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121 result(s) for 'gene editing in the context of an increasingly complex genome ' within BMC Genomics

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  1. Xenorhabdus innexi is a bacterial symbiont of Steinernema scapterisci nematodes, which is a cricket-specialist parasite and together the nematode and bacteria infect and kill crickets....

    Authors: Il-Hwan Kim, Sudarshan K. Aryal, Dariush T. Aghai, Ángel M. Casanova-Torres, Kai Hillman, Michael P. Kozuch, Erin J. Mans, Terra J. Mauer, Jean-Claude Ogier, Jerald C. Ensign, Sophie Gaudriault, Walter G. Goodman, Heidi Goodrich-Blair and Adler R. Dillman
    Citation: BMC Genomics 2017 18:927
    Content type: Research article Published on:

  2. Cilia are microtubule-based organelles protruding from almost all mammalian cells which, when dysfunctional, result in genetic disorders called “ciliopathies”. High-throughput studies have revealed that cilia ...

    Authors: Roberto Amato, Manuela Morleo, Laura Giaquinto, Diego di Bernardo and Brunella Franco
    Citation: BMC Genomics 2014 15:658
    Content type: Research article Published on:

  3. Cysticercosis remains a major neglected tropical disease of humanity in many regions, especially in sub-Saharan Africa, Central America and elsewhere. Owing to the emerging drug resistance and the inability of...

    Authors: Hong-Bin Yan, Zhong-Zi Lou, Li Li, Paul J Brindley, Yadong Zheng, Xuenong Luo, Junling Hou, Aijiang Guo, Wan-Zhong Jia and Xuepeng Cai
    Citation: BMC Genomics 2014 15:428
    Content type: Research article Published on:

  4. Continuing evolution of the Mycobacterium tuberculosis (Mtb) complex genomes associated with resistance to anti-tuberculosis drugs is threatening tuberculosis disease control efforts. Both multi- and extensively ...

    Authors: Yaa E. A. Oppong, Jody Phelan, João Perdigão, Diana Machado, Anabela Miranda, Isabel Portugal, Miguel Viveiros, Taane G. Clark and Martin L. Hibberd
    Citation: BMC Genomics 2019 20:252
    Content type: Research article Published on:

  5. A better understanding of the genetic architecture underlying complex traits (e.g., the distribution of causal variants and their effects) may aid in the genomic prediction. Here, we hypothesized that the geno...

    Authors: Lingzhao Fang, Goutam Sahana, Peipei Ma, Guosheng Su, Ying Yu, Shengli Zhang, Mogens Sandø Lund and Peter Sørensen
    Citation: BMC Genomics 2017 18:604
    Content type: Research article Published on:

  6. Acute myeloid leukemia (AML) is a clonal disorder of the blood forming cells characterized by accumulation of immature blast cells in the bone marrow and peripheral blood. Being a heterogeneous disease, AML ha...

    Authors: Asad Muhammad Ilyas, Sultan Ahmad, Muhammad Faheem, Muhammad Imran Naseer, Taha A Kumosani, Muhammad Hussain Al-Qahtani, Mamdooh Gari and Farid Ahmed
    Citation: BMC Genomics 2015 16(Suppl 1):S5
    Content type: Review Published on:

    This article is part of a Supplement: Volume 16 Supplement 1

  7. miRNAs are small noncoding RNA molecules that play an important role in post-transcriptional regulation of gene expression. Length and/or sequence variants of the same miRNA are termed isomiRs. While most isom...

    Authors: Omar Salem, Nese Erdem, Janine Jung, Ewald Münstermann, Angelika Wörner, Heike Wilhelm, Stefan Wiemann and Cindy Körner
    Citation: BMC Genomics 2016 17:566
    Content type: Research article Published on:

  8. Lysosomes play important roles in multiple aspects of physiology, but the problem of how the transcription of lysosomal genes is coordinated remains incompletely understood. The goal of this study was to illum...

