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1. Characterization of a Salmonella enterica serovar Typhimurium lineage with rough colony morphology and multidrug resistance

Author

Xiang, Ying, Zhu, Kunpeng, Min, Kaiyuan, Zhang, Yaowen, Liu, Jiangfeng, Liu, Kangkang, Han, Yiran, Li, Xinge, Du, Xinying, Wang, Xin, Huang, Ying, Li, Xinping, Peng, Yuqian, Yang, Chaojie, Liu, Hongbo, Liu, HONGBO, Li, Xiaoying, Wang, Hui, Wang, Chao, Wang, Qi, Jia, Huiqun, Yang, Mingjuan, Wang, Ligui, Wu, Yarong, Cui, Yujun, Chen, Fei, Yang, Haiyan, Baker, Stephen, Xu, Xuebin, Yang, Juntao, Song, Hongbin, and Qiu, Shaofu

Published
2024
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3. Genome-wide association studies and fine-mapping identify genomic loci for n-3 and n-6 polyunsaturated fatty acids in Hispanic American and African American cohorts

Author

Yang, Chaojie, Veenstra, Jenna, Bartz, Traci M., Pahl, Matthew C., Hallmark, Brian, Chen, Yii-Der Ida, Westra, Jason, Steffen, Lyn M., Brown, Christopher D., Siscovick, David, Tsai, Michael Y., Wood, Alexis C., Rich, Stephen S., Smith, Caren E., O’Connor, Timothy D., Mozaffarian, Dariush, Grant, Struan F. A., Chilton, Floyd H., Tintle, Nathan L., Lemaitre, Rozenn N., and Manichaikul, Ani

Published
2023
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5. Lymphocyte activation gene-3-associated protein networks are associated with HDL-cholesterol and mortality in the Trans-omics for Precision Medicine program

Author

Manichaikul, Ani, Lin, Honghuang, Kang, Chansuk, Yang, Chaojie, Rich, Stephen S, Taylor, Kent D, Guo, Xiuqing, Rotter, Jerome I, Craig Johnson, W, Cornell, Elaine, Tracy, Russell P, Peter Durda, J, Liu, Yongmei, Vasan, Ramachandran S, Adrienne Cupples, L, Gerszten, Robert E, Clish, Clary B, Jain, Deepti, Conomos, Matthew P, Blackwell, Thomas, Papanicolaou, George J, and Rodriguez, Annabelle

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Heart Disease, Biotechnology, Human Genome, Heart Disease - Coronary Heart Disease, Clinical Research, Cardiovascular, Atherosclerosis, Aging, 2.1 Biological and endogenous factors, Aetiology, Good Health and Well Being, Cholesterol, HDL, Chromatin, Humans, Lymphocyte Activation, Membrane Proteins, Precision Medicine, Biological sciences, Biomedical and clinical sciences
Abstract

Deficiency of the immune checkpoint lymphocyte activation gene-3 (LAG3) protein is significantly associated with both elevated HDL-cholesterol (HDL-C) and myocardial infarction risk. We determined the association of genetic variants within ±500 kb of LAG3 with plasma LAG3 and defined LAG3-associated plasma proteins with HDL-C and clinical outcomes. Whole genome sequencing and plasma proteomics were obtained from the Multi-Ethnic Study of Atherosclerosis (MESA) and the Framingham Heart Study (FHS) cohorts as part of the Trans-Omics for Precision Medicine program. In situ Hi-C chromatin capture was performed in EBV-transformed cell lines isolated from four MESA participants. Genetic association analyses were performed in MESA using multivariate regression models, with validation in FHS. A LAG3-associated protein network was tested for association with HDL-C, coronary heart disease, and all-cause mortality. We identify an association between the LAG3 rs3782735 variant and plasma LAG3 protein. Proteomics analysis reveals 183 proteins significantly associated with LAG3 with four proteins associated with HDL-C. Four proteins discovered for association with all-cause mortality in FHS shows nominal associations in MESA. Chromatin capture analysis reveals significant cis interactions between LAG3 and C1S, LRIG3, TNFRSF1A, and trans interactions between LAG3 and B2M. A LAG3-associated protein network has significant associations with HDL-C and mortality.

Published
2022

7. Whole genome sequence analysis of pulmonary function and COPD in 19,996 multi-ethnic participants.

Author

Zhao, Xutong, Qiao, Dandi, Yang, Chaojie, Kasela, Silva, Kim, Wonji, Ma, Yanlin, Shrine, Nick, Batini, Chiara, Sofer, Tamar, Taliun, Sarah A Gagliano, Sakornsakolpat, Phuwanat, Balte, Pallavi P, Prokopenko, Dmitry, Yu, Bing, Lange, Leslie A, Dupuis, Josée, Cade, Brian E, Lee, Jiwon, Gharib, Sina A, Daya, Michelle, Laurie, Cecelia A, Ruczinski, Ingo, Cupples, L Adrienne, Loehr, Laura R, Bartz, Traci M, Morrison, Alanna C, Psaty, Bruce M, Vasan, Ramachandran S, Wilson, James G, Taylor, Kent D, Durda, Peter, Johnson, W Craig, Cornell, Elaine, Guo, Xiuqing, Liu, Yongmei, Tracy, Russell P, Ardlie, Kristin G, Aguet, François, VanDenBerg, David J, Papanicolaou, George J, Rotter, Jerome I, Barnes, Kathleen C, Jain, Deepti, Nickerson, Deborah A, Muzny, Donna M, Metcalf, Ginger A, Doddapaneni, Harshavardhan, Dugan-Perez, Shannon, Gupta, Namrata, Gabriel, Stacey, Rich, Stephen S, O'Connor, George T, Redline, Susan, Reed, Robert M, Laurie, Cathy C, Daviglus, Martha L, Preudhomme, Liana K, Burkart, Kristin M, Kaplan, Robert C, Wain, Louise V, Tobin, Martin D, London, Stephanie J, Lappalainen, Tuuli, Oelsner, Elizabeth C, Abecasis, Goncalo R, Silverman, Edwin K, Barr, R Graham, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lung Working Group, Cho, Michael H, and Manichaikul, Ani

