Accepted/Published papers

  • Thesis
    October, 2017

  • Using Neural Networks for Reducing the Dimensions of Single-Cell RNA-Seq Data.
    Chieh Lin, Siddhartha Jain, Hannah Kim, Ziv Bar-Joseph
    Nucleic Acids Research

  • Transcriptome analyses identify key cellular factors associated with HIV-1 associated neuropathogenesis in infected men.
    Narasimhan J. Venkatachari, Siddhartha Jain, Leah Walker, Shalmali Bilavaker-Mehla, Ansuman Chattopadhyay, Ziv Bar-Joseph, Charles Rinaldo, Ann Ragin, Eric Seaberg, Andrew Levine, James Becker, Eileen Martin, Ned Sacktor, Velpandi Ayyavoo
    AIDS journal

  • Reconstructing the temporal progression of HIV-1 immune response pathways.
    Siddhartha Jain, Joel Arrais, Narasimhan J. Venkatachari, Velpandi Ayyavoo, Ziv Bar-Joseph.
    International Symposium on Molecular Biology (ISMB), 2016
    [Supporting Website, paper]

  • Thesis proposal
    April, 2016

  • Temporal transcriptional response to latency reversing agents identifies specific factors regulating HIV-1 viral transcriptional switch.
    Narasimhan J Venkatachari, Jennifer M Zerbato, Siddhartha Jain, Allison E Mancini, Ansuman Chattopadhyay, Nicolas Sluis-Cremer, Ziv Bar-Joseph, Velpandi Ayyavoo.
    Retrovirology, 2015

  • Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu
    Siddhartha Jain, Anthony Gitter, Ziv Bar-Joseph.
    PLOS Computational Biology. 10:12, 2014 and
    Society for Laboratory Automation & Screening (SLAS), 2015
    [Supporting Website, paper]

  • Large Neighborhood Search for the Dial-a-Ride Problem.
    Siddhartha Jain, Pascal Van Hentenryck.
    17th International Conference on Principles and Practices of Constraint Programming (CP), 2011 [pdf]

  • A General Nogood-Learning Framework for Pseudo-Boolean Multi-Valued SAT.
    Siddhartha Jain, Ashish Sabharwal, Meinolf Sellmann.
    25th Conference on Artificial Intelligence (AAAI), 2011 [pdf]

  • A Complete Multi-valued SAT Solver.
    Siddhartha Jain, Eoin O'Mahony, Meinolf Sellmann.
    16th International Conference on Principles and Practices of Constraint Programming (CP), 2010 [pdf]

  • Upper Bounds on the Number of Solutions of Binary Integer Programs.
    Siddhartha Jain, Serdar Kadioglu, Meinolf Sellmann.
    7th International Conference on Integration of AI and OR Techniques in Constraint Programming (CPAIOR), 2010 [pdf]