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22 result(s) for 'author#Ziv Bar-Joseph' within BMC

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  1. A response to Combined analysis reveals a core set of cycling genes by Y Lu, S Mahony, PV Benos, R Rosenfeld, I Simon, LL Breeden and Z Bar-Joseph. Genome Biol 2007, 8:R146.

    Authors: Lars Juhl Jensen, Ulrik de Lichtenberg, Thomas Skøt Jensen, Søren Brunak and Peer Bork
    Citation: Genome Biology 2008 9:403
  2. Latent HIV-1 reservoirs are identified as one of the major challenges to achieve HIV-1 cure. Currently available strategies are associated with wide variability in outcomes both in patients and CD4+ T cell models...

    Authors: Narasimhan J. Venkatachari, Jennifer M. Zerbato, Siddhartha Jain, Allison E. Mancini, Ansuman Chattopadhyay, Nicolas Sluis-Cremer, Ziv Bar-Joseph and Velpandi Ayyavoo
    Citation: Retrovirology 2015 12:85
  3. Regulation of meiosis and sporulation in Saccharomyces cerevisiae is a model for a highly regulated developmental process. Meiosis middle phase transcriptional regulation is governed by two transcription factors:...

    Authors: Michael Klutstein, Zahava Siegfried, Ariel Gispan, Shlomit Farkash-Amar, Guy Zinman, Ziv Bar-Joseph, Giora Simchen and Itamar Simon
    Citation: BMC Genomics 2010 11:478
  4. Modeling dynamic regulatory networks is a major challenge since much of the protein-DNA interaction data available is static. The Dynamic Regulatory Events Miner (DREM) uses a Hidden Markov Model-based approac...

    Authors: Marcel H Schulz, William E Devanny, Anthony Gitter, Shan Zhong, Jason Ernst and Ziv Bar-Joseph
    Citation: BMC Systems Biology 2012 6:104
  5. Several years after sequencing the human genome and the mouse genome, much remains to be discovered about the functions of most human and mouse genes. Computational prediction of gene function promises to help...

    Authors: Lourdes Peña-Castillo, Murat Tasan, Chad L Myers, Hyunju Lee, Trupti Joshi, Chao Zhang, Yuanfang Guan, Michele Leone, Andrea Pagnani, Wan Kyu Kim, Chase Krumpelman, Weidong Tian, Guillaume Obozinski, Yanjun Qi, Sara Mostafavi, Guan Ning Lin…
    Citation: Genome Biology 2008 9(Suppl 1):S2

    This article is part of a Supplement: Volume 9 Supplement 1

  6. Carbon catabolite repression (CCR) is critical for optimal bacterial growth, and in bacterial (and yeast) cells it leads to their selective consumption of a single substrate from a complex environment. However...

    Authors: Yi Zhou, Alexei Vazquez, Aaron Wise, Tomoko Warita, Katsuhiko Warita, Ziv Bar-Joseph and Zoltán N Oltvai
    Citation: BMC Systems Biology 2013 7:138
  7. Studies of gene regulation often utilize genome-wide predictions of transcription factor (TF) binding sites. Most existing prediction methods are based on sequence information alone, ignoring biological contex...

    Authors: Shan Zhong, Xin He and Ziv Bar-Joseph
    Citation: BMC Genomics 2013 14:796
  8. Orthologous genes are highly conserved between closely related species and biological systems often utilize the same genes across different organisms. However, while sequence similarity often implies functiona...

    Authors: Guy E Zinman, Shan Zhong and Ziv Bar-Joseph
    Citation: BMC Systems Biology 2011 5:134
  9. Obtaining quantitative predictions for cellular metabolic activities requires the identification and modeling of the physicochemical constraints that are relevant at physiological growth conditions. Molecular ...

    Authors: Alexei Vazquez, Qasim K Beg, Marcio A deMenezes, Jason Ernst, Ziv Bar-Joseph, Albert-László Barabási, László G Boros and Zoltán N Oltvai
    Citation: BMC Systems Biology 2008 2:7
  10. We develop scSTEM, single-cell STEM, a method for clustering dynamic profiles of genes in trajectories inferred from pseudotime ordering of single-cell RNA-seq (scRNA-seq) data. scSTEM uses one of several metr...

    Authors: Qi Song, Jingtao Wang and Ziv Bar-Joseph
    Citation: Genome Biology 2022 23:150
  11. A major advantage of single cell RNA-sequencing (scRNA-Seq) data is the ability to reconstruct continuous ordering and trajectories for cells. Here we present TraSig, a computational method for improving the i...

    Authors: Dongshunyi Li, Jeremy J. Velazquez, Jun Ding, Joshua Hislop, Mo R. Ebrahimkhani and Ziv Bar-Joseph
    Citation: Genome Biology 2022 23:73
  12. Fungal infections are an emerging health risk, especially those involving yeast that are resistant to antifungal agents. To understand the range of mechanisms by which yeasts can respond to anti-fungals, we co...

    Authors: Dwight Kuo, Kai Tan, Guy Zinman, Timothy Ravasi, Ziv Bar-Joseph and Trey Ideker
    Citation: Genome Biology 2010 11:R77
  13. Disease progression in the absence of therapy varies significantly in HIV-1 infected individuals. Both viral and host cellular molecules are implicated; however, the exact role of these factors and/or the mech...

    Authors: Karolina Duskova, Pruthvi Nagilla, Hai-Son Le, Priyadarshini Iyer, Anbupalam Thalamuthu, Jeremy Martinson, Ziv Bar-Joseph, William Buchanan, Charles Rinaldo and Velpandi Ayyavoo
    Citation: BMC Infectious Diseases 2013 13:250
  14. Global transcript levels throughout the cell cycle have been characterized using microarrays in several species. Early analysis of these experiments focused on individual species. More recently, a number of st...

    Authors: Yong Lu, Shaun Mahony, Panayiotis V Benos, Roni Rosenfeld, Itamar Simon, Linda L Breeden and Ziv Bar-Joseph
    Citation: Genome Biology 2007 8:R146
  15. High-throughput methods can directly detect the set of interacting proteins in model species but the results are often incomplete and exhibit high false positive and false negative rates. A number of researche...

    Authors: Yanjun Qi, Judith Klein-Seetharaman and Ziv Bar-Joseph
    Citation: BMC Bioinformatics 2007 8(Suppl 10):S6

    This article is part of a Supplement: Volume 8 Supplement 10

  16. Translating in vitro results to clinical tests is a major challenge in systems biology. Here we present a new Multi-Task learning framework which integrates thousands of cell line expression experiments to rec...

    Authors: Matthew Ruffalo, Petar Stojanov, Venkata Krishna Pillutla, Rohan Varma and Ziv Bar-Joseph
    Citation: BMC Systems Biology 2017 11:96