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  1. When polygenic risk score (PRS) is derived from summary statistics, independence between discovery and test sets cannot be monitored. We compared two types of PRS studies derived from raw genetic data (denoted...

    Authors: David Keetae Park, Mingshen Chen, Seungsoo Kim, Yoonjung Yoonie Joo, Rebekah K. Loving, Hyoung Seop Kim, Jiook Cha, Shinjae Yoo and Jong Hun Kim
    Citation: BMC Genomic Data 2023 24:52
  2. Panax ginseng cultivated under the forest is popular because its shape and effective ingredients are similar to wild ginseng. The growth of P. ginseng in the larch forest is generally better than in the broad-...

    Authors: Tong Aizi, Liu Lijuan, Liu Lihua, Liu Wei and Qin Jiamei
    Citation: BMC Genomic Data 2023 24:51
  3. A relevant part of the genetic architecture of complex traits is still unknown; despite the discovery of many disease-associated common variants. Polygenic risk score (PRS) models are based on the evaluation o...

    Authors: Rana Aldisi, Emadeldin Hassanin, Sugirthan Sivalingam, Andreas Buness, Hannah Klinkhammer, Andreas Mayr, Holger Fröhlich, Peter Krawitz and Carlo Maj
    Citation: BMC Genomic Data 2023 24:50
  4. Providencia is a genus of gram-negative bacteria within the order Enterobacterales, closely related to Proteus and Morganella. While ubiquitous in the environment, some species of Providencia, such as P. rettgeri...

    Authors: Steven Batinovic, Hiu Tat Chan, Jason Stiles and Steve Petrovski
    Citation: BMC Genomic Data 2023 24:49
  5. Sarcopenia is a disease diagnosed in the elderly. In patients with sarcopenia, the muscle mass decreases every year. The occurrence of sarcopenia is greatly affected by extrinsic factors such as eating habits,...

    Authors: Jeong-An Gim, Sang-Yeob Lee, Seung Chan Kim, Kyung-Wan Baek, Sung Hyo Seo and Jun-Il Yoo
    Citation: BMC Genomic Data 2023 24:48
  6. Inherited genetic defects in immune system-related genes can result in Inborn Errors of Immunity (IEI), also known as Primary Immunodeficiencies (PID). Diagnosis of IEI disorders is challenging due to overlapp...

    Authors: Cristina Santos Ferreira, Ronaldo da Silva Francisco Junior, Alexandra Lehmkuhl Gerber, Ana Paula de Campos Guimarães, Flavia Amendola Anisio de Carvalho, Bárbara Carvalho Santos dos Reis, Fernanda Pinto-Mariz, Monica Soares de Souza, Zilton Farias Meira de Vasconcelos, Ekaterini Simões Goudouris and Ana Tereza Ribeiro Vasconcelos
    Citation: BMC Genomic Data 2023 24:47
  7. Thysanoptera, commonly known as thrips, are diverse tiny insects whose earliest fossil record dates back to the Triassic period. Since there are few studies on the divergence time of taxa under Thysanoptera, t...

    Authors: Chunying Wu and Hongrui Zhang
    Citation: BMC Genomic Data 2023 24:46
  8. Distant hybridization is an important breeding technique for creating new strains with superior traits by integrating two different genomes. Successful hybridization of Megalobrama amblycephala (Blunt snout bream...

    Authors: Xue Ding, Yifei Zhang, Die Li, Jia Xu, Chang Wu, Xiaojuan Cui and Yuandong Sun
    Citation: BMC Genomic Data 2023 24:45
  9. The N6-methyladenosine (m6A) RNA modification is the most prevalent and abundant type found in eukaryotic cells. It plays a crucial role in the initiation and progression of cancers. In this study, we aimed to...

    Authors: Jian Ji, Shichao Liu, Yongyuan Liang and Guixi Zheng
    Citation: BMC Genomic Data 2023 24:44
  10. The chloroplast genome of plants is known for its small size and low mutation and recombination rates, making it a valuable tool in plant phylogeny, molecular evolution, and population genetics studies. Codon ...

