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Prokaryote microbial genomics

Section edited by Theo Smits

This section covers the structure and function of the genomes of prokaryotic and archaea microorganisms.

Page 1 of 12

  1. Content type: Research article

    The molecular mechanisms underlying bacterial cell death due to stresses or bactericidal antibiotics are complex and remain puzzling. Due to the current crisis of antibiotic resistance, development of effectiv...

    Authors: Sardar Karash and Young Min Kwon

    Citation: BMC Genomics 2018 19:610

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  2. Content type: Research article

    Mixed, polyclonal Mycobacterium tuberculosis infection occurs in natural populations. Developing an effective method for detecting such cases is important in measuring the success of treatment and reconstruction ...

    Authors: Benjamin Sobkowiak, Judith R. Glynn, Rein M. G. J. Houben, Kim Mallard, Jody E. Phelan, José Afonso Guerra-Assunção, Louis Banda, Themba Mzembe, Miguel Viveiros, Ruth McNerney, Julian Parkhill, Amelia C. Crampin and Taane G. Clark

    Citation: BMC Genomics 2018 19:613

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  3. Content type: Research article

    Host specialization is a hallmark of numerous plant pathogens including bacteria, fungi, oomycetes and viruses. Yet, the molecular and evolutionary bases of host specificity are poorly understood. In some case...

    Authors: Nicolas W. G. Chen, Laurana Serres-Giardi, Mylène Ruh, Martial Briand, Sophie Bonneau, Armelle Darrasse, Valérie Barbe, Lionel Gagnevin, Ralf Koebnik and Marie-Agnès Jacques

    Citation: BMC Genomics 2018 19:606

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  4. Content type: Research article

    Resistance to 3rd-generation cephalosporins in Escherichia coli is mostly mediated by extended-spectrum beta-lactamases (ESBLs) or AmpC beta-lactamases. Besides overexpression of the species-specific chromosomal

    Authors: Michael Pietsch, Alexandra Irrgang, Nicole Roschanski, Geovana Brenner Michael, Axel Hamprecht, Heime Rieber, Annemarie Käsbohrer, Stefan Schwarz, Uwe Rösler, Lothar Kreienbrock, Yvonne Pfeifer, Stephan Fuchs and Guido Werner

    Citation: BMC Genomics 2018 19:601

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  5. Content type: Research article

    Bacteria belonging to the Rhodococcus genus play an important role in the degradation of many contaminants, including methylbenzenes. These bacteria, widely distributed in the environment, are known to be a power...

    Authors: Alessandra Di Canito, Jessica Zampolli, Alessandro Orro, Pasqualina D’Ursi, Luciano Milanesi, Guido Sello, Alexander Steinbüchel and Patrizia Di Gennaro

    Citation: BMC Genomics 2018 19:587

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  6. Content type: Research article

    In order to start to understand the function of individual members of gut microbiota, we cultured, sequenced and analysed bacterial anaerobes from chicken caecum.

    Authors: Matej Medvecky, Darina Cejkova, Ondrej Polansky, Daniela Karasova, Tereza Kubasova, Alois Cizek and Ivan Rychlik

    Citation: BMC Genomics 2018 19:561

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  7. Content type: Research article

    Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a Gram-positive bacterium that colonizes the gastrointestinal and genitourinary tract of humans. This bacterium has also been isolated from ...

    Authors: Ivan Rodrigo Wolf, Alexandre Rossi Paschoal, Cecilia Quiroga, Douglas Silva Domingues, Rogério Fernandes de Souza, Lucienne Garcia Pretto-Giordano and Laurival Antonio Vilas-Boas

    Citation: BMC Genomics 2018 19:556

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  8. Content type: Research article

    Mycobacterium tuberculosis infection in humans is often associated with extended period of latency. To adapt to the hostile hypoxic environment inside a macrophage, M. tuberculosis cells undergo several physiolog...

    Authors: Tungadri Bose, Chandrani Das, Anirban Dutta, Vishnuvardhan Mahamkali, Sudipta Sadhu and Sharmila S. Mande

    Citation: BMC Genomics 2018 19:555

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  9. Content type: Methodology article

    Bacterial genomes have characteristic compositional skews, which are differences in nucleotide frequency between the leading and lagging DNA strands across a segment of a genome. It is thought that these stran...

