feng Guan, Hong Li, Siqi Liu, Yan Ren:
Profiling the Bisecting N-acetylglucosamine Modification in Amniotic Membrane via Mass Spectrometry. 648-656 - Songbiao Zhu, Wenxi Ding, Yuling Chen, Weixuan Wang, Renhua Xu, Chongdong Liu, Xiaohui Liu, Haiteng Deng:
High VHL Expression Reverses Warburg Phenotype and Enhances Immunogenicity in Kidney Tumor Cells. 657-669 - Lei Liu, Jia Wu, Minxin Shi, Fengying Wang, Haimin Lu, Jibing Liu, Weiqin Chen, Guanzhen Yu, Dan Liu, Jing Yang, Qin Luo, Yan Ni, Xing Jin, Xiaoxia Jin, Wenlian Chen:
New Metabolic Alterations and A Predictive Marker Pipecolic Acid in Sera for Esophageal Squamous Cell Carcinoma. 670-687 - Ning Zhang, Lingran Zhang, Linjie Li, Junyou Geng, Lei Zhao, Yan Ren, Zhongdong Dong, Feng Chen:
Global Profiling of 2-hydroxyisobutyrylome in Common Wheat. 688-701 - Xuetong Li, Hongxia Zhou, Ning Xiao, Xueting Wu, Yuanhong Shan, Longxian Chen, Cuiting Wang, Zixuan Wang, Jirong Huang, Aihong Li, Xuan Li:
Expanding the Coverage of Metabolic Landscape in Cultivated Rice with Integrated Computational Approaches. 702-714 - Chen Xu, Bing Wang, Lin Yang, Lucas Zhongming Hu, Lanxing Yi, Yaxuan Wang, Shenglan Chen, Andrew Emili, Cuihong Wan:
Global Landscape of Native Protein Complexes in Synechocystis sp. PCC 6803. 715-727 - Ning Liu, Linlu Qi, Manna Huang, Deng Chen, Changfa Yin, Yiying Zhang, Xingbin Wang, Guixin Yuan, Rui-Jin Wang, Jun Yang, You-Liang Peng, Xunli Lu:
Comparative Secretome Analysis of Magnaporthe oryzae Identified Proteins Involved in Virulence and Cell Wall Integrity. 728-746 - Zhaoxu Gao, Jun Li, Li Li, Yanzhi Yang, Jian Li, Chunxiang Fu, Danmeng Zhu, Hang He, Huaqing Cai, Lei Li:
Structural and Functional Analyses of Hub MicroRNAs in An Integrated Gene Regulatory Network of Arabidopsis. 747-764 - Liu Yang, Wei He, Yuehui Yun, Yongxiang Gao, Zhongliang Zhu, Maikun Teng, Zhi Liang, Liwen Niu:
Defining A Global Map of Functional Group-based 3D Ligand-binding Motifs. 765-779
- Zhongyang Liu, Honglei Li, Zhaoyu Jin, Yang Li, Feifei Guo, Yangzhige He, Xinyue Liu, Yaning Qi, Liying Yuan, Fuchu He, Dong Li:
Exploration of Target Spaces in the Human Genome for Protein and Peptide Drugs. 780-794 - Limin Shang, Yuehui Zhang, Yuchen Liu, Chaozhi Jin, Yanzhi Yuan, Chunyan Tian, Ming Ni, Xiaochen Bo, Li Zhang, Dong Li, Fuchu He, Jian Wang:
A Yeast BiFC-seq Method for Genome-wide Interactome Mapping. 795-807
- Guang Song, Emily M. Lee, Jianbo Pan, Miao Xu, Hee-Sool Rho, Yichen Cheng, Nadia Whitt, Shu Yang, Jennifer Kouznetsova, Carleen Klumpp-Thomas, Samuel G. Michael, Cedric Moore, Ki-Jun Yoon, Kimberly M. Christian, Anton Simeonov, Wenwei Huang, Menghang Xia, Ruili Huang, Madhu Lal-Nag, Hengli Tang, Wei Zheng, Jiang Qian, Hongjun Song, Guo-li Ming, Heng Zhu:
Corrigendum to "An Integrated Systems Biology Approach Identifies the Proteasome as A Critical Host Machinery for ZIKV and DENV Replication" [Genomics Proteomics Bioinformatics19 (1) (2021) 108-122]. 808-809
Volume 20, Number 5, October 2022
- Matthew Brendel, Chang Su, Zilong Bai, Hao Zhang, Olivier Elemento, Fei Wang:
Application of Deep Learning on Single-cell RNA Sequencing Data Analysis: A Review. 814-835 - Stefan Stanojevic, Yijun Li, Aleksandar Ristivojevic, Lana X. Garmire:
