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  1. We have previously suggested a method for proteome wide analysis of variation at functional residues wherein we identified the set of all human genes with nonsynonymous single nucleotide variation (nsSNV) in t...

    Authors: Hayley Dingerdissen, Daniel S Weaver, Peter D Karp, Yang Pan, Vahan Simonyan and Raja Mazumder
    Citation: Biology Direct 2014 9:9
  2. Pannexin1 is ubiquitously expressed in vertebrate tissues, but the role it plays in vascular tone regulation remains unclear. We found that Pannexin1 expression level is much higher in the endothelium relative...

    Authors: Dina Gaynullina, Olga S Tarasova, Oxana O Kiryukhina, Valery I Shestopalov and Yuri Panchin
    Citation: Biology Direct 2014 9:8
  3. Cryptomonads, are a lineage of unicellular and mostly photosynthetic algae, that acquired their plastids through the “secondary” endosymbiosis of a red alga — and still retain the nuclear genome (nucleomorph) ...

    Authors: David R Smith, Serge N Vinogradov and David Hoogewijs
    Citation: Biology Direct 2014 9:7
  4. H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are essential for understanding the infection mechanism of the formidable pathogen M. tuberculosis H37Rv. Computational prediction is an imp...

    Authors: Hufeng Zhou, Shangzhi Gao, Nam Ninh Nguyen, Mengyuan Fan, Jingjing Jin, Bing Liu, Liang Zhao, Geng Xiong, Min Tan, Shijun Li and Limsoon Wong
    Citation: Biology Direct 2014 9:5
  5. For the anucleate platelet it has been unclear how well platelet transcriptomes correlate among different donors or across different RNA profiling platforms, and what the transcriptomes’ relationship is with t...

    Authors: Eric R Londin, Eleftheria Hatzimichael, Phillipe Loher, Leonard Edelstein, Chad Shaw, Kathleen Delgrosso, Paolo Fortina, Paul F Bray, Steven E McKenzie and Isidore Rigoutsos
    Citation: Biology Direct 2014 9:3
  6. A recent study argued, based on data on functional genome size of major phyla, that there is evidence life may have originated significantly prior to the formation of the Earth.

    Authors: Caren Marzban, Raju Viswanathan and Ulvi Yurtsever
    Citation: Biology Direct 2014 9:1
  7. The problem of probabilistic inference of gene content in the last common ancestor of several extant species with completely sequenced genomes is: for each gene that is conserved in all or some of the genomes,...

    Authors: Lavanya Kannan, Hua Li, Boris Rubinstein and Arcady Mushegian
    Citation: Biology Direct 2013 8:32
  8. The generation of interferon-gamma (IFN-γ) by MHC class II activated CD4+ T helper cells play a substantial contribution in the control of infections such as caused by Mycobacterium tuberculosis. In the past, num...

    Authors: Sandeep Kumar Dhanda, Pooja Vir and Gajendra PS Raghava
    Citation: Biology Direct 2013 8:30
  9. Translation elongation factors eEF1A1 and eEF1A2 are 92% identical but exhibit non-overlapping expression patterns. While the two proteins are predicted to have similar tertiary structures, it is notable that ...

    Authors: Dinesh C Soares and Catherine M Abbott
    Citation: Biology Direct 2013 8:29
  10. In the past, numerous methods have been developed for predicting antigenic regions or B-cell epitopes that can induce B-cell response. To the best of authors’ knowledge, no method has been developed for predic...

    Authors: Sudheer Gupta, Hifzur Rahman Ansari, Ankur Gautam and Gajendra PS Raghava
    Citation: Biology Direct 2013 8:27
  11. The recently discovered Pandoraviruses are by far the largest viruses known, with their 2 megabase genomes exceeding in size the genomes of numerous bacteria and archaea. Pandoraviruses show a distant relation...

    Authors: Natalya Yutin and Eugene V Koonin
    Citation: Biology Direct 2013 8:25
  12. Significant efforts have been made to address the problem of identifying short genes in prokaryotic genomes. However, most known methods are not effective in detecting short genes. Because of the limited infor...

    Authors: Sun Chen, Chun-ying Zhang and Kai Song
    Citation: Biology Direct 2013 8:23
  13. The bacterial SOS response is an elaborate program for DNA repair, cell cycle regulation and adaptive mutagenesis under stress conditions. Using sensitive sequence and structure analysis, combined with context...

    Authors: L Aravind, Swadha Anand and Lakshminarayan M Iyer
    Citation: Biology Direct 2013 8:20
  14. It is commonly assumed that a heterotrophic ancestor of the supergroup Archaeplastida/Plantae engulfed a cyanobacterium that was transformed into a primary plastid; however, it is still unclear how nuclear-enc...

    Authors: Przemysław Gagat, Andrzej Bodył and Paweł Mackiewicz
    Citation: Biology Direct 2013 8:18
  15. RNA-seq is a next generation sequencing method with a wide range of applications including single nucleotide polymorphism (SNP) detection, splice junction identification, and gene expression level measurement....

    Authors: Changhoon Lee, R Adron Harris, Jason K Wall, R Dayne Mayfield and Claus O Wilke
    Citation: Biology Direct 2013 8:16
  16. The major role of enzymatic toxins that target nucleic acids in biological conflicts at all levels has become increasingly apparent thanks in large part to the advances of comparative genomics. Typically, toxi...

