István Albert, Bioinformatics, Penn State

Publications

List of Publications

  1. Horton, William J; Jensen, Matthew; Sebastian, Aswathy; Praul, Craig A; Albert, Istvan; Bartell, Paul A;
    Transcriptome Analyses of Heart and Liver Reveal Novel Pathways for Regulating Songbird Migration
    Scientific reports, 2019
  2. Liang, Xiaoying; Hart, Kevin J; Dong, Gang; Siddiqui, Faiza A; Sebastian, Aswathy; Li, Xiaolian; Albert, Istvan; Miao, Jun; Lindner, Scott E; Cui, Liwang;
    Puf3 participates in ribosomal biogenesis in malaria parasites
    J Cell Sci, 2018
  3. Palchak, Kay; Chothe, Shubhada K; Sebastian, Aswathy; Nissly, Ruth H; Barry, Rhiannon; Albert, Istvan; Jayarao, Bhushan M; Kuchipudi, Suresh V;
    Whole-Genome Sequence of Infectious Pancreatic Necrosis Virus Isolated from Farmed Brook Trout (Salvelinus fontinalis) in Pennsylvania
    Genome Announc., 2018
  4. Chothe, Shubhada K; Sebastian, Aswathy; Thomas, Asha; Nissly, Ruth; Byukusenge, Maurice; Wolfgang, David; Mor, Sunil Kumar; Goyal, Sagar; Albert, Istvan; Jayarao, Bhushan;
    Whole-Genome Sequences of 18 Bovine Alphaherpesvirus 1 Field Isolates from Pennsylvania and Minnesota
    Genome Announc., 2018
  5. Shabbir, M Zubair; Nissly, Ruth Helmus; Ahad, Abdul; Rabbani, Masood; Chothe, Shubhada K; Sebastian, Aswathy; Albert, Istvan; Jayarao, Bhushan M; Kuchipudi, Suresh V;
    Complete genome sequences of three related avian avulavirus 1 isolates from poultry farmers in Pakistan
    Genome Announc., 2018
  6. Silva, Constanza P; Horton, William J; Caruso, Michael J; Sebastian, Aswathy; Klein, Laura C; Albert, Istvan; Kamens, Helen M;
    The influence of adolescent nicotine exposure on ethanol intake and brain gene expression
    PloS one, 2018
  7. Chothe, Shubhada K; Sebastian, Aswathy; Thomas, Asha; Nissly, Ruth H; Wolfgang, David; Byukusenge, Maurice; Mor, Sunil Kumar; Goyal, Sagar M; Albert, Istvan; Tewari, Deepanker;
    Whole-genome sequence analysis reveals unique SNP profiles to distinguish vaccine and wild-type strains of bovine herpesvirus-1 (BoHV-1)
    Virology, 2018
  8. Painter, Heather J; Chung, Neo Christopher; Sebastian, Aswathy; Albert, Istvan; Storey, John D; Llinás, Manuel;
    Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development
    Nature communications, 2018
  9. Niu, Ben; Coslo, Denise M; Bataille, Alain R; Albert, Istvan; Pugh, B Franklin; Omiecinski, Curtis J;
    In vivo genome-wide binding interactions of mouse and human constitutive androstane receptors reveal novel gene targets
    Nucleic acids research, 2018
  10. Wan, Yuan; Cheng, Gong; Liu, Xin; Hao, Si-Jie; Nisic, Merisa; Zhu, Chuan-Dong; Xia, Yi-Qiu; Li, Wen-Qing; Wang, Zhi-Gang; Zhang, Wen-Long;
    Rapid magnetic isolation of extracellular vesicles via lipid-based nanoprobes
    Nature biomedical engineering, 2017
  11. Huang, Kuan-Hsun; Nichols, Robert G; Sebastian, Aswathy; Albert, István; Patterson, Andrew D; Ross, A Catharine;
    Gut microbiota increased by omega-3 fatty acids is negatively correlated with hepatic lipid metabolism-associated genes in mice with high carbohydrate diet-induced steatosis
    The FASEB Journal, 2017
  12. 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
  13. Mondal, Smarajit; Yakhnin, Alexander V; Sebastian, Aswathy; Albert, Istvan; Babitzke, Paul;
    NusA-dependent transcription termination prevents misregulation of global gene expression
    Nature microbiology, 2016
  14. Bishop, EL; Pecchia, John Andrew; Wilkinson, V; Albert, Istvan; Royse, DJ;
    Effects of spent mushroom compost (SMC) as an ingredient in phase I compost on production of Agaricus bisporus
    Compost Science & Utilization, 2016
  15. 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
  16. 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
  17. 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
  18. Yeh, Yin-Ting; Tang, Yi; Sebastian, Aswathy; Dasgupta, Archi; Perea-Lopez, Nestor; Albert, Istvan; Lu, Huaguang; Terrones, Mauricio; Zheng, Si-Yang;
    Tunable and label-free virus enrichment for ultrasensitive virus detection using carbon nanotube arrays
    Science advances, 2016
  19. McSweeney, C; Zou, D; Sebastian, A; Albert, I; Mao, Y;
    RBM8a regulates neural progenitor proliferation.
    MOLECULAR BIOLOGY OF THE CELL, 2016
  20. 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
  21. 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
  22. 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
  23. 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, 2015
  24. 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
  25. Wan, Yinan; Renner, Daniel W; Albert, Istvan; Szpara, Moriah L;
    VirAmp: a galaxy-based viral genome assembly pipeline
    Gigascience, 2015
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. Katani, Robab; Cote, Rebecca; Moreau, Matthew R; Kudva, Indira T; Brandl, Maria T; Carter, Michelle Q; Arthur, T; DebRoy, Chitria; Mwangi, M; Albert, Istvan;