    Authors: Louise M Brignull, Zsolt Czimmerer, Hafida Saidi, Bence Daniel, Izabel Villela, Nathan W Bartlett, Sebastian L Johnston, Lisiane B Meira, Laszlo Nagy and Axel Nohturfft
    Citation: BMC Genomics 2013 14:853
    Content type: Research article Published on:

  9. Genomic tools are increasingly being used on non-model organisms to provide insights into population structure and variability, including signals of selection. However, most studies are carried out in regions ...

    Authors: Erica S. Nielsen, Romina Henriques, Robert J. Toonen, Ingrid S. S. Knapp, Baocheng Guo and Sophie von der Heyden
    Citation: BMC Genomics 2018 19:347
    Content type: Research article Published on:

  10. The fucoid brown algae (Heterokontophyta, Phaeophyceae) are increasingly the focus of ecological genetics, biodiversity, biogeography and speciation research. The molecular genetics underlying mating system va...

    Authors: Maria João F Martins, Catarina F Mota and Gareth A Pearson
    Citation: BMC Genomics 2013 14:294
    Content type: Research article Published on:

  11. Research using the Pacific oyster Crassostrea gigas as a model organism has experienced rapid growth in recent years due to the development of high-throughput molecular technologies. As many as 56,268 EST sequenc...

    Authors: Nolwenn M Dheilly, Christophe Lelong, Arnaud Huvet and Pascal Favrel
    Citation: BMC Genomics 2011 12:468
    Content type: Research article Published on:

  12. Most molecular studies of plant stress tolerance have been performed with Arabidopsis thaliana, although it is not particularly stress tolerant and may lack protective mechanisms required to survive extreme envir...

    Authors: Yang Ping Lee, Federico M Giorgi, Marc Lohse, Kotryna Kvederaviciute, Sven Klages, Björn Usadel, Irute Meskiene, Richard Reinhardt and Dirk K Hincha
    Citation: BMC Genomics 2013 14:793
    Content type: Research article Published on:

  13. The introduction of benchtop sequencers has made adoption of whole genome sequencing possible for a broader community of researchers than ever before. Concurrently, metagenomic sequencing (MGS) is rapidly emer...

    Authors: Kenneth G Frey, Jesus Enrique Herrera-Galeano, Cassie L Redden, Truong V Luu, Stephanie L Servetas, Alfred J Mateczun, Vishwesh P Mokashi and Kimberly A Bishop-Lilly
    Citation: BMC Genomics 2014 15:96
    Content type: Research article Published on:

  14. Charting the interactions among genes and among their protein products is essential for understanding biological systems. A flood of interaction data is emerging from high throughput technologies, computationa...

    Authors: Jingkai Yu, Svetlana Pacifico, Guozhen Liu and Russell L Finley Jr
    Citation: BMC Genomics 2008 9:461
    Content type: Database Published on:

  15. Cryptic unstable transcripts (CUTs) are a largely unexplored class of nuclear exosome degraded, non-coding RNAs in budding yeast. It is highly debated whether CUT transcription has a functional role in the cell o...

    Authors: Jessica M. Vera and Robin D. Dowell
    Citation: BMC Genomics 2016 17:305
    Content type: Research article Published on:

  17. Previous whole-genome shotgun bisulfite sequencing experiments showed that DNA cytosine methylation in the honey bee (Apis mellifera) is almost exclusively at CG dinucleotides in exons. However, the most commonly...

    Authors: Pablo Cingolani, Xiaoyi Cao, Radhika S Khetani, Chieh-Chun Chen, Melissa Coon, Alya’a Sammak, Aliccia Bollig-Fischer, Susan Land, Yun Huang, Matthew E Hudson, Mark D Garfinkel, Sheng Zhong, Gene E Robinson and Douglas M Ruden
    Citation: BMC Genomics 2013 14:666
    Content type: Research article Published on:

  18. Non-human primates (NHPs), particularly macaques, serve as critical and highly relevant pre-clinical models of human disease. The similarity in human and macaque natural disease susceptibility, along with para...

