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  1. Pathway analysis is one of the later stage data analysis steps essential in interpreting high-throughput gene expression data. We propose a set of algorithms which given gene expression data can recognize whic...

    Authors: Yue Zhao, Stephanie Piekos, Tham H. Hoang and Dong-Guk Shin
    Citation: BMC Genomics 2020 21(Suppl 1):834
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 21 Supplement 1

  2. Growth is a major economic production trait in aquaculture. Improvements in growth performance will reduce time and cost for fish to reach market size. However, genes underlying growth have not been fully expl...

    Authors: Ali Ali, Rafet Al-Tobasei, Daniela Lourenco, Tim Leeds, Brett Kenney and Mohamed Salem
    Citation: BMC Genomics 2020 21:209
    Content type: Research article Published on:

  3. Horizontal gene transfer (HGT) is the event of a DNA sequence being transferred between species not by inheritance. HGT is a crucial factor in prokaryotic evolution and is a significant source for genomic nove...

    Authors: Gur Sevillya, Orit Adato and Sagi Snir
    Citation: BMC Genomics 2020 21(Suppl 1):106
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 1

  4. Postpartum developmental delay has been proposed as an important phenotype of human evolution which contributes to many human-specific features including the increase in brain size and the advanced human-speci...

    Authors: Hui Tang, Ying Tang, Tao Zeng and Luonan Chen
    Citation: BMC Genomics 2020 21(Suppl 1):74
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 1

  5. Gills of euryhaline fishes possess great physiological and structural plasticity to adapt to large changes in external osmolality and to participate in ion uptake/excretion, which is essential for the re-estab...

    Authors: Hoi Man Ng, Jeff Cheuk Hin Ho, Wenyan Nong, Jerome Ho Lam Hui, Keng Po Lai and Chris Kong Chu Wong
    Citation: BMC Genomics 2020 21:208
    Content type: Research article Published on:

  6. Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of...

    Authors: Zeinab Amiri Ghanatsaman, Guo-Dong Wang, Hojjat Asadollahpour Nanaei, Masood Asadi Fozi, Min-Sheng Peng, Ali Esmailizadeh and Ya-Ping Zhang
    Citation: BMC Genomics 2020 21:207
    Content type: Research article Published on:

  7. Rye (Secale cereale L., 2n = 2x = 14, RR), a relative of common wheat, is a large gene resource pool for wheat improvement. Accurate and convenient identification of the rye chromatin in wheat background will fac...

    Authors: Guohao Han, Shiyu Liu, Yuli Jin, Mengshu Jia, Pengtao Ma, Hong Liu, Jing Wang and Diaoguo An
    Citation: BMC Genomics 2020 21:206
    Content type: Research article Published on:

  8. The trading of individual animal genotype information often involves only the exchange of the called genotypes and not necessarily the additional information required to effectively call structural variants. T...

    Authors: Pierce Rafter, Isobel Claire Gormley, Andrew C. Parnell, John Francis Kearney and Donagh P. Berry
    Citation: BMC Genomics 2020 21:205
    Content type: Research article Published on:

  9. In response to ecological niche of domestication, domesticated mammals and birds developed adaptively phenotypic homoplasy in behavior modifications like fearlessness, altered sociability, exploration and cogn...

    Authors: Yali Hou, Furong Qi, Xue Bai, Tong Ren, Xu Shen, Qin Chu, Xiquan Zhang and Xuemei Lu
    Citation: BMC Genomics 2020 21:204
    Content type: Research article Published on:

  10. Unravelling the genetic architecture of agronomic traits in walnut such as budbreak date and bearing habit, is crucial for climate change adaptation and yield improvement. A Genome-Wide Association Study (GWAS...

    Authors: Anthony Bernard, Annarita Marrano, Armel Donkpegan, Patrick J. Brown, Charles A. Leslie, David B. Neale, Fabrice Lheureux and Elisabeth Dirlewanger
    Citation: BMC Genomics 2020 21:203
    Content type: Research article Published on:

  11. Salmonella enterica subsp. enterica serovar Napoli (S. Napoli) is among the top serovars causing human infections in Italy, although it is relatively uncommon in other European countries; it is mainly isolated fr...