Subjects
NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lung Working Group, Lung, Humans, Pulmonary Disease, Chronic Obstructive, Genetic Predisposition to Disease, Intracellular Signaling Peptides and Proteins, Calcium-Binding Proteins, Small Ubiquitin-Related Modifier Proteins, Follow-Up Studies, Feasibility Studies, Polymorphism, Single Nucleotide, Adult, Aged, Aged, 80 and over, Middle Aged, African Americans, Female, Male, Protein Inhibitors of Activated STAT, Respiratory Physiological Phenomena, Genome-Wide Association Study, Genetic Loci, Alpha-Ketoglutarate-Dependent Dioxygenase FTO, Whole Genome Sequencing, and over, Polymorphism, Single Nucleotide, Pulmonary Disease, Chronic Obstructive
Abstract

Chronic obstructive pulmonary disease (COPD), diagnosed by reduced lung function, is a leading cause of morbidity and mortality. We performed whole genome sequence (WGS) analysis of lung function and COPD in a multi-ethnic sample of 11,497 participants from population- and family-based studies, and 8499 individuals from COPD-enriched studies in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program. We identify at genome-wide significance 10 known GWAS loci and 22 distinct, previously unreported loci, including two common variant signals from stratified analysis of African Americans. Four novel common variants within the regions of PIAS1, RGN (two variants) and FTO show evidence of replication in the UK Biobank (European ancestry n ~ 320,000), while colocalization analyses leveraging multi-omic data from GTEx and TOPMed identify potential molecular mechanisms underlying four of the 22 novel loci. Our study demonstrates the value of performing WGS analyses and multi-omic follow-up in cohorts of diverse ancestry.

Published
2020

8. Stroke genetics informs drug discovery and risk prediction across ancestries

Author

Mishra, Aniket, Malik, Rainer, Hachiya, Tsuyoshi, Jürgenson, Tuuli, Namba, Shinichi, Posner, Daniel C., Kamanu, Frederick K., Koido, Masaru, Le Grand, Quentin, Shi, Mingyang, He, Yunye, Georgakis, Marios K., Caro, Ilana, Krebs, Kristi, Liaw, Yi-Ching, Vaura, Felix C., Lin, Kuang, Winsvold, Bendik Slagsvold, Srinivasasainagendra, Vinodh, Parodi, Livia, Bae, Hee-Joon, Chauhan, Ganesh, Chong, Michael R., Tomppo, Liisa, Akinyemi, Rufus, Roshchupkin, Gennady V., Habib, Naomi, Jee, Yon Ho, Thomassen, Jesper Qvist, Abedi, Vida, Cárcel-Márquez, Jara, Nygaard, Marianne, Leonard, Hampton L., Yang, Chaojie, Yonova-Doing, Ekaterina, Knol, Maria J., Lewis, Adam J., Judy, Renae L., Ago, Tetsuro, Amouyel, Philippe, Armstrong, Nicole D., Bakker, Mark K., Bartz, Traci M., Bennett, David A., Bis, Joshua C., Bordes, Constance, Børte, Sigrid, Cain, Anael, Ridker, Paul M., Cho, Kelly, Chen, Zhengming, Cruchaga, Carlos, Cole, John W., de Jager, Phil L., de Cid, Rafael, Endres, Matthias, Ferreira, Leslie E., Geerlings, Mirjam I., Gasca, Natalie C., Gudnason, Vilmundur, Hata, Jun, He, Jing, Heath, Alicia K., Ho, Yuk-Lam, Havulinna, Aki S., Hopewell, Jemma C., Hyacinth, Hyacinth I., Inouye, Michael, Jacob, Mina A., Jeon, Christina E., Jern, Christina, Kamouchi, Masahiro, Keene, Keith L., Kitazono, Takanari, Kittner, Steven J., Konuma, Takahiro, Kumar, Amit, Lacaze, Paul, Launer, Lenore J., Lee, Keon-Joo, Lepik, Kaido, Li, Jiang, Li, Liming, Manichaikul, Ani, Markus, Hugh S., Marston, Nicholas A., Meitinger, Thomas, Mitchell, Braxton D., Montellano, Felipe A., Morisaki, Takayuki, Mosley, Thomas H., Nalls, Mike A., Nordestgaard, Børge G., O’Donnell, Martin J., Okada, Yukinori, Onland-Moret, N. Charlotte, Ovbiagele, Bruce, Peters, Annette, Psaty, Bruce M., Rich, Stephen S., Rosand, Jonathan, Sabatine, Marc S., Sacco, Ralph L., Saleheen, Danish, Sandset, Else Charlotte, Salomaa, Veikko, Sargurupremraj, Muralidharan, Sasaki, Makoto, Satizabal, Claudia L., Schmidt, Carsten O., Shimizu, Atsushi, Smith, Nicholas L., Sloane, Kelly L., Sutoh, Yoichi, Sun, Yan V., Tanno, Kozo, Tiedt, Steffen, Tatlisumak, Turgut, Torres-Aguila, Nuria P., Tiwari, Hemant K., Trégouët, David-Alexandre, Trompet, Stella, Tuladhar, Anil Man, Tybjærg-Hansen, Anne, van Vugt, Marion, Vibo, Riina, Verma, Shefali S., Wiggins, Kerri L., Wennberg, Patrik, Woo, Daniel, Wilson, Peter W. F., Xu, Huichun, Yang, Qiong, Yoon, Kyungheon, Millwood, Iona Y., Gieger, Christian, Ninomiya, Toshiharu, Grabe, Hans J., Jukema, J. Wouter, Rissanen, Ina L., Strbian, Daniel, Kim, Young Jin, Chen, Pei-Hsin, Mayerhofer, Ernst, Howson, Joanna M. M., Irvin, Marguerite R., Adams, Hieab, Wassertheil-Smoller, Sylvia, Christensen, Kaare, Ikram, Mohammad A., Rundek, Tatjana, Worrall, Bradford B., Lathrop, G. Mark, Riaz, Moeen, Simonsick, Eleanor M., Kõrv, Janika, França, Paulo H. C., Zand, Ramin, Prasad, Kameshwar, Frikke-Schmidt, Ruth, de Leeuw, Frank-Erik, Liman, Thomas, Haeusler, Karl Georg, Ruigrok, Ynte M., Heuschmann, Peter Ulrich, Longstreth, W. T., Jung, Keum Ji, Bastarache, Lisa, Paré, Guillaume, Damrauer, Scott M., Chasman, Daniel I., Rotter, Jerome I., Anderson, Christopher D., Zwart, John-Anker, Niiranen, Teemu J., Fornage, Myriam, Liaw, Yung-Po, Seshadri, Sudha, Fernández-Cadenas, Israel, Walters, Robin G., Ruff, Christian T., Owolabi, Mayowa O., Huffman, Jennifer E., Milani, Lili, Kamatani, Yoichiro, Dichgans, Martin, and Debette, Stephanie