    Authors: Yaqi Li, Xiang Hu, Mingkun Xiao, Jiaxiong Huang, Yuqiang Lou, Faguang Hu, Xingfei Fu, Yanan Li, Hongyan He and Jinhuan Cheng
    Citation: BMC Genomic Data 2023 24:42
  11. At present, donkey meat in the market shows an imbalance between supply and demand, and there is an urgent need to cultivate a meat-type Dezhou donkey breed. On the one hand, it can improve the imbalance in th...

    Authors: Xinrui Wang, Tianqi Wang, Huili Liang, Liyuan Wang, Faheem Akhtar, Xiaoyuan Shi, Wei Ren, Bingjian Huang, Xiyan Kou, Yinghui Chen, Yandong Zhan and Changfa Wang
    Citation: BMC Genomic Data 2023 24:41
  12. Essential thrombocythemia (ET) is one of the most common types of Ph-negative myeloproliferative neoplasms, an infrequent group of blood cancers that arise from a CD34 + hematopoietic stem cell (HSC) in the bone ...

    Authors: Ana Guijarro-Hernández and José Luis Vizmanos
    Citation: BMC Genomic Data 2023 24:40
  13. This study was performed in the frame of a more extensive study dedicated to the integrated analysis of the single-cell transcriptome and chromatin accessibility datasets of peripheral blood mononuclear cells ...

    Authors: Xiao Wang, Yahui Gao, Cong-jun Li, Lingzhao Fang, George E. Liu, Xiuxin Zhao, Yuanpei Zhang, Gaozhan Cai, Guanghui Xue, Yan Liu, Lingling Wang, Fan Zhang, Kun Wang, Miao Zhang, Rongling Li, Yundong Gao…
    Citation: BMC Genomic Data 2023 24:39
  14. The frequency of droughts has dramatically increased over the last 50 years, causing yield declines in cereals, including wheat. Crop varieties with efficient root systems show great potential for plant adapta...

    Authors: Nurealam Siddiqui, Melesech T. Gabi, Mohammad Kamruzzaman, Abebaw M. Ambaw, Tesfaye J. Teferi, Said Dadshani, Jens Léon and Agim Ballvora
    Citation: BMC Genomic Data 2023 24:38
  15. The Golden2-like (GLK) transcription factors are plant-specific transcription factors (TFs) that perform extensive and significant roles in regulating chloroplast development. Here, genome-wide identification, cl...

    Authors: Ruihua Wu, Lin Guo, Yueyang Guo, Lehang Ma, Kehang Xu, Boyu Zhang and Liang Du
    Citation: BMC Genomic Data 2023 24:37
  16. Inborn error of immunity (IEI) comprises a broad group of inherited immunological disorders that usually display an overlap in many clinical manifestations challenging their diagnosis. The identification of di...

    Authors: Cristina Santos Ferreira, Ronaldo da Silva Francisco Junior, Alexandra Lehmkuhl Gerber, Ana Paula de Campos Guimarães, Flávia Anisio Amendola, Fernanda Pinto-Mariz, Monica Soares de Souza, Patrícia Carvalho Batista Miranda, Zilton Farias Meira de Vasconcelos, Ekaterini Simões Goudouris and Ana Tereza Ribeiro Vasconcelos
    Citation: BMC Genomic Data 2023 24:36
  17. A haplotype is a set of DNA variants inherited together from one parent or chromosome. Haplotype information is useful for studying genetic variation and disease association. Haplotype assembly (HA) is a proce...

    Authors: Shuying Sun, Flora Cheng, Daphne Han, Sarah Wei, Alice Zhong, Sherwin Massoudian and Alison B. Johnson
    Citation: BMC Genomic Data 2023 24:35
  18. Evidence shows that genetic factors play important roles in the severity of coronavirus disease 2019 (COVID-19). Sulfatase modifying factor 1 (SUMF1) gene is involved in alveolar damage and systemic inflammatory ...