    Authors: Benjamin N. Bimber, Melissa Y. Yan, Samuel M. Peterson and Betsy Ferguson
    Citation: BMC Genomics 2019 20:176
    Content type: Database Article Published on:

  20. Copy number variation is an important dimension of genetic diversity and has implications in development and disease. As an important model organism, the mouse is a prime candidate for copy number variant (CNV...

    Authors: M Elizabeth O Locke, Maja Milojevic, Susan T Eitutis, Nisha Patel, Andrea E Wishart, Mark Daley and Kathleen A Hill
    Citation: BMC Genomics 2015 16:497
    Content type: Research article Published on:

  21. Internal circadian (circa, about; dies, day) clocks enable organisms to maintain adaptive timing of their daily behavioral activities and physiological functions. Eukaryotic clocks consist of core transcription-t...

    Authors: Duncan Tormey, John K. Colbourne, Keithanne Mockaitis, Jeong-Hyeon Choi, Jacqueline Lopez, Joshua Burkhart, William Bradshaw and Christina Holzapfel
    Citation: BMC Genomics 2015 16:754
    Content type: Research article Published on:

  22. The major intrinsic protein (MIP) family is a family of proteins, including aquaporins, which facilitate water and small molecule transport across plasma membranes. In plants, MIPs function in a huge variety o...

    Authors: Darren Chern Jan Wong, Li Zhang, Isabelle Merlin, Simone D. Castellarin and Gregory A. Gambetta
    Citation: BMC Genomics 2018 19:248
    Content type: Research article Published on:

  23. Parasitic nematodes, significant pathogens for humans, animals, and plants, depend on diverse organ systems for intra-host survival. Understanding the cellular diversity and molecular variations underlying the...

    Authors: Rahul Tyagi, Bruce A Rosa, Amanda Swain, Maxim N Artyomov, Douglas P Jasmer and Makedonka Mitreva
    Citation: BMC Genomics 2024 25:341
    Content type: Research Published on:

  24. Mate preference behavior is an essential first step in sexual selection and is a critical determinant in evolutionary biology. Previously an environmental compound (the fungicide vinclozolin) was found to prom...

    Authors: Michael K Skinner, Marina I Savenkova, Bin Zhang, Andrea C Gore and David Crews
    Citation: BMC Genomics 2014 15:377
    Content type: Research article Published on:

  25. Chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) is increasingly being applied to study genome-wide binding sites of transcription factors. There is an increasing interest in...

    Authors: Hatice Ulku Osmanbeyoglu, Ryan J Hartmaier, Steffi Oesterreich and Xinghua Lu
    Citation: BMC Genomics 2012 13(Suppl 1):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 1

  26. Feline immunodeficiency virus (FIV) naturally infects multiple species of cat and is related to human immunodeficiency virus in humans. FIV infection causes AIDS-like disease and mortality in the domestic cat (Fe...

    Authors: Jill Pecon-Slattery, Carrie L McCracken, Jennifer L Troyer, Sue VandeWoude, Melody Roelke, Kerry Sondgeroth, Christiaan Winterbach, Hanlie Winterbach and Stephen J O'Brien
    Citation: BMC Genomics 2008 9:66
    Content type: Research article Published on:

  27. Single-cell chromatin accessibility has emerged as a powerful means of understanding the epigenetic landscape of diverse tissues and cell types, but profiling cells from many independent specimens is challengi...

    Authors: Gregory T. Booth, Riza M. Daza, Sanjay R. Srivatsan, José L. McFaline-Figueroa, Rula Green Gladden, Andrew C. Mullen, Scott N. Furlan, Jay Shendure and Cole Trapnell
    Citation: BMC Genomics 2023 24:737
    Content type: Research Published on:

  28. Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So ...

    Authors: Sèyi Fridaïus Ulrich Vanvanhossou, Carsten Scheper, Luc Hippolyte Dossa, Tong Yin, Kerstin Brügemann and Sven König
    Citation: BMC Genomics 2020 21:783
    Content type: Research article Published on:

  30. Modern broiler chickens exhibit very rapid growth and high feed efficiency compared to unselected chicken breeds. The improved production efficiency in modern broiler chickens was achieved by the intensive gen...