    Authors: Eleonora Mastrorilli, Sara Petrin, Massimiliano Orsini, Alessandra Longo, Debora Cozza, Ida Luzzi, Antonia Ricci, Lisa Barco and Carmen Losasso
    Citation: BMC Genomics 2020 21:202
    Content type: Research article Published on:

  12. The yak is a species of livestock which is crucial for local communities of the Qinghai-Tibet Plateau and adjacent regions and naturally owns one more thoracic vertebra than cattle. Recently, a sub-population ...

    Authors: Yu Wang, Haoyang Cai, Xiaolin Luo, Yi Ai, Mingfeng Jiang and Yongli Wen
    Citation: BMC Genomics 2020 21:201
    Content type: Research article Published on:

  13. PhasiRNAs (phased secondary siRNAs) play important regulatory roles in the development processes and biotic or abiotic stresses in plants. Some of phasiRNAs involve in the reproductive development in grasses, ...

    Authors: Rongzhi Zhang, Siyuan Huang, Shiming Li, Guoqi Song, Yulian Li, Wei Li, Jihu Li, Jie Gao, Tiantian Gu, Dandan Li, Shujuan Zhang and Genying Li
    Citation: BMC Genomics 2020 21:200
    Content type: Research article Published on:

  14. Breeding for new macadamia cultivars with high nut yield is expensive in terms of time, labour and cost. Most trees set nuts after four to five years, and candidate varieties for breeding are evaluated for at ...

    Authors: Katie O’Connor, Ben Hayes, Craig Hardner, Catherine Nock, Abdul Baten, Mobashwer Alam, Robert Henry and Bruce Topp
    Citation: BMC Genomics 2020 21:199
    Content type: Research article Published on:

  15. Purple-fleshed sweetpotato (PFSP) is one of the most important crops in the word which helps to bridge the food gap and contribute to solve the malnutrition problem especially in developing countries. Salt str...

    Authors: Mohamed Hamed Arisha, Hesham Aboelnasr, Muhammad Qadir Ahmad, Yaju Liu, Wei Tang, Runfei Gao, Hui Yan, Meng Kou, Xin Wang, Yungang Zhang and Qiang Li
    Citation: BMC Genomics 2020 21:197
    Content type: Research article Published on:

  16. Olfactory receptor (OR) genes are the largest multi-gene family in the mammalian genome, with 874 in human and 1483 loci in mouse (including pseudogenes). The expansion of the OR gene repertoire has occurred t...

    Authors: If H. A. Barnes, Ximena Ibarra-Soria, Stephen Fitzgerald, Jose M. Gonzalez, Claire Davidson, Matthew P. Hardy, Deepa Manthravadi, Laura Van Gerven, Mark Jorissen, Zhen Zeng, Mona Khan, Peter Mombaerts, Jennifer Harrow, Darren W. Logan and Adam Frankish
    Citation: BMC Genomics 2020 21:196
    Content type: Research article Published on:

  17. Read coverage of RNA sequencing data reflects gene expression and RNA processing events. Single-cell RNA sequencing (scRNA-seq) methods, particularly “full-length” ones, provide read coverage of many individua...

    Authors: Haruka Ozaki, Tetsutaro Hayashi, Mana Umeda and Itoshi Nikaido
    Citation: BMC Genomics 2020 21:177
    Content type: Software Published on:

  18. The H+-PPase (pyrophosphatase) gene family is an important class of proton transporters that play key roles in plant development and stress resistance. Although the physiological and biochemical functions of H+-P...

    Authors: Yiming Zhang, Xue Feng, Lihui Wang, Yanping Su, Zhuodong Chu and Yanxiang Sun
    Citation: BMC Genomics 2020 21:195
    Content type: Research article Published on:

  20. Genome assemblies are foundational for understanding the biology of a species. They provide a physical framework for mapping additional sequences, thereby enabling characterization of, for example, genomic div...