    Authors: Lena M. Joesch-Cohen, Max Robinson, Neda Jabbari, Christopher G. Lausted and Gustavo Glusman

    Citation: BMC Genomics 2018 19:528

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  10. Content type: Methodology article

    Mycoplasma hominis is a human urogenital pathogen involved in gynaecological, neonatal and extra-genital infections. However, no versatile genetic tools are currently available to study the pathogenicity of this ...

    Authors: S. Pereyre, C. Bénard, C. Brès, C. Le Roy, J. P. Mauxion, F. Rideau, P. Sirand-Pugnet, B. Henrich and C. Bébéar

    Citation: BMC Genomics 2018 19:525

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  11. Content type: Research article

    Streptomyces species produce a vast diversity of secondary metabolites of clinical and biotechnological importance, in particular antibiotics. Recent developments in metabolic engineering, synthetic and systems b...

    Authors: Adam Amara, Eriko Takano and Rainer Breitling

    Citation: BMC Genomics 2018 19:519

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  12. Content type: Methodology article

    Cronobacter species are associated with severe foodborne infections in neonates and infants, with particular pathovars associated with specific clinical presentations. However, before 2008 the genus was regarded ...

    Authors: Qingyan Guo, Jielin Yang, S. J. Forsythe, Yuan Jiang, Wei Han, Yuping He and Bing Niu

    Citation: BMC Genomics 2018 19:506

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  13. Content type: Research article

    In streptococci of the mitis group, competence for natural transformation is a transient physiological state triggered by competence stimulating peptides (CSPs). Although low transformation yields and the abse...

    Authors: G. Salvadori, R. Junges, H. A. Åmdal, T. Chen, D. A. Morrison and F. C. Petersen

    Citation: BMC Genomics 2018 19:453

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  14. Content type: Research article

    Cyanobacteria of the genus Nostoc are capable of forming symbioses with a wide range of organism, including a diverse assemblage of cyanolichens. Only certain lineages of Nostoc appear to be able to form a close,...

    Authors: Andrey N. Gagunashvili and Ólafur S. Andrésson

    Citation: BMC Genomics 2018 19:434

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  15. Content type: Research article

    Thinning supplies of natural resources increase attention to sustainable microbial production of bio-based fuels. The strain Clostridium beijerinckii NRRL B-598 is a relatively well-described butanol producer reg...

    Authors: Karel Sedlar, Pavlina Koscova, Maryna Vasylkivska, Barbora Branska, Jan Kolek, Kristyna Kupkova, Petra Patakova and Ivo Provaznik

    Citation: BMC Genomics 2018 19:415

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  16. Content type: Research article

    Type strains of the genus Porphyrobacter belonging to the family Erythrobacteraceae and the class Alphaproteobacteria have been isolated from various environments, such as swimming pools, lake water and hot sprin...

    Authors: Lin Xu, Yue-Hong Wu, Peng Zhou, Hong Cheng, Qian Liu and Xue-Wei Xu

    Citation: BMC Genomics 2018 19:385

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  17. Content type: Research article

    Streptococcus salivarius is an abundant isolate of the human oral microbiota. Since both pH and glucose availability fluctuate frequently in the oral cavity, the goal of this study was to investigate regulation b...

    Authors: Jianing Geng, Szu-Chuan Huang, Yueh-Ying Chen, Cheng-Hsun Chiu, Songnian Hu and Yi-Ywan M. Chen

    Citation: BMC Genomics 2018 19:386

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  18. Content type: Research article

    The increasing spectrum of multidrug-resistant bacteria is a major global public health concern, necessitating discovery of novel antimicrobial agents. Here, members of the genus Bacillus are investigated as a po...