    Authors: Shaohui Liang, Huixia Gao, Tongxin He, Li Li, Xin Zhang, Lei Zhao, Jie Chen, Yanyan Xie, Jie Bao, Yong Gao, Erhei Dai and Yuling Wang
    Citation: BMC Genomic Data 2023 24:34
  19. Complex physiological adaptations often involve the coordination of molecular responses across multiple tissues. Establishing transcriptomic resources for non-traditional model organisms with phenotypes of int...

    Authors: Blair W. Perry, Michael W. Saxton, Heiko T. Jansen, Corey R. Quackenbush, Brandon D. Evans Hutzenbiler, Charles T. Robbins, Joanna L. Kelley and Omar E. Cornejo
    Citation: BMC Genomic Data 2023 24:33
  20. Considering the co-morbidity of major psychiatric disorders and intelligence with smoking, to increase our understanding of why some people take up smoking or continue to smoke, while others stop smoking witho...

    Authors: Olesya Ajnakina and Andrew Steptoe
    Citation: BMC Genomic Data 2023 24:31
  21. Allele counts of sequence variants obtained by whole genome sequencing (WGS) often play a central role in interpreting the results of genetic and genomic research. However, such variant counts are not readily ...

    Authors: Karina Banasik, Peter L. Møller, Tanya R. Techlo, Peter C. Holm, G. Bragi Walters, Andrés Ingason, Anders Rosengren, Palle D. Rohde, Lisette J. A. Kogelman, David Westergaard, Troels Siggaard, Piotr J. Chmura, Mona A. Chalmer, Ólafur Þ. Magnússon, Guðmundur Á. Þórisson, Hreinn Stefánsson…
    Citation: BMC Genomic Data 2023 24:30
  22. This report provides information about the public release of the 2018–2019 Maize G X E project of the Genomes to Fields (G2F) Initiative datasets. G2F is an umbrella initiative that evaluates maize hybrids and...

    Authors: Dayane Cristina Lima, Alejandro Castro Aviles, Ryan Timothy Alpers, Bridget A. McFarland, Shawn Kaeppler, David Ertl, Maria Cinta Romay, Joseph L. Gage, James Holland, Timothy Beissinger, Martin Bohn, Edward Buckler, Jode Edwards, Sherry Flint-Garcia, Candice N. Hirsch, Elizabeth Hood…
    Citation: BMC Genomic Data 2023 24:29
  23. Polygenic scores (PGSs) combining genetic variants found to be associated with creatinine-based estimated glomerular filtration rate (eGFRcrea) have been applied in various study populations with different age ra...

    Authors: Janina M. Herold, Jana Nano, Mathias Gorski, Thomas W. Winkler, Kira J. Stanzick, Martina E. Zimmermann, Caroline Brandl, Annette Peters, Wolfgang Koenig, Ralph Burkhardt, André Gessner, Iris M. Heid, Christian Gieger and Klaus J. Stark
    Citation: BMC Genomic Data 2023 24:28
  24. With the release of genomic data for B.rapa, B.oleracea, and B.napus, research on the genetic and molecular functions of Brassica spp. has entered a new stage. PEBP genes in plants play an important role in the t...

    Authors: Yanling Li, Lu Xiao, Zhi Zhao, Hongping Zhao and Dezhi Du
    Citation: BMC Genomic Data 2023 24:27
  25. HostSeq was launched in April 2020 as a national initiative to integrate whole genome sequencing data from 10,000 Canadians infected with SARS-CoV-2 with clinical information related to their disease experienc...

    Authors: S Yoo, E Garg, LT Elliott, RJ Hung, AR Halevy, JD Brooks, SB Bull, F Gagnon, CMT Greenwood, JF Lawless, AD Paterson, L Sun, MH Zawati, J Lerner-Ellis, RJS Abraham, I Birol…
    Citation: BMC Genomic Data 2023 24:26
  26. Recently, deep neural networks have been successfully applied in many biological fields. In 2020, a deep learning model AlphaFold won the protein folding competition with predicted structures within the error ...