    Authors: Byung-Whi Kong, Nicholas Hudson, Dongwon Seo, Seok Lee, Bhuwan Khatri, Kentu Lassiter, Devin Cook, Alissa Piekarski, Sami Dridi, Nicholas Anthony and Walter Bottje
    Citation: BMC Genomics 2017 18:82
    Content type: Research article Published on:

  31. MicroRNA-regulation of gene expression plays a key role in the development and response to biotic and abiotic stresses. Deep sequencing analyses accelerate the process of small RNA discovery in many plants and...

    Authors: Flávia Thiebaut, Clícia Grativol, Mariana Carnavale-Bottino, Cristian Antonio Rojas, Milos Tanurdzic, Laurent Farinelli, Robert A Martienssen, Adriana Silva Hemerly and Paulo Cavalcanti Gomes Ferreira
    Citation: BMC Genomics 2012 13:290
    Content type: Research article Published on:

  32. Effective bioinformatics solutions are needed to tackle challenges posed by industrial-scale genome annotation. We present Bcheck, a wrapper tool which predicts RNase P RNA genes by combining the speed of pattern...

    Authors: Dilmurat Yusuf, Manja Marz, Peter F Stadler and Ivo L Hofacker
    Citation: BMC Genomics 2010 11:432
    Content type: Methodology article Published on:

  34. Increases in ocean temperatures and in the frequency and severity of hypoxic events are expected with climate change, and may become a challenge for cultured Atlantic salmon and negatively affect their growth,...

    Authors: Anne Beemelmanns, Fábio S. Zanuzzo, Xi Xue, Rebeccah M. Sandrelli, Matthew L. Rise and A. Kurt Gamperl
    Citation: BMC Genomics 2021 22:261
    Content type: Research article Published on:

  37. Recent studies have demonstrated an unexpected complexity of transcription in eukaryotes. The majority of the genome is transcribed and only a little fraction of these transcripts is annotated as protein codin...

    Authors: Claudia Calabrese, Marina Mangiulli, Caterina Manzari, Anna Maria Paluscio, Mariano Francesco Caratozzolo, Flaviana Marzano, Ivana Kurelac, Anna Maria D’Erchia, Domenica D’Elia, Flavio Licciulli, Sabino Liuni, Ernesto Picardi, Marcella Attimonelli, Giuseppe Gasparre, Anna Maria Porcelli, Graziano Pesole…
    Citation: BMC Genomics 2013 14:855
    Content type: Methodology article Published on:

  38. The maturation of the brain involves the coordinated expression of thousands of genes, proteins and regulatory elements over time. In sensory pathways, gene expression profiles are modified by age and sensory ...

    Authors: Troy A. Hackett, Yan Guo, Amanda Clause, Nicholas J. Hackett, Krassimira Garbett, Pan Zhang, Daniel B. Polley and Karoly Mirnics
    Citation: BMC Genomics 2015 16:606
    Content type: Research article Published on:

  39. Human immunodeficiency virus-1 (HIV-1) has a minimal genome of only 9 genes, which encode 15 proteins. HIV-1 thus depends on the human host for virtually every aspect of its life cycle. The universal language ...

    Authors: Sivaraman Balakrishnan, Oznur Tastan, Jaime Carbonell and Judith Klein-Seetharaman
    Citation: BMC Genomics 2009 10(Suppl 3):S30
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  40. The lined sea anemone Edwardsiella lineata is an informative model system for evolutionary-developmental studies of parasitism. In this species, it is possible to compare alternate developmental pathways leading ...

    Authors: Derek J Stefanik, Tristan J Lubinski, Brian R Granger, Allyson L Byrd, Adam M Reitzel, Lukas DeFilippo, Allison Lorenc and John R Finnerty
    Citation: BMC Genomics 2014 15:71
    Content type: Database Published on:

  41. DNA methylation (DNAm) profiling has emerged as a powerful tool for characterizing the placental methylome. However, previous studies have focused primarily on whole placental tissue, which is a mixture of epi...