    Authors: Ghofran Othoum, Salim Bougouffa, Rozaimi Razali, Ameerah Bokhari, Soha Alamoudi, André Antunes, Xin Gao, Robert Hoehndorf, Stefan T. Arold, Takashi Gojobori, Heribert Hirt, Ivan Mijakovic, Vladimir B. Bajic, Feras F. Lafi and Magbubah Essack

    Citation: BMC Genomics 2018 19:382

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  19. Content type: Research article

    Drug resistance in Mycobacterium tuberculosis (MTB) is one of the major challenges in tuberculosis (TB) treatment. However, known mutations cannot explain all of the cases of resistance and little research has fo...

    Authors: Xi Zeng, Jamie Sui-Lam Kwok, Kevin Yi Yang, Kenneth Siu-Sing Leung, Mai Shi, Zhiyuan Yang, Wing-Cheong Yam and Stephen Kwok-Wing Tsui

    Citation: BMC Genomics 2018 19:365

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  20. Content type: Research article

    Recent experimental evidence showed that lactobacilli could be used as potential therapeutic agents for hyperammonemia. However, lack of understanding on how lactobacilli reduce blood ammonia levels limits app...

    Authors: Parul Singh, Hea-Jong Chung, In-Ah Lee, Roshan D’Souza, Hyeon-Jin Kim and Seong-Tshool Hong

    Citation: BMC Genomics 2018 19:292

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  21. Content type: Research article

    Bacterial taxonomy aims to classify bacteria based on true evolutionary events and relies on a polyphasic approach that includes phenotypic, genotypic and chemotaxonomic analyses. Until now, complete genomes a...

    Authors: Raffael C. Inglin, Leo Meile and Marc J. A. Stevens

    Citation: BMC Genomics 2018 19:284

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  22. Content type: Research article

    In shotgun metagenomics, microbial communities are studied through direct sequencing of DNA without any prior cultivation. By comparing gene abundances estimated from the generated sequencing reads, functional...

    Authors: Mariana Buongermino Pereira, Mikael Wallroth, Viktor Jonsson and Erik Kristiansson

    Citation: BMC Genomics 2018 19:274

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  23. Content type: Research article

    Species of the genus Halomonas are salt-tolerant organisms that have a versatile metabolism and can degrade a variety of xenobiotic compounds, utilizing them as their sole carbon source. In this study, we examine...

    Authors: Ana Florencia Gasperotti, María Victoria Revuelta, Claudia Alicia Studdert and María Karina Herrera Seitz

    Citation: BMC Genomics 2018 19:266

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    The Correction to this article has been published in BMC Genomics 2018 19:442

  24. Content type: Research article

    Many cyanobacteria are capable of fixing atmospheric nitrogen, playing a crucial role in biogeochemical cycling. Little is known about freshwater unicellular cyanobacteria Synechococcus spp. at the genomic level,...

    Authors: Andrea Di Cesare, Pedro J. Cabello-Yeves, Nathan A. M. Chrismas, Patricia Sánchez-Baracaldo, Michaela M. Salcher and Cristiana Callieri

    Citation: BMC Genomics 2018 19:259

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  25. Content type: Research article

    Coxiella burnetii is a Gram-negative gammaproteobacterium and zoonotic agent of Q fever. C. burnetii’s genome contains an abundance of pseudogenes and numerous selfish genetic elements. MITEs (miniature inverted-...

    Authors: Shaun Wachter, Rahul Raghavan, Jenny Wachter and Michael F. Minnick

    Citation: BMC Genomics 2018 19:247

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  26. Content type: Research article

    There is a worldwide interest for sustainable and environmentally-friendly ways to produce fuels and chemicals from renewable resources. Among them, the production of acetone, butanol and ethanol (ABE) or Isop...

    Authors: Hadrien Máté de Gérando, François Wasels, Angélique Bisson, Benjamin Clement, Frédérique Bidard, Etienne Jourdier, Ana María López-Contreras and Nicolas Lopes Ferreira

    Citation: BMC Genomics 2018 19:242

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    The Correction to this article has been published in BMC Genomics 2018 19:423

  27. Content type: Research article

    Strains of Lactobacillus paracasei are present in many diverse environments, including dairy and plant materials and the intestinal tracts of humans and animals. Their adaptation to various niches is correlated t...