Published
2022
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9. Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries.

Author

Zekavat, Seyedeh M, Ruotsalainen, Sanni, Handsaker, Robert E, Alver, Maris, Bloom, Jonathan, Poterba, Timothy, Seed, Cotton, Ernst, Jason, Chaffin, Mark, Engreitz, Jesse, Peloso, Gina M, Manichaikul, Ani, Yang, Chaojie, Ryan, Kathleen A, Fu, Mao, Johnson, W Craig, Tsai, Michael, Budoff, Matthew, Vasan, Ramachandran S, Cupples, L Adrienne, Rotter, Jerome I, Rich, Stephen S, Post, Wendy, Mitchell, Braxton D, Correa, Adolfo, Metspalu, Andres, Wilson, James G, Salomaa, Veikko, Kellis, Manolis, Daly, Mark J, Neale, Benjamin M, McCarroll, Steven, Surakka, Ida, Esko, Tonu, Ganna, Andrea, Ripatti, Samuli, Kathiresan, Sekar, Natarajan, Pradeep, and NHLBI TOPMed Lipids Working Group

Subjects
NHLBI TOPMed Lipids Working Group
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

15. The Complex FtBBX22 and FtHY5 Positively Regulates Light-Induced Anthocyanin Accumulation by Activating FtMYB42 in Tartary Buckwheat Sprouts.

Author

Deng, Jiao, Zhang, Lan, Wang, Lijuan, Zhao, Jiali, Yang, Chaojie, Li, Hongyou, Huang, Juan, Shi, Taoxiong, Zhu, Liwei, Damaris, Rebecca Njeri, and Chen, Qingfu

Subjects
TRANSCRIPTION factors, GERMPLASM, ANTHOCYANINS, GENETIC transcription, BIOSYNTHESIS, BUCKWHEAT
Abstract

Anthocyanin is one important nutrition composition in Tartary buckwheat (Fagopyrum tataricum) sprouts, a component missing in its seeds. Although anthocyanin biosynthesis requires light, the mechanism of light-induced anthocyanin accumulation in Tartary buckwheat is unclear. Here, comparative transcriptome analysis of Tartary buckwheat sprouts under light and dark treatments and biochemical approaches were performed to identify the roles of one B-box protein BBX22 and ELONGATED HYPOCOTYL 5 (HY5). The overexpression assay showed that FtHY5 and FtBBX22 could both promote anthocyanin synthesis in red-flower tobacco. Additionally, FtBBX22 associated with FtHY5 to form a complex that activates the transcription of MYB transcription factor genes FtMYB42 and FtDFR, leading to anthocyanin accumulation. These findings revealed the regulation mechanism of light-induced anthocyanin synthesis and provide excellent gene resources for breeding high-quality Tartary buckwheat. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Genomic and Phenotypic Analysis of blaKPC-2 Associated Carbapenem Resistance in Klebsiella aerogenes: Insights into Clonal Spread and Resistance Mechanisms Across Hospital Departments in Beijing.

Author

Jin, Hang, Yan, Zhongqiang, Ge, Xin, Wang, Qi, Wang, Hui, Du, Xinying, Liu, Hongbo, Yang, Chaojie, Xiang, Ying, Tian, Sai, Qiu, Shaofu, and Zhou, Yu

Subjects
WHOLE genome sequencing, GENOMICS, SINGLE nucleotide polymorphisms, MICROBIAL sensitivity tests, DRUG resistance in microorganisms
Abstract