Computational Methods for Single-cell Multi-omics Integration and Alignment. 836-849 - Yawei Li, Xin Wu, Ping Yang, Guoqian Jiang, Yuan Luo:
Machine Learning for Lung Cancer Diagnosis, Treatment, and Prognosis. 850-866 - Yuguo Zha, Hui Chong, Pengshuo Yang, Kang Ning:
Microbial Dark Matter: from Discovery to Applications. 867-881
- Wubing Zhang, Shourya S. Roy Burman, Jiaye Chen, Katherine A. Donovan, Yang Cao, Chelsea Shu, Boning Zhang, Zexian Zeng, Shengqing Gu, Yi Zhang, Dian Li, Eric S. Fischer, Collin Tokheim, X. Shirley Liu:
Machine Learning Modeling of Protein-intrinsic Features Predicts Tractability of Targeted Protein Degradation. 882-898 - Yongbing Zhao, Jinfeng Shao, Yan W. Asmann:
Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data. 899-911
- Alexandra J. Lee, Dallas L. Mould, Jake Crawford, Dongbo Hu, Rani K. Powers, Georgia Doing, James C. Costello, Deborah A. Hogan, Casey S. Greene:
SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses. 912-927 - Shao-Wu Zhang, Jing-Yu Xu, Tong Zhang:
DGMP: Identifying Cancer Driver Genes by Jointing DGCN and MLP from Multi-omics Genomic Data. 928-938 - Hui Wan, Liang Chen, Minghua Deng:
scEMAIL: Universal and Source-free Annotation Method for scRNA-seq Data with Novel Cell-type Perception. 939-958 - Juexiao Zhou, Bin Zhang, Haoyang Li, Longxi Zhou, Zhongxiao Li, Yongkang Long, Wenkai Han, Meng-Ran Wang, Huanhuan Cui, Jingjing Li, Wei Chen, Xin Gao:
Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-seq Data via DeeReCT-TSS. 959-973 - Yiran Shan, Qian Zhang, Wenbo Guo, Yanhong Wu, Yuxin Miao, Hongyi Xin, Qiuyu Lian, Jin Gu:
TIST: Transcriptome and Histopathological Image Integrative Analysis for Spatial Transcriptomics. 974-988 - Sen Yang, Tao Shen, Yuqi Fang, Xiyue Wang, Jun Zhang, Wei Yang, Junzhou Huang, Xiao Han:
DeepNoise: Signal and Noise Disentanglement Based on Classifying Fluorescent Microscopy Images via Deep Learning. 989-1001 - Hao-Dong Xu, Zhongming Zhao:
NetBCE: An Interpretable Deep Neural Network for Accurate Prediction of Linear B-cell Epitopes. 1002-1012 - Yi-Heng Zhu, Chengxin Zhang, Yan Liu, Gilbert S. Omenn, Peter L. Freddolino, Dong-Jun Yu, Yang Zhang:
TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction. 1013-1027 - Zhiting Wei, Sheng Zhu, Xiaohan Chen, Chen-Yu Zhu, Bin Duan, Qi Liu:
DrSim: Similarity Learning for Transcriptional Phenotypic Drug Discovery. 1028-1036
Volume 20, Number 6, December 2022
- Yixue Li:
A Beloved Bioinformatician Buddy - In Memory of Professor Weimin Zhu. 1037-1039
- Mingpeng Zhang, Qiang Yang, Huashui Ai, Lusheng Huang:
Revisiting the Evolutionary History of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree. 1040-1052 - Min Li, Baosheng Wu, Peng Zhang, Ye Li, Wenjie Xu, Kun Wang, Qiang Qiu, Jun Zhang, Jie Li, Chi Zhang, Jiangtao Fan, Chenguang Feng, Zuozhi Chen:
Genomes of Two Flying Squid Species Provide Novel Insights into Adaptations of Cephalopods to Pelagic Life. 1053-1065 - Yuli Li, Yaran Liu, Hongwei Yu, Fuyun Liu, Wentao Han, Qifan Zeng, Yuehuan Zhang, Lingling Zhang, Jingjie Hu, Zhenmin Bao, Shi Wang:
