István Albert, Bioinformatics, Penn State

Publications

List of Publications

  1. Galbraith, David A; Kocher, Sarah D; Glenn, Tom; Albert, Istvan; Hunt, Greg J; Strassmann, Joan E; Queller, David C; Grozinger, Christina M;
    Testing the kinship theory of intragenomic conflict in honey bees (Apis mellifera)
    Proceedings of the National Academy of Sciences, 2016
  2. Mondal, Smarajit; Yakhnin, Alexander V; Sebastian, Aswathy; Albert, Istvan; Babitzke, Paul;
    NusA-dependent transcription termination prevents misregulation of global gene expression
    Nature Microbiology, 2016
  3. Bishop, EL; Pecchia, JA; Wilkinson, V; Albert, I; Royse, DJ;
    Effects of Spent Mushroom Compost (SMC) as an Ingredient in Phase I Compost on Production of Agaricus bisporus
    Compost Science & Utilization, 2016
  4. Hao, Ruixin; Su, Shengzhong; Wan, Yinan; Shen, Frank; Niu, Ben; Coslo, Denise M; Albert, Istvan; Han, Xing; Omiecinski, Curtis J;
    Bioinformatic analysis of microRNA networks following the activation of the constitutive androstane receptor (CAR) in mouse liver
    Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 2016
  5. Jung, Huihun; Pena-Francesch, Abdon; Saadat, Alham; Sebastian, Aswathy; Kim, Dong Hwan; Hamilton, Reginald F; Albert, Istvan; Allen, Benjamin D; Demirel, Melik C;
    Molecular tandem repeat strategy for elucidating mechanical properties of high-strength proteins
    Proceedings of the National Academy of Sciences, 2016
  6. Cattadori, Isabella M; Sebastian, Aswathy; Hao, Han; Katani, Robab; Albert, Istvan; Eilertson, Kirsten E; Kapur, Vivek; Pathak, Ashutosh; Mitchell, Susan;
    Impact of Helminth Infections and Nutritional Constraints on the Small Intestine Microbiota
    PloS one, 2016
  7. Liermann, Laura J; Albert, Istvan; Buss, Heather L; Minyard, Morgan; Brantley, Susan L;
    Relating Microbial Community Structure and Geochemistry in Deep Regolith Developed on Volcaniclastic Rock in the Luquillo Mountains, Puerto Rico
    Geomicrobiology Journal, 2015
  8. Jiang, Changtao; Xie, Cen; Li, Fei; Zhang, Limin; Nichols, Robert G; Krausz, Kristopher W; Cai, Jingwei; Qi, Yunpeng; Fang, Zhong-Ze; Takahashi, Shogo;
    Intestinal farnesoid X receptor signaling promotes nonalcoholic fatty liver disease
    The Journal of clinical investigation, 2015
  9. Cote, Rebecca; Katani, Robab; Moreau, Matthew R; Kudva, Indira T; Arthur, Terrance M; DebRoy, Chitrita; Mwangi, Michael M; Albert, Istvan; Garay, Juan Antonio Raygoza; Li, Lingling;
    Comparative analysis of super-shedder strains of Escherichia coli O157: H7 reveals distinctive genomic features and a strongly aggregative adherent phenotype on bovine rectoanal junction squamous epithelial cells
    PloS one, 2015
  10. Zhang, Limin; Nichols, Robert G; Correll, Jared; Murray, Iain A; Tanaka, Naoki; Smith, Philip B; Hubbard, Troy D; Sebastian, Aswathy; Albert, Istvan; Hatzakis, Emmanuel;
    Persistent organic pollutants modify gut microbiota-host metabolic homeostasis in mice through aryl hydrocarbon receptor activation
    Environmental Health Perspectives (Online), 2015
  11. Tang, Yi; Lu, Huaguang; Sebastian, Aswathy; Yeh, Yin-Ting; Praul, Craig A; Albert, Istvan U; Zheng, Si-Yang;
    Genomic characterization of a turkey reovirus field strain by Next-Generation Sequencing
    Infection, Genetics and Evolution, 2015
  12. Wan, Yinan; Renner, Daniel W; Albert, Istvan; Szpara, Moriah L;
    VirAmp: a galaxy-based viral genome assembly pipeline
    GigaScience, 2015
  13. Zou, Donghua; McSweeney, Colleen; Sebastian, Aswathy; Reynolds, Derrick James; Dong, Fengping; Zhou, Yijing; Deng, Dazhi; Wang, Yonggang; Liu, Long; Zhu, Jun;
    A critical role of RBM8a in proliferation and differentiation of embryonic neural progenitors
    Neural development, 2015
  14. de Bekker, Charissa; Ohm, Robin A; Loreto, Raquel G; Sebastian, Aswathy; Albert, Istvan; Merrow, Martha; Brachmann, Andreas; Hughes, David P;
    Gene expression during zombie ant biting behavior reflects the complexity underlying fungal parasitic behavioral manipulation