Purpose: This study conducted an phenotypic and whole-genome sequencing analysis with Klebsiella aerogenes to elucidate its clinical epidemiological characteristics, antimicrobial resistance (AMR) phenotype, biofilm formation ability and hemolytic activity testing, AMR genes and phylogenetic relationships, so as to provide a further understanding of the intra-hospital strain transmission. Methods: Samples were collected from a hospital in Beijing between 2020 and 2022. All strains underwent bacterial identification, antimicrobial susceptibility testing (AST) using the VITEK-2 compact system. Biofilm formation ability and hemolytic activity were tested. Second-generation sequencing was applied to all strains, with those carrying the blaKPC gene were selected for third-generation sequencing. Whole-genome analysis identified resistance genes, plasmid types, MLST typing, and phylogenetic relationships. Plasmids were assembled to detect plasmid structures and AMR gene location. Results: Among the 42 K. aerogenes isolates, 21 were carbapenem-resistant K. aerogenes (CRKA). All strains exhibited strong biofilm formation and no hemolytic activity. Most were sourced from sputum (83.3%). CRKA demonstrated extensive resistance to antibiotics, particularly β-lactamase inhibitors and Cefotetan. This resistance pattern was closely associated with the presence of an IncFII(pHN7A8) plasmid, which carried multiple resistance genes, including blaKPC-2, blaCTX-M-65, blaTEM-1, rmtB and a large number of mobile elements. The majority of CRKA strains clustered within the same branch of the phylogenetic tree, exhibiting minimal single nucleotide polymorphism (0– 13 SNPs) differences, and they shared the same sequence type (ST292), resistance genes, and plasmids, originating from different departments, suggesting clonal transmission among the hospital. Conclusion: Our research reveals that the clonal transmission of CRKA occurs across various departments within the hospital. The widespread resistance observed in CRKA, attributed to the presence of blaKPC and ESBLs genes, underscores the need for heightened vigilance to prevent the further dissemination of CRKA within the hospital and, potentially, throughout the wider community. [ABSTRACT FROM AUTHOR]

Published
2024
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17. Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries.

Author

Zekavat, Seyedeh M, Ruotsalainen, Sanni, Handsaker, Robert E, Alver, Maris, Bloom, Jonathan, Poterba, Timothy, Seed, Cotton, Ernst, Jason, Chaffin, Mark, Engreitz, Jesse, Peloso, Gina M, Manichaikul, Ani, Yang, Chaojie, Ryan, Kathleen A, Fu, Mao, Johnson, W Craig, Tsai, Michael, Budoff, Matthew, Vasan, Ramachandran S, Cupples, L Adrienne, Rotter, Jerome I, Rich, Stephen S, Post, Wendy, Mitchell, Braxton D, Correa, Adolfo, Metspalu, Andres, Wilson, James G, Salomaa, Veikko, Kellis, Manolis, Daly, Mark J, Neale, Benjamin M, McCarroll, Steven, Surakka, Ida, Esko, Tonu, Ganna, Andrea, Ripatti, Samuli, Kathiresan, Sekar, Natarajan, Pradeep, and NHLBI TOPMed Lipids Working Group

Subjects
NHLBI TOPMed Lipids Working Group
Abstract

The original version of this article contained an error in the name of the author Ramachandran S. Vasan, which was incorrectly given as Vasan S. Ramachandran. This has now been corrected in both the PDF and HTML versions of the article.

Published
2018

18. Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries.

Author

Zekavat, Seyedeh M, Ruotsalainen, Sanni, Handsaker, Robert E, Alver, Maris, Bloom, Jonathan, Poterba, Timothy, Seed, Cotton, Ernst, Jason, Chaffin, Mark, Engreitz, Jesse, Peloso, Gina M, Manichaikul, Ani, Yang, Chaojie, Ryan, Kathleen A, Fu, Mao, Johnson, W Craig, Tsai, Michael, Budoff, Matthew, Vasan, Ramachandran S, Cupples, L Adrienne, Rotter, Jerome I, Rich, Stephen S, Post, Wendy, Mitchell, Braxton D, Correa, Adolfo, Metspalu, Andres, Wilson, James G, Salomaa, Veikko, Kellis, Manolis, Daly, Mark J, Neale, Benjamin M, McCarroll, Steven, Surakka, Ida, Esko, Tonu, Ganna, Andrea, Ripatti, Samuli, Kathiresan, Sekar, Natarajan, Pradeep, and NHLBI TOPMed Lipids Working Group

Subjects
NHLBI TOPMed Lipids Working Group, Humans, Cardiovascular Diseases, Lipoprotein(a), Adaptor Proteins, Vesicular Transport, Risk Factors, Gene Expression, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Genome, Human, African Continental Ancestry Group, European Continental Ancestry Group, Cholesterol, LDL, Genome-Wide Association Study, DNA Copy Number Variations, Whole Genome Sequencing, Atherosclerosis, Genetics, Cardiovascular, Prevention, Human Genome, Heart Disease, 2.1 Biological and endogenous factors
Abstract

Lipoprotein(a), Lp(a), is a modified low-density lipoprotein particle that contains apolipoprotein(a), encoded by LPA, and is a highly heritable, causal risk factor for cardiovascular diseases that varies in concentrations across ancestries. Here, we use deep-coverage whole genome sequencing in 8392 individuals of European and African ancestry to discover and interpret both single-nucleotide variants and copy number (CN) variation associated with Lp(a). We observe that genetic determinants between Europeans and Africans have several unique determinants. The common variant rs12740374 associated with Lp(a) cholesterol is an eQTL for SORT1 and independent of LDL cholesterol. Observed associations of aggregates of rare non-coding variants are largely explained by LPA structural variation, namely the LPA kringle IV 2 (KIV2)-CN. Finally, we find that LPA risk genotypes confer greater relative risk for incident atherosclerotic cardiovascular diseases compared to directly measured Lp(a), and are significantly associated with measures of subclinical atherosclerosis in African Americans.