    Authors: Ewelina Stefanovic and Olivia McAuliffe

    Citation: BMC Genomics 2018 19:205

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  28. Content type: Research article

    Neisseria gonorrhoeae causes gonorrhoea, the second most commonly notified sexually transmitted infection in Australia. One of the highest notification rates of gonorrhoea is found in the remote regions of Wester...

    Authors: Barakat A. Al Suwayyid, Geoffrey W. Coombs, David J. Speers, Julie Pearson, Michael J. Wise and Charlene M. Kahler

    Citation: BMC Genomics 2018 19:165

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  29. Content type: Research article

    Our previous comparative genomic analysis of Staphylococcus equorum KS1039 with five S. equorum strains illuminated the genomic basis of its safety and salt tolerance. However, a comprehensive picture of the cell...

    Authors: Jong-Hoon Lee, Sojeong Heo and Do-Won Jeong

    Citation: BMC Genomics 2018 19:136

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  30. Content type: Research article

    Rhizobial symbionts belong to the classes Alphaproteobacteria and Betaproteobacteria (called “alpha” and “beta”-rhizobia). Most knowledge on the genetic basis of symbiosis is based on model strains belonging t...

    Authors: Agnieszka Klonowska, Rémy Melkonian, Lucie Miché, Pierre Tisseyre and Lionel Moulin

    Citation: BMC Genomics 2018 19:105

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  31. Content type: Research article

    The human pathogen Corynebacterium diphtheriae is the causative agent of diphtheria. In the 1990s a large diphtheria outbreak in Eastern Europe was caused by the strain C. diphtheriae NCTC 13129. Although the gen...

    Authors: Manuel Wittchen, Tobias Busche, Andrew H. Gaspar, Ju Huck Lee, Hung Ton-That, Jörn Kalinowski and Andreas Tauch

    Citation: BMC Genomics 2018 19:82

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  32. Content type: Research article

    Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes...

    Authors: Luis Acuña-Amador, Aline Primot, Edouard Cadieu, Alain Roulet and Frédérique Barloy-Hubler

    Citation: BMC Genomics 2018 19:54

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  33. Content type: Research article

    The protean chemical properties of mercury have long made it attractive for diverse applications, but its toxicity requires great care in its use, disposal, and recycling. Mercury occurs in multiple chemical f...

    Authors: Stephen P. LaVoie and Anne O. Summers

    Citation: BMC Genomics 2018 19:52

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    The Correction to this article has been published in BMC Genomics 2018 19:268

  34. Content type: Research article

    Among naturally occurring small molecules, tRNA-derived cyclodipeptides are a class that have attracted attention for their diverse and desirable biological activities. However, no tools are available to link ...

    Authors: Michael A. Skinnider, Chad W. Johnston, Nishanth J. Merwin, Chris A. Dejong and Nathan A. Magarvey

    Citation: BMC Genomics 2018 19:45

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  35. Content type: Software

    Expression screening of environmental DNA (eDNA) libraries is a popular approach for the identification and characterization of novel microbial enzymes with promising biotechnological properties. In such “func...

    Authors: Matteo Chiara, Antonio Placido, Ernesto Picardi, Luigi Ruggiero Ceci, David Stephen Horner and Graziano Pesole

    Citation: BMC Genomics 2018 19:44

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  36. Content type: Research article

    Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe r...

    Authors: Silvia Arboleya, Francesca Bottacini, Mary O’Connell-Motherway, C. Anthony Ryan, R. Paul Ross, Douwe van Sinderen and Catherine Stanton

    Citation: BMC Genomics 2018 19:33

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  37. Content type: Research article

    The acetic acid bacterium Gluconobacter oxydans 621H is characterized by its exceptional ability to incompletely oxidize a great variety of carbohydrates in the periplasm. The metabolism of this α-proteobacterium...

    Authors: Angela Kranz, Tobias Busche, Alexander Vogel, Björn Usadel, Jörn Kalinowski, Michael Bott and Tino Polen

    Citation: BMC Genomics 2018 19:24

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  38. Content type: Research article

    Due to the predominant usage of short-read sequencing to date, most bacterial genome sequences reported in the last years remain at the draft level. This precludes certain types of analyses, such as the in-dep...