    Complete genome sequence and adherence characteristics of Escherichia coli O157: H7 isolated from super-shedder cattle
    114th American Society for Microbiology General Meeting, 2014
  33. 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
  34. 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
  35. 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
  36. 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 computational biology, 2011
  37. Waagmeester, Andra; Palidwor, Gareth; Szczesny, Pawel; Albert, Istvan; Mangan, Mary; Miller, Chris; Cockell, Simon; Lindenbaum, Pierre; Silvestre, Daniel AMM; Dall’Olio, Giovanni Marco;
    Acknowledging contributions to online expert assistance
    , 2011
  38. 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 computational biology, 2011
  39. 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
    PLOS Computational Biology (online), 2011
  40. Christensen, Claire; Albert, István; Grenfell, Bryan; Albert, Réka;
    Disease dynamics in a dynamic social network
    Physica A: Statistical Mechanics and its Applications, 2010
  41. Saadatpour, Assieh; Albert, István; Albert, Réka;
    Attractor analysis of asynchronous Boolean models of signal transduction networks
    Journal of theoretical biology, 2010
  42. 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
  43. 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
  44. Albert, István; Thakar, Juilee; Li, Song; Zhang, Ranran; Albert, Réka;
    Boolean network simulations for life scientists
    Source code for biology and medicine, 2008
  45. Albert, Istvan; Wachi, Shinichiro; Jiang, Cizhong; Pugh, B Franklin;
    GeneTrack—a genomic data processing and visualization framework
    Bioinformatics, 2008
  46. 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 Saccharomycescerevisiae genome
    Nature, 2007
  47. 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
  48. Veeraraghavan, Istvan Albert; Miller, Webb; Makova, Kateryna D; Hardison, Ross C; Nekrutenko, Anton;
    A framework for collaborative analysis of ENCODE data: Making
    , 2007
  49. Ioshikhes, Ilya P; Albert, Istvan; Zanton, Sara J; Pugh, B Franklin;
    Nucleosome positions predicted through comparative genomics
    Nature genetics, 2006
  50. 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
  51. 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
  52. Albert, Réka; Albert, István; Nakarado, Gary L;
    Structural vulnerability of the North American power grid
    Physical review E, 2004
  53. Albert, István; Albert, Réka;
    Conserved network motifs allow protein–protein interaction prediction
    Bioinformatics, 2004
  54. Racunas, Stephen A; Shah, NH; Albert, I; Fedoroff, Nina V;
    HyBrow: a prototype system for computer-aided hypothesis evaluation
    Bioinformatics, 2004
  55. 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
  56. 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
  57. 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
  58. 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
  59. 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
  60. Luo, Jiawei; Zhu, Fengrong; Milo, R; Shen-Orr, S; Itzkovitz, S; Kashtan, N; Chklovskii, D; Alon, U; Kong, D; He, J;
    Sampling Technique.
    Information Technology Journal, 2002
  61. Luo, Jiawei; Zhou, Hanqi; Milo, R; Shen-Orr, S; Itzkovitz, S; Kashtan, N; Chklovskii, D; Alon, U; Alon, U; Albert, I;
    A comprehensive analysis of protein-protein interactions in saccharomyces cerevisiae.
    Information Technology Journal, 2002
  62. Albert, Istvan;
    Drag force in dense granular media.
    , 2002
  63. Albert, Istvan; Tegzes, Pal; Albert, R; Sample, JG; Barabási, A-L; Vicsek, T; Kahng, B; Schiffer, P;
    Stick-slip fluctuations in granular drag
    Physical Review E, 2001
  64. 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
  65. Kahng, B; Albert, I; Schiffer, P; Barabási, A-L;
    Modeling relaxation and jamming in granular media
    Physical review E, 2001
  66. Schiffer, P; Albert, I; Sample, J; Barabasi, AL;
    The drag force in granular media
    Powders and grains 2001: proceedings of the fourth international conference on micromechanics of granular media, Sendai, Japan, 21–25 May 2001, 2001
  67. Albert, I; Tegzes, P; Albert, R; Sample, J; Barabasi, AL; Vicsek, T; Kahng, B; Schiffer, P;
    An Experimental Study of the Fluctuations in Granular Drag
    MATERIALS RESEARCH SOCIETY SYMPOSIUM PROCEEDINGS, 2001
  68. 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
  69. 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 Online Proceedings Library Archive, 2000
  70. Hornbaker, DJ; Albert, Réka; Albert, István; Barabási, A-L; Schiffer, Peter;
    What keeps sandcastles standing?
    Nature, 1997
  71. 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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