Published
2018

21. Comparative de novo transcriptomics reveal the effect of lead on Leech in aquaculture environment

Author

Wang Kun, Meng Jieqin, Cheng Liangke, Shi Fujuan, Yang Chaojie, Maiheliya Mijiti, and Yang Yaojun

Subjects
Whitmania pigra, Culturing environment, Lead contamination, Comparative transcriptomics，differentially expressed genes, Aquaculture. Fisheries. Angling, SH1-691
Abstract

Whitmania pigra Whitman is a non-bloodsucking leech, which is included in the Pharmacopoeia of the People's Republic of China. As a traditional Chinese medicine, its main function is to remove the blood stasis. In the process of breeding, Whitmania pigra Whitman is easily affected by the pollution of the heavy metal lead. This study simulated the pond culture environment in the aquarium with the soil in the bottom. The soil lead contamination was caused by adding lead nitrate to the soil. The blank leech group and lead contaminated leech group were obtained after 50 days of culturing in the aquariums. Denovo assembly and analysis were performed to reveal the changes of gene expression in Whitmania pigra Whitman after lead contamination. The sequencing results showed that each sample had more than 45 million Raw Reads and the percentage of Clean reads was more than 96%. There were altogether 120,684 transcripts which average length is 1590.42 bp. 34,612 unigenes were annotated based on the sequence homology. In result, a total of 1110 differentially expressed genes were obtained, including 694 up-regulated genes and 416 down-regulated genes. The GO enrichment analysis of differentially expressed genes was significantly enriched to 85 GO entries. In the other hand, the KEGG enrichment analysis of differentially expressed genes was significantly enriched to 5 pathways, among which arachidonic acid metabolism and lysosomes were important pathways. In conclusion, the results of this study can provide data support for future studies on the quality of leech and provide a reference for the effects of heavy metal lead accumulation in the culture environment on aquatic organisms.

Published
2022
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22. Publisher Correction: Stroke genetics informs drug discovery and risk prediction across ancestries

Author

Mishra, Aniket, Malik, Rainer, Hachiya, Tsuyoshi, Jürgenson, Tuuli, Namba, Shinichi, Posner, Daniel C., Kamanu, Frederick K., Koido, Masaru, Le Grand, Quentin, Shi, Mingyang, He, Yunye, Georgakis, Marios K., Caro, Ilana, Krebs, Kristi, Liaw, Yi-Ching, Vaura, Felix C., Lin, Kuang, Winsvold, Bendik Slagsvold, Srinivasasainagendra, Vinodh, Parodi, Livia, Bae, Hee-Joon, Chauhan, Ganesh, Chong, Michael R., Tomppo, Liisa, Akinyemi, Rufus, Roshchupkin, Gennady V., Habib, Naomi, Jee, Yon Ho, Thomassen, Jesper Qvist, Abedi, Vida, Cárcel-Márquez, Jara, Nygaard, Marianne, Leonard, Hampton L., Yang, Chaojie, Yonova-Doing, Ekaterina, Knol, Maria J., Lewis, Adam J., Judy, Renae L., Ago, Tetsuro, Amouyel, Philippe, Armstrong, Nicole D., Bakker, Mark K., Bartz, Traci M., Bennett, David A., Bis, Joshua C., Bordes, Constance, Børte, Sigrid, Cain, Anael, Ridker, Paul M., Cho, Kelly, Chen, Zhengming, Cruchaga, Carlos, Cole, John W., de Jager, Phil L., de Cid, Rafael, Endres, Matthias, Ferreira, Leslie E., Geerlings, Mirjam I., Gasca, Natalie C., Gudnason, Vilmundur, Hata, Jun, He, Jing, Heath, Alicia K., Ho, Yuk-Lam, Havulinna, Aki S., Hopewell, Jemma C., Hyacinth, Hyacinth I., Inouye, Michael, Jacob, Mina A., Jeon, Christina E., Jern, Christina, Kamouchi, Masahiro, Keene, Keith L., Kitazono, Takanari, Kittner, Steven J., Konuma, Takahiro, Kumar, Amit, Lacaze, Paul, Launer, Lenore J., Lee, Keon-Joo, Lepik, Kaido, Li, Jiang, Li, Liming, Manichaikul, Ani, Markus, Hugh S., Marston, Nicholas A., Meitinger, Thomas, Mitchell, Braxton D., Montellano, Felipe A., Morisaki, Takayuki, Mosley, Thomas H., Nalls, Mike A., Nordestgaard, Børge G., O’Donnell, Martin J., Okada, Yukinori, Onland-Moret, N. Charlotte, Ovbiagele, Bruce, Peters, Annette, Psaty, Bruce M., Rich, Stephen S., Rosand, Jonathan, Sabatine, Marc S., Sacco, Ralph L., Saleheen, Danish, Sandset, Else Charlotte, Salomaa, Veikko, Sargurupremraj, Muralidharan, Sasaki, Makoto, Satizabal, Claudia L., Schmidt, Carsten O., Shimizu, Atsushi, Smith, Nicholas L., Sloane, Kelly L., Sutoh, Yoichi, Sun, Yan V., Tanno, Kozo, Tiedt, Steffen, Tatlisumak, Turgut, Torres-Aguila, Nuria P., Tiwari, Hemant K., Trégouët, David-Alexandre, Trompet, Stella, Tuladhar, Anil Man, Tybjærg-Hansen, Anne, van Vugt, Marion, Vibo, Riina, Verma, Shefali S., Wiggins, Kerri L., Wennberg, Patrik, Woo, Daniel, Wilson, Peter W. F., Xu, Huichun, Yang, Qiong, Yoon, Kyungheon, Millwood, Iona Y., Gieger, Christian, Ninomiya, Toshiharu, Grabe, Hans J., Jukema, J. Wouter, Rissanen, Ina L., Strbian, Daniel, Kim, Young Jin, Chen, Pei-Hsin, Mayerhofer, Ernst, Howson, Joanna M. M., Irvin, Marguerite R., Adams, Hieab, Wassertheil-Smoller, Sylvia, Christensen, Kaare, Ikram, Mohammad A., Rundek, Tatjana, Worrall, Bradford B., Lathrop, G. Mark, Riaz, Moeen, Simonsick, Eleanor M., Kõrv, Janika, França, Paulo H. C., Zand, Ramin, Prasad, Kameshwar, Frikke-Schmidt, Ruth, de Leeuw, Frank-Erik, Liman, Thomas, Haeusler, Karl Georg, Ruigrok, Ynte M., Heuschmann, Peter Ulrich, Longstreth, W. T., Jung, Keum Ji, Bastarache, Lisa, Paré, Guillaume, Damrauer, Scott M., Chasman, Daniel I., Rotter, Jerome I., Anderson, Christopher D., Zwart, John-Anker, Niiranen, Teemu J., Fornage, Myriam, Liaw, Yung-Po, Seshadri, Sudha, Fernández-Cadenas, Israel, Walters, Robin G., Ruff, Christian T., Owolabi, Mayowa O., Huffman, Jennifer E., Milani, Lili, Kamatani, Yoichiro, Dichgans, Martin, and Debette, Stephanie