    Authors: Nancy Manchanda, John L. Portwood II, Margaret R. Woodhouse, Arun S. Seetharam, Carolyn J. Lawrence-Dill, Carson M. Andorf and Matthew B. Hufford
    Citation: BMC Genomics 2020 21:193
    Content type: Software Published on:

  22. Cyclic nucleotide gated channels (CNGCs) play multifaceted roles in plant physiological processes, especially with respect to signalling processes, plant development, and responses to environmental stresses. H...

    Authors: Lixin Wang, Min Li, Zhiguo Liu, Li Dai, Mengling Zhang, Lili Wang, Jin Zhao and Mengjun Liu
    Citation: BMC Genomics 2020 21:191
    Content type: Research article Published on:

  23. The AIG (avrRpt2-induced gene) family of GTPases, characterized by the presence of a distinctive AIG1 domain, is mysterious in having a peculiar phylogenetic distribution, a predilection for undergoing expansi...

    Authors: Lijun Lu, Eric S. Loker, Si-Ming Zhang, Sarah K. Buddenborg and Lijing Bu
    Citation: BMC Genomics 2020 21:190
    Content type: Research article Published on:

  26. Aohan fine wool sheep (AFWS) is a historically bred fine wool sheep, cultivated in China. The wool has excellent quality and good textile performance. Investigating the molecular mechanisms that regulate wool ...

    Authors: Ranran Zhao, Nan Liu, Fuhui Han, Hegang Li, Jifeng Liu, Lanlan Li, Guoyi Wang and Jianning He
    Citation: BMC Genomics 2020 21:187
    Content type: Research article Published on:

  27. Phaseolus vulgaris (common bean) microsymbionts belonging to the bacterial genera Rhizobium, Bradyrhizobium, and Ensifer (Sinorhizobium) have been isolated across the globe. Individual symbiosis genes (e.g., nodC

    Authors: Wenjun Tong, Xiangchen Li, Entao Wang, Ying Cao, Weimin Chen, Shiheng Tao and Gehong Wei
    Citation: BMC Genomics 2020 21:186
    Content type: Research article Published on:

  28. Growth regulation is a complex process influenced by genetic and environmental factors. We examined differences between growth hormone (GH) transgenic (T) and non-transgenic (NT) coho salmon to elucidate wheth...

    Authors: Erin Kathleen McClelland, Michelle T. T. Chan, Xiang Lin, Dionne Sakhrani, Felicia Vincelli, Jin-Hyoung Kim, Daniel D. Heath and Robert H. Devlin
    Citation: BMC Genomics 2020 21:185
    Content type: Research article Published on:

  30. Whole-genome approaches are widely preferred for species delineation in prokaryotes. However, these methods require pairwise alignments and calculations at the whole-genome level and thus are computationally i...

    Authors: Yizhuang Zhou, Jifang Zheng, Yepeng Wu, Wenting Zhang and Junfei Jin
    Citation: BMC Genomics 2020 21:183
    Content type: Methodology article Published on:

  32. Sporobolomyces pararoseus is regarded as an oleaginous red yeast, which synthesizes numerous valuable compounds with wide industrial usages. This species hold biotechnological interests in biodiesel, food and cos...

    Authors: Chun-Ji Li, Die Zhao, Bing-Xue Li, Ning Zhang, Jian-Yu Yan and Hong-Tao Zou
    Citation: BMC Genomics 2020 21:181
    Content type: Research article Published on:

  33. In silico functional genomics have become a driving force in the way we interpret and use gene expression data, enabling researchers to understand which biological pathways are likely to be affected by the tre...

    Authors: Jeffrey A. Thompson and Devin C. Koestler
    Citation: BMC Genomics 2020 21:180
    Content type: Methodology article Published on:

  34. The filamentous fungus Fusarium graminearum causes devastating crop diseases and produces harmful mycotoxins worldwide. Understanding the complex F. graminearum transcriptional regulatory networks (TRNs) is vital...