Adaptive Bird-like Genome Miniaturization During the Evolution of Scallop Swimming Lifestyle. 1066-1077 - Yang Zhang, Fan Mao, Shu Xiao, Haiyan Yu, Zhiming Xiang, Fei Xu, Jun Li, Lili Wang, Yuanyan Xiong, Mengqiu Chen, Yongbo Bao, Yuewen Deng, Quan Huo, Lvping Zhang, Wenguang Liu, Xuming Li, Haitao Ma, Yuehuan Zhang, Xiyu Mu, Min Liu, Hongkun Zheng, Nai-Kei Wong, Ziniu Yu:
Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-right Shell Asymmetry in Bivalves. 1078-1091 - Qian Zhao, Longqing Shi, Weiyi He, Jinyu Li, Shijun You, Shuai Chen, Jing Lin, Yibin Wang, Liwen Zhang, Guang Yang, Liette Vasseur, Minsheng You:
Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution. 1092-1105 - Yinqing Yang, Kang Zhang, Ya Xiao, Lingkui Zhang, Yile Huang, Xing Li, Shumin Chen, Yansong Peng, Shuhua Yang, Yongbo Liu, Feng Cheng:
Genome Assembly and Population Resequencing Reveal the Geographical Divergence of Shanmei (Rubus corchorifolius). 1106-1118 - Zhongqiang Xia, Xuelei Dai, Wei Fan, Changying Liu, Meirong Zhang, Peipei Bian, Yuping Zhou, Liang Li, Baozhong Zhu, Shuman Liu, Zhengang Li, Xiling Wang, Maode Yu, Zhonghuai Xiang, Yu Jiang, Aichun Zhao:
Chromosome-level Genomes Reveal the Genetic Basis of Descending Dysploidy and Sex Determination in Morus Plants. 1119-1137 - Duo Chen, Xue Yuan, Xuehai Zheng, Jingping Fang, Gang Lin, Rongmao Li, Jiannan Chen, Wenjin He, Zhen Huang, Wenfang Fan, Limin Liang, Chentao Lin, Jinmao Zhu, Youqiang Chen, Ting Xue:
Multi-omics Analyses Provide Insight into the Biosynthesis Pathways of Fucoxanthin in Isochrysis galbana. 1138-1153 - Cuidan Li, Xiaoyuan Jiang, Tingting Yang, Yingjiao Ju, Zhe Yin, Liya Yue, Guannan Ma, Xuebing Wang, Ying Jing, Xinhua Luo, Shuangshuang Li, Xue Yang, Fei Chen, Dongsheng Zhou:
Genomic Epidemiology of Carbapenemase-producing Klebsiella pneumoniae in China. 1154-1167 - Yingbo Shen, Rong Zhang, Dongyan Shao, Lu Yang, Jiayue Lu, Congcong Liu, Xueyang Wang, Junyao Jiang, Boxuan Wang, Congming Wu, Julian Parkhill, Yang Wang, Timothy R. Walsh, George F. Gao, Zhangqi Shen:
Genomic Shift in Population Dynamics of mcr-1-positive Escherichia coli in Human Carriage. 1168-1179 - Khaista Rahman, Muhammad Jamal, Xi Chen, Wei Zhou, Bin Yang, Yanyan Zou, Weize Xu, Yingying Lei, Chengchao Wu, Xiaojian Cao, Rohit Tyagi, Muhammad Ahsan Naeem, Da Lin, Zeshan Habib, Nan Peng, Zhen-Hua Feng, Gang Cao:
Reprogramming Mycobacterium tuberculosis CRISPR System for Gene Editing and Genome-wide RNA Interference Screening. 1180-1196
- Wan-Ping Lee, Qihui Zhu, Xiaofei Yang, Silvia Liu, Eliza Cerveira, Mallory Ryan, Adam Mil-Homens, Lauren Bellfy, Kai Ye, Charles Lee, Chengsheng Zhang:
JAX-CNV: A Whole-genome Sequencing-based Algorithm for Copy Number Detection at Clinical Grade Level. 1197-1206
- Mei-Jing Dong, Hao Luo, Feng Gao:
Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins. 1207-1213
- Yali Hou, Shilei Zhao, Qi Liu, Xiaolong Zhang, Tong Sha, Yankai Su, Wenming Zhao, Yiming Bao, Yongbiao Xue, Hua Chen:
Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes. 1214-1223 - Yuan Gao, Jinning Zhang, Zhenyu Liu, Shuyue Qi, Xinmeng Guo, Hui Wang, Yanfei Cheng, Shuang Tian, Minyue Ma, Hongmei Peng, Lu Wen, Fuchou Tang, Yuanqing Yao:
Single-cell Sequencing Reveals Clearance of Blastula Chromosomal Mosaicism in In Vitro Fertilization Babies. 1224-1231
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