Published
2022
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24. Impact of Amerind ancestry and FADS genetic variation on omega-3 deficiency and cardiometabolic traits in Hispanic populations

Author

Yang, Chaojie, Hallmark, Brian, Chai, Jin Choul, O’Connor, Timothy D., Reynolds, Lindsay M., Wood, Alexis C., Seeds, Michael, Chen, Yii-Der Ida, Steffen, Lyn M., Tsai, Michael Y., Kaplan, Robert C., Daviglus, Martha L., Mandarino, Lawrence J., Fretts, Amanda M., Lemaitre, Rozenn N., Coletta, Dawn K., Blomquist, Sarah A., Johnstone, Laurel M., Tontsch, Chandra, Qi, Qibin, Ruczinski, Ingo, Rich, Stephen S., Mathias, Rasika A., Chilton, Floyd H., and Manichaikul, Ani

Published
2021
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25. Genetic characterization of a Salmonella enterica serovar Typhimurium isolated from an infant with concurrent resistance to ceftriaxone, ciprofloxacin and azithromycin

Author

Liu, Meiling, primary, Zhu, Kunpeng, additional, Li, Xinge, additional, Han, Yiran, additional, Yang, Chaojie, additional, Liu, Hongbo, additional, Du, Xinyin, additional, Xu, Xuebin, additional, Yang, Haiyan, additional, Song, Hongbin, additional, Qiu, Shaofu, additional, and Xiang, Ying, additional

Published
2023
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26. NAD(P)H Activated Fluorescent Probe for Rapid Intraoperative Pathological Diagnosis and Tumor Histological Grading

Author

Yang, Chaojie, primary, Jiang, Chenxia, additional, Yang, Majun, additional, Bai, Qingqing, additional, Zhen, Yaya, additional, Zhang, Yuxue, additional, Yin, Weiyi, additional, Wang, Jian, additional, Zhou, Xiaobo, additional, Li, Guo, additional, Wu, Mingmin, additional, Qin, Yuling, additional, Wang, Qi, additional, Ji, Haiwei, additional, and Wu, Li, additional

Published
2023
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27. Genome-Wide Identification of R2R3-MYB Transcription Factor Family in Tartary Buckwheat (Fagopyrum tataricum) Identifies a Member Involved in Anthocyanin Biosynthesis

Author

Deng, Jiao, primary, Wang, Lijuan, additional, Damaris, Rebecca Njeri, additional, Zhao, Jiali, additional, Zhang, Lan, additional, Wang, Tingting, additional, Yang, Chaojie, additional, Huang, Juan, additional, Shi, Taoxiong, additional, Zhu, Liwei, additional, Meng, Ziye, additional, Cai, Fang, additional, and Chen, Qingfu, additional

Published
2023
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28. The complete mitochondrial genome of Indo-Pacific soft coral Sinularia acuta Manuputty and van Ofwegen, 2007 (Octocorallia: Alcyonacea)

Author

Yang, Chaojie, Shikhsarmast, Farnaz Mahmoudi, Fu, Chunzheng, and Shen, Chun-Yang

Subjects
Genetics, Molecular Biology
Abstract

The complete mitochondrial genome (mitogenome) of the soft coral Sinularia acuta Manuputty and van Ofwegen, 2007 was sequenced and annotated using Illumina next-generation sequencing (NGS). The mitogenome of S. acuta was 18,730 bp in length and consisted of 14 protein-coding genes (PCGs), two ribosomal RNA genes (rRNA), and only one transfer RNA gene (tRNA-Met). The base composition was 30.18% A, 16.46% C, 19.35% G, and 34.00% T, with a total A + T content of 64.19%. The phylogenetic analysis demonstrated a close evolutionary relationship among Sinularia acuta, Sinularia penghuensis, and Sinularia maxima.