    Authors: Li Guo, Mengjie Ji and Kai Ye
    Citation: BMC Genomics 2020 21:179
    Content type: Research article Published on:

  35. The basic helix–loop–helix (bHLH) is the second largest gene family in the plant, some members play important roles in pistil development and response to drought, waterlogging, cold stress and salt stress. The...

    Authors: Liming Miao, Yingying Gao, Kun Zhao, Lijun Kong, Shubo Yu, Rongrong Li, Kaiwen Liu and Xiaolin Yu
    Citation: BMC Genomics 2020 21:178
    Content type: Research article Published on:

  36. Vaccines have greatly reduced the burden of infectious disease, ranking in their impact on global health second only after clean water. Most vaccines confer protection by the production of antibodies with bind...

    Authors: Anna Fowler, Jacob D. Galson, Johannes Trück, Dominic F. Kelly and Gerton Lunter
    Citation: BMC Genomics 2020 21:176
    Content type: Methodology Article Published on:

  37. Proximity ligation based techniques, like Hi-C, involve restriction digestion followed by ligation of formaldehyde cross-linked chromatin. Distinct chromatin states can impact the restriction digestion, and he...

    Authors: Keerthivasan Raanin Chandradoss, Prashanth Kumar Guthikonda, Srinivas Kethavath, Monika Dass, Harpreet Singh, Rakhee Nayak, Sreenivasulu Kurukuti and Kuljeet Singh Sandhu
    Citation: BMC Genomics 2020 21:175
    Content type: Research article Published on:

  38. Tuberculosis (TB), particularly multi- and or extensive drug resistant TB, is still a global medical emergency. Whole genome sequencing (WGS) is a current alternative to the WHO-approved probe-based methods fo...

    Authors: Bugwesa Z. Katale, Peter M. Mbelele, Nsiande A. Lema, Susana Campino, Stephen E. Mshana, Mark M. Rweyemamu, Jody E. Phelan, Julius D. Keyyu, Mtebe Majigo, Erasto V. Mbugi, Hazel M. Dockrell, Taane G. Clark, Mecky I. Matee and Stellah Mpagama
    Citation: BMC Genomics 2020 21:174
    Content type: Research article Published on:

  39. Recently, a new strain of Cercospora sojina (Race15) has been identified, which has caused the breakdown of resistance in most soybean cultivars in China. Despite this serious yield reduction, little is known abo...

    Authors: Xin Gu, Junjie Ding, Wei Liu, Xiaohe Yang, Liangliang Yao, Xuedong Gao, Maoming Zhang, Shuai Yang and Jingzhi Wen
    Citation: BMC Genomics 2020 21:172
    Content type: Research article Published on:

  40. Lepidoptera is one group of the largest plant-feeding insects and Spodoptera litura (Lepidoptera: Noctuidae) is one of the most serious agricultural pests in Asia countries. An interesting and unique phenomenon f...

    Authors: Yaqing Chen, Jun Ou, Yucheng Liu, Qiong Wu, Liang Wen, Sichun Zheng, Sheng Li, Qili Feng and Lin Liu
    Citation: BMC Genomics 2020 21:171
    Content type: Research article Published on:

  41. Semantic similarity between Gene Ontology (GO) terms is a fundamental measure for many bioinformatics applications, such as determining functional similarity between genes or proteins. Most previous research e...

    Authors: Xiaoshi Zhong, Rama Kaalia and Jagath C. Rajapakse
    Citation: BMC Genomics 2020 20(Suppl 9):918
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

  42. To date, four thrips vectors have been reported to transmit five different tospoviruses in India. Their identification at an early stage is crucial in formulating appropriate pest management strategies. Since ...

    Authors: Sumit Jangra, Anubha Mittal, Heena Dhall, Rakesh Kumar Jain and Amalendu Ghosh
    Citation: BMC Genomics 2020 21:170
    Content type: Research article Published on:

  43. Matricaria recutita (German chamomile) and Chamaemelum nobile (Roman chamomile) belong to the botanical family Asteraceae. These two herbs are not only morphologically distinguishable, but their secondary metabol...