    Authors: Victor Yuan, Desmond Hui, Yifan Yin, Maria S. Peñaherrera, Alexander G. Beristain and Wendy P. Robinson
    Citation: BMC Genomics 2021 22:6
    Content type: Research article Published on:

  42. We present a computational framework tailored for the modeling of the complex, dynamic relationships that are encountered in splicing regulation. The starting point is whole-genome transcriptomic data from hig...

    Authors: Panagiotis Papasaikas, Arvind Rao, Peter Huggins, Juan Valcarcel and A Javier Lopez
    Citation: BMC Genomics 2015 16(Suppl 10):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 10

  43. InCoB became since its inception in 2002 one of the largest annual bioinformatics conferences in the Asia-Pacific region with attendance ranging between 150 and 250 delegates depending on the venue location. I...

    Authors: Christian Schönbach, Chandra Verma, Lawrence Jin Kiat Wee, Peter John Bond and Shoba Ranganathan
    Citation: BMC Genomics 2016 17(Suppl 13):1036
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 17 Supplement 13

  44. During embryogenesis, the developmental potential of initially pluripotent cells becomes progressively restricted as they transit to lineage restricted states. The pluripotent cells of Xenopus blastula-stage embr...

    Authors: Kristin Johnson, Simon Freedman, Rosemary Braun and Carole LaBonne
    Citation: BMC Genomics 2022 23:723
    Content type: Research Published on:

  45. Micro-RNAs (miRNA) are attributed to the systems biological role of a regulatory mechanism of the expression of protein coding genes. Research has identified miRNAs dysregulations in several but distinct patho...

    Authors: Alfred Ultsch and Jörn Lötsch
    Citation: BMC Genomics 2014 15:976
    Content type: Research article Published on:

  46. Accurate variant detection in the coding regions of the human genome is a key requirement for molecular diagnostics of Mendelian disorders. Efficiency of variant discovery from next-generation sequencing (NGS)...

    Authors: Yury A. Barbitoff, Ruslan Abasov, Varvara E. Tvorogova, Andrey S. Glotov and Alexander V. Predeus
    Citation: BMC Genomics 2022 23:155
    Content type: Research article Published on:

  47. Progressive CO2-induced ocean acidification (OA) impacts marine life in ways that are difficult to predict but are likely to become exacerbated over generations. Although marine fishes can balance acid–base homeo...

    Authors: Mishal Cohen-Rengifo, Morgane Danion, Anne-Alicia Gonzalez, Marie-Laure Bégout, Alexandre Cormier, Cyril Noël, Joëlle Cabon, Thomas Vitré, Felix C. Mark and David Mazurais
    Citation: BMC Genomics 2022 23:448
    Content type: Research Published on:

    The Correction to this article has been published in BMC Genomics 2023 24:284

  48. Single-cell sequencing techniques are revolutionizing every field of biology by providing the ability to measure the abundance of biological molecules at a single-cell resolution. Although single-cell sequenci...

    Authors: Lucas Kuijpers, Bastian Hornung, Mirjam C. G. N. van den Hout - van Vroonhoven, Wilfred F. J. van IJcken, Frank Grosveld and Eskeatnaf Mulugeta
    Citation: BMC Genomics 2024 25:361
    Content type: Research Published on:

  49. Trichoderma spp. are majorly composed of plant-beneficial symbionts widely used in agriculture as bio-control agents. Studying the mechanisms behind Trichoderma-derived plant benefits has yielded tangible bio-ind...

    Authors: Elizabeth A. Malinich, Ken Wang, Prasun K. Mukherjee, Michael Kolomiets and Charles M. Kenerley
    Citation: BMC Genomics 2019 20:280
    Content type: Research article Published on:

  50. Individuals with schizophrenia (SCZ) have, on average, a 10- to 20-year shorter expected life span than the rest of the population, primarily due to cardiovascular disease comorbidity. Genome-wide association ...

    Authors: Qian He, Adam N. Bennett, Jundong Liu, Beifang Fan, Xue Han, Lu Cheng, Yan Chen, Xia Yang and Kei Hang Katie Chan
    Citation: BMC Genomics 2022 23:617
    Content type: Research Published on:

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