Published
2023

29. Dietary Sources of Linoleic Acid (LA) Differ by Race/Ethnicity in Adults Participating in the National Health and Nutrition Examination Survey (NHANES) between 2017–2018

Author

Momin, Shabnam R., primary, Senn, Mackenzie K., additional, Manichaikul, Ani, additional, Yang, Chaojie, additional, Mathias, Rasika, additional, Phan, Mimi, additional, Rich, Stephen S., additional, Sergeant, Susan, additional, Seeds, Michael, additional, Reynolds, Lindsay, additional, Chilton, Floyd H., additional, and Wood, Alexis C., additional

Published
2023
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30. FHL5 Controls Vascular Disease–Associated Gene Programs in Smooth Muscle Cells

Author

Wong, Doris, primary, Auguste, Gaëlle, additional, Lino Cardenas, Christian L., additional, Turner, Adam W., additional, Chen, Yixuan, additional, Song, Yipei, additional, Ma, Lijiang, additional, Perry, R. Noah, additional, Aherrahrou, Redouane, additional, Kuppusamy, Maniselvan, additional, Yang, Chaojie, additional, Mosquera, Jose Verdezoto, additional, Dube, Collin J., additional, Khan, Mohammad Daud, additional, Palmore, Meredith, additional, Kalra, Jaspreet K., additional, Kavousi, Maryam, additional, Peyser, Patricia A., additional, Matic, Ljubica, additional, Hedin, Ulf, additional, Manichaikul, Ani, additional, Sonkusare, Swapnil K., additional, Civelek, Mete, additional, Kovaci, Jason C., additional, Björkegren, Johan L.M., additional, Malhotra, Rajeev, additional, and Miller, Clint L., additional

Published
2023
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33. Genome-Wide Analysis of Left Ventricular Image-Derived Phenotypes Identifies Fourteen Loci Associated With Cardiac Morphogenesis and Heart Failure Development

Author

Aung, Nay, Vargas, Jose D., Yang, Chaojie, Cabrera, Claudia P., Warren, Helen R., Fung, Kenneth, Tzanis, Evan, Barnes, Michael R., Rotter, Jerome I., Taylor, Kent D., Manichaikul, Ani W., Lima, Joao A.C., Bluemke, David A., Piechnik, Stefan K., Neubauer, Stefan, Munroe, Patricia B., and Petersen, Steffen E.

Published
2019
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37. Genetic characterization of a Salmonella entericaserovar Typhimurium isolated from an infant with concurrent resistance to ceftriaxone, ciprofloxacin and azithromycin

Author

Liu, Meiling, Zhu, Kunpeng, Li, Xinge, Han, Yiran, Yang, Chaojie, Liu, Hongbo, Du, Xinyin, Xu, Xuebin, Yang, Haiyan, Song, Hongbin, Qiu, Shaofu, and Xiang, Ying

Abstract

•We describe a strain of S. Typhimurium resistant to 28 antibiotics.•The strain carried 54 AMR genes, and blaOKP-B-10was found in Salmonellafirst.•The strain carried two novel plasmids.•pSH11G993-1 carried 14 AMR genes, including blaCMY-2, mphA, and ermB.•pSH11G993-2 endowed the strain virulence and resistance.

Published
2023
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43. Corrigendum: A Severe Gastroenteritis Outbreak of Salmonella enterica Serovar Enteritidis Linked to Contaminated Egg Fried Rice, China, 2021

Author

Zhang, Yaowen, primary, Liu, Kangkang, additional, Zhang, Zhenbiao, additional, Tian, Sai, additional, Liu, Xiong, additional, Qi, Hongjuan, additional, Dong, Derong, additional, Wang, Yong, additional, Liu, Meiling, additional, Li, Xinge, additional, Han, Yiran, additional, Zhu, Kunpeng, additional, Liu, Hongbo, additional, Yang, Chaojie, additional, Liu, HONGBO, additional, Du, Xinying, additional, Wang, Qi, additional, Wang, Hui, additional, Yang, Mingjuan, additional, Wang, Ligui, additional, Song, Hongbin, additional, Yang, Haiyan, additional, Xiang, Ying, additional, and Qiu, Shaofu, additional

Published
2022
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44. Interpreting Clinical Trials With Omega-3 Supplements in the Context of Ancestry and FADS Genetic Variation

Author

Chilton, Floyd H., primary, Manichaikul, Ani, additional, Yang, Chaojie, additional, O'Connor, Timothy D., additional, Johnstone, Laurel M., additional, Blomquist, Sarah, additional, Schembre, Susan M., additional, Sergeant, Susan, additional, Zec, Manja, additional, Tsai, Michael Y., additional, Rich, Stephen S., additional, Bridgewater, Susan J., additional, Mathias, Rasika A., additional, and Hallmark, Brian, additional

Published
2022
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45. Genetic Characterization of mcr-1-Positive Multidrug-Resistant Salmonella enterica Serotype Typhimurium Isolated From Intestinal Infection in Children and Pork Offal in China

Author

Zhang, Haoran, primary, Xiang, Ying, additional, Huang, Yong, additional, Liang, Beibei, additional, Xu, Xuebin, additional, Xie, Jing, additional, Du, Xinying, additional, Yang, Chaojie, additional, Liu, Hongbo, additional, Wang, Hui, additional, Yang, Mingjuan, additional, Wang, Ligui, additional, Hu, Xiaofeng, additional, Jin, Lianqun, additional, Li, Jinsong, additional, Jiang, Yongqiang, additional, Qiu, Shaofu, additional, and Song, Hongbin, additional

Published
2022
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46. A Severe Gastroenteritis Outbreak of Salmonella enterica Serovar Enteritidis Linked to Contaminated Egg Fried Rice, China, 2021

Author

Zhang, Yaowen, primary, Liu, Kangkang, additional, Zhang, Zhenbiao, additional, Tian, Sai, additional, Liu, Xiong, additional, Qi, Hongjuan, additional, Dong, Derong, additional, Wang, Yong, additional, Liu, Meiling, additional, Li, Xinge, additional, Han, Yiran, additional, Zhu, Kunpeng, additional, Liu, Hongbo, additional, Yang, Chaojie, additional, Liu, HONGBO, additional, Du, Xinying, additional, Wang, Qi, additional, Wang, Hui, additional, Yang, Mingjuan, additional, Wang, Ligui, additional, Song, Hongbin, additional, Yang, Haiyan, additional, Xiang, Ying, additional, and Qiu, Shaofu, additional