    Authors: Yuling Tai, Xiaojuan Hou, Chun Liu, Jiameng Sun, Chunxiao Guo, Ling Su, Wei Jiang, Chengcheng Ling, Chengxiang Wang, Huanhuan Wang, Guifang Pan, Xiongyuan Si and Yi Yuan
    Citation: BMC Genomics 2020 21:169
    Content type: Research article Published on:

  44. Taxus cells are a potential sustainable and environment-friendly source of taxol, but they have low survival ratios and slow grow rates. Despite these limitations, Taxus callus cells induced through 6 months of c...

    Authors: Ying Chen, Meng Zhang, Xiaofei Jin, Haoran Tao, Yamin Wang, Bo Peng, Chunhua Fu and Longjiang Yu
    Citation: BMC Genomics 2020 21:168
    Content type: Research article Published on:

  45. Tuberculosis remains one of the leading causes of morbidity and mortality worldwide. Therefore, understanding the pathophysiology of Mycobacterium tuberculosis is imperative for developing new drugs. Post-transcr...

    Authors: Vimla Kany G. Ami, Rami Balasubramanian and Shubhada R. Hegde
    Citation: BMC Genomics 2020 21:167
    Content type: Research article Published on:

  46. The state-of-the-art in nucleic acid based biodetection continues to be polymerase chain reaction (PCR), and many real-time PCR assays targeting biodefense pathogens for biosurveillance are in widespread use. ...

    Authors: Robert Player, Kathleen Verratti, Andrea Staab, Christopher Bradburne, Sarah Grady, Bruce Goodwin and Shanmuga Sozhamannan
    Citation: BMC Genomics 2020 21:166
    Content type: Methodology article Published on:

  47. MicroRNAs (miRNAs) are a class of noncoding small RNAs that play important roles in many physiological processes by regulating gene expression. Previous studies have shown that the expression levels of total m...

    Authors: Hua Xu, Xin Wang, Zhikai Wang, Jianhui Li, Zhiming Xu, Maohua Miao, Guowu Chen, Xiangdong Lei, Jun Wu, Huijuan Shi, Ke Wang, Tiancheng Zhang and Xiaoxi Sun
    Citation: BMC Genomics 2020 21:165
    Content type: Research article Published on:

  48. MicroRNAs (miRNAs), a class of small regulatory RNAs, have been proven to play important roles in plant growth, development and stress responses. Sweet potato (Ipomoea batatas L.) is an important food and industr...

    Authors: Zhengmei Yang, Panpan Zhu, Hunseung Kang, Lin Liu, Qinghe Cao, Jian Sun, Tingting Dong, Mingku Zhu, Zongyun Li and Tao Xu
    Citation: BMC Genomics 2020 21:164
    Content type: Research article Published on:

  49. Gang goose is a native species with gray plumage in Sichuan, China. As a result of overhunting, the number of gray Gang geese has decreased dramatically. To keep the species from extinction, conservation work ...

    Authors: Yang Xi, Lei Wang, Hehe Liu, Shengchao Ma, Yanying Li, Liang Li, Jiwen Wang, Han Chunchun, Lili Bai, Ahsan Mustafa and Hua He
    Citation: BMC Genomics 2020 21:162
    Content type: Research article Published on:

  50. Climate plays an essential role in forest health, and climate change may increase forest productivity losses due to abiotic and biotic stress. Increased temperature leads to the increased formation of ozone (O3)....

    Authors: Nourolah Soltani, Teo Best, Dantria Grace, Christen Nelms, Ketia Shumaker, Jeanne Romero-Severson, Daniela Moses, Stephan Schuster, Margaret Staton, John Carlson and Kimberly Gwinn
    Citation: BMC Genomics 2020 21:160
    Content type: Research article Published on:

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BMC Genomics

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