    Authors: Katarína Grešová, Vlastimil Martinek, David Čechák, Petr Šimeček and Panagiotis Alexiou
    Citation: BMC Genomic Data 2023 24:25
  27. Gastric cancer (GC) is the fourth most common cancer worldwide, with the highest incidence and mortality regardless of sex. Despite technological advances in diagnosing and treating gastric cancer, GC still ha...

    Authors: Eun-Hye Seo, Yun-Jae Shin, Hee-Jin Kim, Jeong-Hwan Kim, Yong Sung Kim and Seon-Young Kim
    Citation: BMC Genomic Data 2023 24:24
  28. As part of a research aiming at presenting an alternative approach for rapid determination of antimicrobial susceptibility by quantification of changes in expression levels of specific marker genes and gene se...

    Authors: Galia Zaide, Inbar Cohen-Gihon, Ohad Shifman, Ofir Israeli, Moshe Aftalion, Sharon Maoz, Theodor Chitlaru, Raphael Ber, Anat Zvi and Ida Steinberger-Levy
    Citation: BMC Genomic Data 2023 24:23
  29. Previous reports revealed that a history of major depressive disorder (MDD) increased the risk of Alzheimer’s disease (AD). The immune disorder is associated with MDD and AD pathophysiology. We aimed to identi...

    Authors: Jin Song, Zilong Ma, Huishi Zhang, Ting Liang and Jun Zhang
    Citation: BMC Genomic Data 2023 24:22
  30. Nepenthes belongs to the monotypic family Nepenthaceae, one of the largest carnivorous plant families. Nepenthes species show impressive adaptive radiation and suffer from being overexploited in nature. Nepenthes...

    Authors: Yuan Gao, Hao-Bin Liao, Ting-Hong Liu, Jia-Ming Wu, Zheng-Feng Wang and Hong-Lin Cao
    Citation: BMC Genomic Data 2023 24:21
  31. Intracranial aneurysm (IA) is a common cerebrovascular disease. The immune mechanism of IA is more complicated, and it is unclear so far. Therefore, it is necessary to continue to explore the immune related mo...

    Authors: Zhengfei Ma, Ping Zhong, Peidong Yue and Zhongwu Sun
    Citation: BMC Genomic Data 2023 24:20
  32. Streptococcus pneumoniae (pneumococcus) represents an important human pathogen, responsible for respiratory and invasive infections in the community. The efficacy of polysaccharide conjugate vaccines formulated a...

    Authors: Weronika Puzia, Jan Gawor, Robert Gromadka, Anna Skoczyńska and Ewa Sadowy
    Citation: BMC Genomic Data 2023 24:19
  33. Diospyros oleifera, one of the most economically important Diospyros species, is an ideal model for studying the fruit development of persimmon. While, the lack of whole-transcriptome has hindered the complex tra...

    Authors: Yang Xu, Cui-yu Liu, Wen-qiang Cheng, Kai-yun Wu and Bang-chu Gong
    Citation: BMC Genomic Data 2023 24:17
  34. The Enterobacter cloacae complex is considered an important opportunistic pathogen. It comprises many members that remain difficult to delineate by phenotypic approaches. Despite its importance in human infection...

    Authors: Matthieu Pot, Célia Ducat, Yann Reynaud, David Couvin, Séverine Ferdinand, Sébastien Breurec, Antoine Talarmin and Stéphanie Guyomard-Rabenirina
    Citation: BMC Genomic Data 2023 24:16
  35. Petrea volubilis, a member of the Order Lamiales and the Verbenaceae family, is an important horticultural species that has been used in traditional folk medicine. To provide a genome sequence for comparative st...

    Authors: John P. Hamilton, Brieanne Vaillancourt, Joshua C. Wood and C. Robin Buell
    Citation: BMC Genomic Data 2023 24:14
  36. Genome Wide Association Studies (GWAS) are based on the observation of genome-wide sets of genetic variants – typically single-nucleotide polymorphisms (SNPs) – in different individuals that are associated wit...