Published
2021
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47. Source-tracking of the Chinese Chikungunya viruses suggests that Indian subcontinent and Southeast Asia act as major hubs for the recent global spread of Chikungunya virus

Author

Qiu, Shaofu, primary, Guo, Jinpeng, additional, Li, Peihan, additional, Li, Peng, additional, Du, Xinying, additional, Hao, Rongzhang, additional, Yang, Chaojie, additional, Wang, Qi, additional, Liu, Hongbo, additional, Zhang, Haoran, additional, Tian, Sai, additional, Shi, Hua, additional, Wen, Liang, additional, An, Daizhi, additional, Yang, Xiaocui, additional, An, Xiaoyuan, additional, Wang, Ligui, additional, Wang, Changjun, additional, and Song, Hongbin, additional

Published
2021
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48. Localization and Surface Characterization by Zhurong Mars Rover at Utopia Planitia

Author

Jia Yang, Haibo Gao, Zongquan Deng, Chuankai Liu, Liang Ding, Ziqing Cheng, Zhao Huang, Lutz Richter, Zhen Liu, Niu Fuliang, Jian Li, Li Nan, He Ximing, Yuyan Zhao, Huanan Qi, Dang Zhaolong, Zhengyin Wang, Gang Bao, Wenhao Feng, Wan Wenhui, Zuoyu Zhang, Hui Zhang, Yang Huaiguang, Baichao Chen, Guanyu Wang, Wang Xiaoxue, Ruyi Zhou, Hongjun Xing, Jitao Zhang, Jia Wang, Fan Wu, Guangjun Liu, Tianyi Yu, Lan Huang, Baofeng Yuan, Peng Xu, Xiaofeng Cui, Lichun Li, Zhao Rui, Shu Li, Yuan Ye, Xiyu Wang, Hao Lu, Qian Xu, Mingming Zhang, Yang Chaojie, Niu Lizhou, and Kaichang Di

Subjects
Mars rover, Surface (mathematics), Utopia (typeface), Geology, Characterization (materials science), Astrobiology
Abstract

China’s first Mars rover, Zhurong, has successfully touched down on the southern Utopia Planitia of Mars at 109.925° E, 25.066° N, and since performed cooperative multiscale investigations with the Tianwen-1 orbiter. Here we present primary localization and surface characterization results based on complementary data of the first 60 sols. The Zhurong rover has traversed 450.9 m southwards over a flat surface with mild wheel slippage (less than 0.2 in slip ratio). The encountered crescent-shaped sand dune indicates a NE-SW local wind direction, consistent with larger-range remote-sensing observations. Soil parameter analysis based on terramechanics indicates that the topsoil has high bearing strength and cohesion, and its equivalent stiffness and internal friction angle are ~1390-5872 kPa∙m-n and ~21°-34° respectively. Rocks observed strewn with dense pits, or showing layered and flaky structures, are presumed to be involved in physical weathering like severe wind erosion and potential chemical weathering processes. These preliminary observations suggest great potential of in-situ investigations by the scientific payload suite of the Zhurong rover in obtaining new clues of the region’s aeolian and aqueous history. Cooperative investigations using the related payloads on both the rover and the obiter could peek into the habitability evolution of the northern lowlands on Mars.

Published
2021

49. Pneumonia Patients Caused by Co-infection With SARS-CoV-2 and Human Adenovirus in China

Author

Qiu, Shaofu, primary, Zeng, Ge, additional, Li, Peihan, additional, Li, Xiaohui, additional, Liu, Hongbo, additional, Du, Xinying, additional, Zhang, Heng, additional, Xiang, Xingyu, additional, Wang, Hui, additional, Chen, Xiangbing, additional, Yang, Guangyao, additional, Tian, Sai, additional, Wang, Ligui, additional, Yang, Mingjuan, additional, Yang, Chaojie, additional, Gao, Lidong, additional, Hu, Shixiong, additional, Song, Hongbin, additional, and Zhan, Zhifei, additional

Published
2021
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50. Feasibility of Wrist-Worn, Cancelable, Real-Time Biometric Authentication via HD-sEMG and Dynamic Gestures

Author

Qiu, Haomeng, Chen, Yan, Chen, Zhitao, Yang, Chaojie, Wu, Sihan, Li, Fanglin, and Xie, Longhan

Abstract

In recent years, high-density surface electromyography (HD-sEMG) has been applied for cancelable authentication of wearable devices used in healthcare applications. However, previous studies focused on the forearm or hand, whereas the wrist is more comfortable for practical use. Covering a larger area with fewer electrodes (16 channels on the wrist versus 256 channels on the forearm) also reduces the chance of electrode corruption and improves the stability of the authentication system. In addition, fast dynamic gestures are more desirable than static gestures for real-time authentication. Shorter gesture execution time also makes dynamic gesture codes harder to record by imposters. We propose a cancelable real-time biometric system via wrist-worn HD-sEMG and dynamic gestures. A wearable wristband was designed to collect HD-sEMG signals. Based on a dataset with 12 dynamic gestures, we realized a fast real-time authentication. It achieved an equal error rate (EER) of 0.0039 even when imposters entered a correct gesture code. The cancelability was confirmed with an EER of 0.0018. The real-time authentication with an authentication accuracy of 96.7% and a low latency of 64 ms makes it practical in healthcare applications. These results demonstrate the feasibility of wrist-worn biometrics, which allows secure healthcare applications without compromising the user experience.

Published
2023
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