    Authors: Friedhelm Pfeiffer, Maria-Antonia Zamora-Lagos, Martin Blettinger, Assa Yeroslaviz, Andreas Dahl, Stephan Gruber and Bianca H. Habermann

    Citation: BMC Genomics 2018 19:20

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  39. Content type: Research article

    Xanthomonas citri, a causal agent of citrus canker, has been a well-studied model system due to recent availability of whole genome sequences of multiple strains from different geographical regions. Major limitat...

    Authors: Alberto M. Gochez, Jose C. Huguet-Tapia, Gerald V. Minsavage, Deepak Shantaraj, Neha Jalan, Annett Strauß, Thomas Lahaye, Nian Wang, Blanca I. Canteros, Jeffrey B. Jones and Neha Potnis

    Citation: BMC Genomics 2018 19:16

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  40. Content type: Research article

    In recent years, the idea of a highly immunogenic protein-based vaccine to combat Streptococcus pneumoniae and its severe invasive infectious diseases has gained considerable interest. However, the target protein...

    Authors: Gustavo Gámez, Andrés Castro, Alejandro Gómez-Mejia, Mauricio Gallego, Alejandro Bedoya, Mauricio Camargo and Sven Hammerschmidt

    Citation: BMC Genomics 2018 19:10

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  41. Content type: Research article

    Bovine tuberculosis (bTB) poses serious risks to animal welfare and economy, as well as to public health as a zoonosis. Its etiological agent, Mycobacterium bovis, belongs to the Mycobacterium tuberculosis comple...

    Authors: Moira Lasserre, Pablo Fresia, Gonzalo Greif, Gregorio Iraola, Miguel Castro-Ramos, Arturo Juambeltz, Álvaro Nuñez, Hugo Naya, Carlos Robello and Luisa Berná

    Citation: BMC Genomics 2018 19:2

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  42. Content type: Research article

    Bifidobacterium breve represents a common member of the infant gut microbiota and its presence in the gut has been associated with host well being. For this reason it is relevant to in...

    Authors: Francesca Bottacini, Aldert Zomer, Christian Milani, Chiara Ferrario, Gabriele Andrea Lugli, Muireann Egan, Marco Ventura and Douwe van Sinderen

    Citation: BMC Genomics 2017 18:991

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  43. Content type: Research article

    Brevibacterium strains are widely used for the manufacturing of surface-ripened cheeses, contributing to the breakdown of lipids and proteins and producing volatile sulfur compounds an...

    Authors: Nguyen-Phuong Pham, Séverine Layec, Eric Dugat-Bony, Marie Vidal, Françoise Irlinger and Christophe Monnet

    Citation: BMC Genomics 2017 18:955

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  44. Content type: Research article

    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

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  45. Content type: Methodology article

    Microbiome/host interactions describe characteristics that affect the host's health. Shotgun metagenomics includes sequencing a random subset of the microbiome to analyze its taxonomic and metabolic potential....

    Authors: Bhavya Papudeshi, J. Matthew Haggerty, Michael Doane, Megan M. Morris, Kevin Walsh, Douglas T. Beattie, Dnyanada Pande, Parisa Zaeri, Genivaldo G. Z. Silva, Fabiano Thompson, Robert A. Edwards and Elizabeth A. Dinsdale

    Citation: BMC Genomics 2017 18:915

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  46. Content type: Research article

    Household contacts of cholera patients have a 100 times higher risk of developing a cholera infection than the general population. To compare the genetic relatedness of clinical and water source Vibrio cholerae i...

    Authors: Christine Marie George, Mahamud Rashid, Mathieu Almeida, K. M. Saif-Ur-Rahman, Shirajum Monira, Md. Sazzadul Islam Bhuyian, Khaled Hasan, Toslim T. Mahmud, Shan Li, Jessica Brubaker, Jamie Perin, Zillur Rahman, Munshi Mustafiz, David A. Sack, R. Bradley Sack, Munirul Alam…

    Citation: BMC Genomics 2017 18:903

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