    Authors: Anna Bernasconi, Arif Canakoglu and Federico Comolli
    Citation: BMC Genomic Data 2023 24:13

    The Correction to this article has been published in BMC Genomic Data 2023 24:32

  37. The peaberry bean in Arabica coffee has exceptional quality compared to the regular coffee bean. Understanding the molecular mechanism of bean quality is imperative to introduce superior coffee quality traits....

    Authors: Xingfei Fu, Guiping Li, Faguang Hu, Jiaxiong Huang, Yuqiang Lou, Yaqi Li, Yanan Li, Hongyan He, YuLan Lv and Jinhuan Cheng
    Citation: BMC Genomic Data 2023 24:12
  38. The marine cyanobacterium Prochlorococcus is a critical part of warm ocean ecosystems and a model for studying microbial evolution and ecology. To expand the representation of this organism’s vast wild diversity ...

    Authors: Jessie W. Berta-Thompson, Elaina Thomas, Andrés Cubillos-Ruiz, Thomas Hackl, Jamie W. Becker, Allison Coe, Steven J. Biller, Paul M. Berube and Sallie W. Chisholm
    Citation: BMC Genomic Data 2023 24:11
  39. The fungal pathogen Thecaphora frezii Carranza & Lindquist causes peanut smut, a severe disease currently endemic in Argentina. To study the ecology of T. frezii and to understand the mechanisms of smut resistanc...

    Authors: Renee S. Arias, Cinthia Conforto, Valerie A. Orner, Edgardo J. Carloni, Juan H. Soave, Alicia N. Massa, Marshall C. Lamb, Nelson Bernardi-Lima and Alejandro M. Rago
    Citation: BMC Genomic Data 2023 24:9
  40. Rice is one of the most important food crops in the world and mainly cultivated in paddy field by transplanting seedlings. However, increasing water scarcity due to climate change, labor cost for transplanting...

    Authors: Wisdom Mawuli Edzesi, Xiaojing Dang, Erbao Liu, William Kwame Nuako Bandoh, Patience Mansa Gakpetor, Daniel Aninagyei Ofori and Delin Hong
    Citation: BMC Genomic Data 2023 24:8
  41. High-density single nucleotide polymorphisms (SNPs) are the most abundant and robust form of genetic variants and hence make highly favorable markers to determine the genetic diversity and relationship, enhanc...

    Authors: Mihret Yirgu, Mulugeta Kebede, Tileye Feyissa, Berhane Lakew, Aemiro Bezabih Woldeyohannes and Mulusew Fikere
    Citation: BMC Genomic Data 2023 24:7
  42. Thrombocytopenia is a condition that causes a low amount of blood platelets. Platelets are blood cells that play an essential role in blood coagulation. Therefore, thrombocytopenia can put the patient at risk ...

    Authors: Eun-Hye Seo, Jeong-Hwan Kim, Da-Hee Kim, Jung-Hwa Oh and Seon-Young Kim
    Citation: BMC Genomic Data 2023 24:6
  43. Microsatellites are a ubiquitous occurrence in prokaryotic and eukaryotic genomes. Microsatellites have become one of the most popular classes of genetic markers due to their high reproducibility, multi-alleli...

    Authors: Weiwei Shao, Wei Cai, Fen Qiao, Zhihua Lin and Li Wei
    Citation: BMC Genomic Data 2023 24:5
  44. Cytoskeleton-related proteins are essential for cell shape maintenance and cytoskeleton remodeling. The spermatozoa of Eriocheir sinensis (Chinese mitten crab) have a unique cellular structure, and the mechanism ...

    Authors: Yulian Tang, Lishuang Sun, Shu Li, Huiting Liu, Lvjing Luo, Zhengyu Chen and Genliang Li
    Citation: BMC Genomic Data 2023 24:4
  45. The Phenomenon of codon usage bias exists in the genomes of prokaryotes and eukaryotes. The codon usage pattern is affected by environmental factors, base mutation, gene flow and gene expression level, among w...

    Authors: Yingzhe Wang, Dacheng Jiang, Kun Guo, Lei Zhao, Fangfang Meng, Jinglei Xiao, Yuan Niu and Yunlong Sun
    Citation: BMC Genomic Data 2023 24:3

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