    Authors: Vivek Anantharaman, Kira S Makarova, A Maxwell Burroughs, Eugene V Koonin and L Aravind
    Citation: Biology Direct 2013 8:15
  17. The PIWI module, found in the PIWI/AGO superfamily of proteins, is a critical component of several cellular pathways including germline maintenance, chromatin organization, regulation of splicing, RNA interfer...

    Authors: A Maxwell Burroughs, Lakshminarayan M Iyer and L Aravind
    Citation: Biology Direct 2013 8:13
  18. MicroRNAs (miRNAs) are non-uniformly distributed in genomes and ~30% of the miRNAs in the human genome are clustered. In this study we have focused on the imprinted miRNA cluster miR-379/miR-656 on 14q32.31 (h...

    Authors: Saurabh V Laddha, Subhashree Nayak, Deepanjan Paul, Rajasekhara Reddy, Charu Sharma, Prerana Jha, Manoj Hariharan, Anurag Agrawal, Shantanu Chowdhury, Chitra Sarkar and Arijit Mukhopadhyay
    Citation: Biology Direct 2013 8:10
  19. A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes.

    Authors: Mircea Podar, Kira S Makarova, David E Graham, Yuri I Wolf, Eugene V Koonin and Anna-Louise Reysenbach
    Citation: Biology Direct 2013 8:9
  20. Invasive cell growth and migration is usually considered a specifically metazoan phenomenon. However, common features and mechanisms of cytoskeletal rearrangements, membrane trafficking and signalling processe...

    Authors: Katarína Vaškovičová, Viktor Žárský, Daniel Rösel, Margaret Nikolič, Roberto Buccione, Fatima Cvrčková and Jan Brábek
    Citation: Biology Direct 2013 8:8
  21. The Michaelis-Menten equation, proposed a century ago, describes the kinetics of enzyme-catalyzed biochemical reactions. Since then, this equation has been used in countless, increasingly complex models of cel...

    Authors: Ed Reznik, Stefan Yohe and Daniel Segrè
    Citation: Biology Direct 2013 8:7
  22. tRNA-derived RNA fragments (tRFs) are 19mer small RNAs that associate with Argonaute (AGO) proteins in humans. However, in plants, it is unknown if tRFs bind with AGO proteins. Here, using public deep sequenci...

    Authors: Guilherme Loss-Morais, Peter M Waterhouse and Rogerio Margis
    Citation: Biology Direct 2013 8:6
  23. Twintrons represent a special intronic arrangement in which introns of two different types occupy the same gene position. Consequently, alternative splicing of these introns requires two different spliceosomes...

    Authors: Jessin Janice, Marcin Jąkalski and Wojciech Makałowski
    Citation: Biology Direct 2013 8:4
  24. Thanks to advances in next-generation technologies, genome sequences are now being generated at breadth (e.g. across environments) and depth (thousands of closely related strains, individuals or samples) unimagin...

    Authors: Cheong Xin Chan and Mark A Ragan
    Citation: Biology Direct 2013 8:3
  25. Alvinella pompejana is an annelid worm that inhabits deep-sea hydrothermal vent sites in the Pacific Ocean. Living at a depth of approximately 2500 meters, these worms experience extreme environmental conditions,...

    Authors: Thomas Holder, Claire Basquin, Judith Ebert, Nadine Randel, Didier Jollivet, Elena Conti, Gáspár Jékely and Fulvia Bono
    Citation: Biology Direct 2013 8:2
  26. Clusters of localized hypermutation in human breast cancer genomes, named “kataegis” (from the Greek for thunderstorm), are hypothesized to result from multiple cytosine deaminations catalyzed by AID/APOBEC pr...

    Authors: Artem G Lada, Alok Dhar, Robert J Boissy, Masayuki Hirano, Aleksandr A Rubel, Igor B Rogozin and Youri I Pavlov
    Citation: Biology Direct 2012 7:47
  27. Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made...

    Authors: Yuri I Wolf, Kira S Makarova, Natalya Yutin and Eugene V Koonin
    Citation: Biology Direct 2012 7:46
  28. Ethanolamine is used as an energy source by phylogenetically diverse bacteria including pathogens, by the concerted action of proteins from the eut-operon. Previous studies have revealed the presence of eutBC gen...

    Authors: Neelam Khatri, Indu Khatri, Srikrishna Subramanian and Saumya Raychaudhuri
    Citation: Biology Direct 2012 7:45
  29. High-dimensional gene expression data provide a rich source of information because they capture the expression level of genes in dynamic states that reflect the biological functioning of a cell. For this reaso...

    Authors: Frank Emmert-Streib, Shailesh Tripathi and Ricardo de Matos Simoes
    Citation: Biology Direct 2012 7:44
  30. As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computin...

    Authors: Lin Dai, Xin Gao, Yan Guo, Jingfa Xiao and Zhang Zhang
    Citation: Biology Direct 2012 7:43
  31. It has been recently discovered that transposable elements show high activity in the brain of mammals, however, the magnitude of their influence on its functioning is unclear so far. In this paper, I use flux ...

    Authors: György Abrusán
    Citation: Biology Direct 2012 7:41

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