    BMC genomics, 2015
  15. Ooi, Jot Hui; Waddell, Amanda; Lin, Yang-Ding; Albert, Istvan; Rust, Laura T; Holden, Victoria; Cantorna, Margherita T;
    Dominant effects of the diet on the microbiome and the local and systemic immune response in mice
    PloS one, 2014
  16. Maalouf, Samar W; Liu, Wan-Sheng; Albert, Istvan; Pate, Joy L;
    Regulating life or death: potential role of microRNA in rescue of the corpus luteum
    Molecular and cellular endocrinology, 2014
  17. Pena‐Francesch, Abdon; Florez, Sergio; Jung, Huihun; Sebastian, Aswathy; Albert, Istvan; Curtis, Wayne; Demirel, Melik C;
    Proteins: Materials Fabrication from Native and Recombinant Thermoplastic Squid Proteins (Adv. Funct. Mater. 47/2014)
    Advanced Functional Materials, 2014
  18. Pena‐Francesch, Abdon; Florez, Sergio; Jung, Huihun; Sebastian, Aswathy; Albert, Istvan; Curtis, Wayne; Demirel, Melik C;
    Materials fabrication from native and recombinant thermoplastic squid proteins
    Advanced Functional Materials, 2014
  19. Varshney, Jyotika; Ooi, Jot Hui; Jayarao, Bhushan M; Albert, Istvan; Fisher, Jenny; Smith, Rhonda L; Patterson, Andrew D; Cantorna, Margherita T;
    White button mushrooms increase microbial diversity and accelerate the resolution of Citrobacter rodentium infection in mice
    The Journal of nutrition, 2013
  20. Li, Fei; Jiang, Changtao; Krausz, Kristopher W; Li, Yunfei; Albert, Istvan; Hao, Haiping; Fabre, Kristin M; Mitchell, James B; Patterson, Andrew D; Gonzalez, Frank J;
    Microbiome remodelling leads to inhibition of intestinal farnesoid X receptor signalling and decreased obesity
    Nature communications, 2013
  21. Vargas, Ignacio T; Albert, Istvan U; Regan, John M;
    Spatial distribution of bacterial communities on volumetric and planar anodes in single‐chamber air‐cathode microbial fuel cells
    Biotechnology and bioengineering, 2013
  22. Parnell, Laurence D; Lindenbaum, Pierre; Shameer, Khader; Dall'Olio, Giovanni Marco; Swan, Daniel C; Jensen, Lars Juhl; Cockell, Simon J; Pedersen, Brent S; Mangan, Mary E; Miller, Christopher A;
    BioStar: an online question & answer resource for the bioinformatics community
    PLoS Comput Biol, 2011
  23. Saadatpour, Assieh; Wang, Rui-Sheng; Liao, Aijun; Liu, Xin; Loughran, Thomas P; Albert, István; Albert, Réka;
    Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia
    PLoS Comput Biol, 2011
  24. Christensen, Claire; Albert, István; Grenfell, Bryan; Albert, Réka;
    Disease dynamics in a dynamic social network
    Physica A: Statistical Mechanics and its Applications, 2010
  25. Saadatpour, Assieh; Albert, István; Albert, Réka;
    Attractor analysis of asynchronous Boolean models of signal transduction networks
    Journal of theoretical biology, 2010
  26. Mavrich, Travis N; Jiang, Cizhong; Ioshikhes, Ilya P; Li, Xiaoyong; Venters, Bryan J; Zanton, Sara J; Tomsho, Lynn P; Qi, Ji; Glaser, Robert L; Schuster, Stephan C;
    Nucleosome organization in the Drosophila genome
    Nature, 2008
  27. Mavrich, Travis N; Ioshikhes, Ilya P; Venters, Bryan J; Jiang, Cizhong; Tomsho, Lynn P; Qi, Ji; Schuster, Stephan C; Albert, Istvan; Pugh, B Franklin;
    A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
    Genome research, 2008
  28. Albert, István; Thakar, Juilee; Li, Song; Zhang, Ranran; Albert, Réka;
    Boolean network simulations for life scientists
    Source code for biology and medicine, 2008
  29. Albert, Istvan; Wachi, Shinichiro; Jiang, Cizhong; Pugh, B Franklin;
    GeneTrack—a genomic data processing and visualization framework
    Bioinformatics, 2008
  30. Albert, Istvan; Mavrich, Travis N; Tomsho, Lynn P; Qi, Ji; Zanton, Sara J; Schuster, Stephan C; Pugh, B Franklin;
    Translational and rotational settings of H2A. Z nucleosomes across the Saccharomyces cerevisiae genome
    Nature, 2007
  31. Blankenberg, Daniel; Taylor, James; Schenck, Ian; He, Jianbin; Zhang, Yi; Ghent, Matthew; Veeraraghavan, Narayanan; Albert, Istvan; Miller, Webb; Makova, Kateryna D;
    A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly
    Genome research, 2007
  32. Ioshikhes, Ilya P; Albert, Istvan; Zanton, Sara J; Pugh, B Franklin;
    Nucleosome positions predicted through comparative genomics
    Nature genetics, 2006
  33. Chung, Wen-Yu; Albert, Reka; Albert, Istvan; Nekrutenko, Anton; Makova, Kateryna D;
    Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network
    BMC bioinformatics, 2006
  34. Giardine, Belinda; Riemer, Cathy; Hardison, Ross C; Burhans, Richard; Elnitski, Laura; Shah, Prachi; Zhang, Yi; Blankenberg, Daniel; Albert, Istvan; Taylor, James;
    Galaxy: a platform for interactive large-scale genome analysis
    Genome research, 2005
  35. Albert, Réka; Albert, István; Nakarado, Gary L;
    Structural vulnerability of the North American power grid
    Physical review E, 2004
  36. Albert, István; Albert, Réka;
    Conserved network motifs allow protein–protein interaction prediction
    Bioinformatics, 2004
  37. Racunas, Stephen A; Shah, NH; Albert, I; Fedoroff, Nina V;
    HyBrow: a prototype system for computer-aided hypothesis evaluation
    Bioinformatics, 2004
  38. Miller, Bradley N; Albert, Istvan; Lam, Shyong K; Konstan, Joseph A; Riedl, John;
    Movielens unplugged: experiences with a recommender system on four mobile devices
    People and Computers XVII—Designing for Society, 2004
  39. Miller, Bradley N; Albert, Istvan; Lam, Shyong K; Konstan, Joseph A; Riedl, John;
    MovieLens unplugged: experiences with an occasionally connected recommender system
    Proceedings of the 8th international conference on Intelligent user interfaces, 2003
  40. Cosley, Dan; Lam, Shyong K; Albert, Istvan; Konstan, Joseph A; Riedl, John;
    Is seeing believing?: how recommender system interfaces affect users' opinions
    Proceedings of the SIGCHI conference on Human factors in computing systems, 2003
  41. Miller, Bradley N; Albert, Istvan; Lam, Shyong K; Konstan, Joseph A; Riedl, John; Riedl, Joseph A Konstan John;
    Movielens unplugged: Experiences with a recommender system on four mobile devices
    In Proceedings of the 2003 Conference on Intelligent User Interfaces, 2003
  42. Rashid, Al Mamunur; Albert, Istvan; Cosley, Dan; Lam, Shyong K; McNee, Sean M; Konstan, Joseph A; Riedl, John;
    Getting to know you: learning new user preferences in recommender systems
    Proceedings of the 7th international conference on Intelligent user interfaces, 2002
  43. McNee, Sean M; Albert, Istvan; Cosley, Dan; Gopalkrishnan, Prateep; Lam, Shyong K; Rashid, Al Mamunur; Konstan, Joseph A; Riedl, John;
    On the recommending of citations for research papers
    Proceedings of the 2002 ACM conference on Computer supported cooperative work, 2002
  44. Albert, I; Tegzes, P; Albert, R; Sample, JG; Barabási, A-L; Vicsek, T; Kahng, B; Schiffer, P;
    Stick-slip fluctuations in granular drag
    Physical Review E, 2001
  45. Albert, I; Sample, JG; Morss, AJ; Rajagopalan, S; Barabási, A-L; Schiffer, P;
    Granular drag on a discrete object: Shape effects on jamming
    Physical review E, 2001
  46. Kahng, B; Albert, I; Schiffer, P; Barabási, A-L;
    Modeling relaxation and jamming in granular media
    Physical review E, 2001
  47. Schiffer, P; Albert, I; Sample, J; Barabasi, AL;
    The drag force in granular media
    Powders and grains, 2001
  48. Albert, I; Tegzes, P; Kahng, B; Albert, R; Sample, JG; Pfeifer, M; Barabasi, A-L; Vicsek, T; Schiffer, P;
    Jamming and fluctuations in granular drag
    Physical review letters, 2000
  49. Albert, István; Tegzes, Pál; Albert, Réka; Sample, John; Barabási, Albert-László; Vicsek, Tamás; Kahng, B; Schiffer, Peter;
    An experimental study of the fluctuations in granular drag
    MRS Proceedings, 2000
  50. Hornbaker, DJ; Albert, Réka; Albert, István; Barabási, Albert-Lázló; Schiffer, Peter;
    What keeps sandcastles standing?
    Nature, 1997
  51. Albert, Réka; Albert, István; Hornbaker, Daniel; Schiffer, Peter; Barabási, Albert-László;
    Maximum angle of stability in wet and dry spherical granular media
    Physical Review E, 1997
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