All Stories

  1. Transcriptional Regulators Compete with Nucleosomes Post-replication

    Article • Cell, April 2016, Elsevier

    Dr Srinivas Ramachandran

  2. Nucleosome dynamics during chromatin remodelingin vivo

    Article • Nucleus, March 2016, Taylor & Francis

    Dr Srinivas Ramachandran

  3. Replicating nucleosomes

    Article • Science Advances, August 2015, American Association for the Advancement of Science

    Steven Henikoff, Dr Srinivas Ramachandran

  4. Non-canonical Bromodomain within DNA-PKcs Promotes DNA Damage Response and Radioresistance through Recognizing an IR-Induced Acetyl-Lysine on H2AX

    Article • Chemistry & Biology, July 2015, Elsevier

    Dr Srinivas Ramachandran

  5. Asymmetric nucleosomes flank promoters in the budding yeast genome

    Article • Genome Research, December 2014, Cold Spring Harbor Laboratory Press

    Dr Srinivas Ramachandran

  6. Faculty Opinions recommendation of A chromatin structure-based model accurately predicts DNA replication timing in human cells.

    Article • September 2014, F1000Research

    Dr Srinivas Ramachandran

  7. Pore Dynamics and Conductance of RyR1 Transmembrane Domain

    Article • Biophysical Journal, June 2014, Elsevier

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  8. The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo

    Article • eLife, April 2014, eLife

    Kristina Krassovsky, Steven Henikoff, Dr Srinivas Ramachandran

  9. Computational approaches to understanding protein aggregation in neurodegeneration

    Article • Journal of Molecular Cell Biology, March 2014, Oxford University Press (OUP)

    Dr Srinivas Ramachandran

  10. Nucleosomes Are Context-Specific, H2A.Z-Modulated Barriers to RNA Polymerase

    Article • Molecular Cell, March 2014, Elsevier

    Dr Srinivas Ramachandran

  11. Statistical Analysis of SHAPE-Directed RNA Secondary Structure Modeling

    Article • Biochemistry, January 2013, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  12. Structural Determinants of Skeletal Muscle Ryanodine Receptor Gating

    Article • Journal of Biological Chemistry, January 2013, American Society for Biochemistry & Molecular Biology (ASBMB)

    Dr Srinivas Ramachandran

  13. Recognition of Platinum–DNA Adducts by HMGB1a

    Article • Biochemistry, September 2012, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  14. Faculty Opinions recommendation of Dynamics and memory of heterochromatin in living cells.

    Article • June 2012, F1000Research

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  15. Faculty Opinions recommendation of Direct-coupling analysis of residue coevolution captures native contacts across many protein families.

    Article • March 2012, F1000Research

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  16. Discrete Molecular Dynamics: An Efficient And Versatile Simulation Method For Fine Protein Characterization

    Article • The Journal of Physical Chemistry B, February 2012, American Chemical Society (ACS)

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  17. Homology Modeling: Generating Structural Models to Understand Protein Function and Mechanism

    Article • January 2012, Springer Science + Business Media

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  18. Faculty Opinions recommendation of Aspartate 112 is the selectivity filter of the human voltage-gated proton channel.

    Article • December 2011, F1000Research

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  19. Faculty Opinions recommendation of Mapping intact protein isoforms in discovery mode using top-down proteomics.

    Article • December 2011, F1000Research

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  20. ATP hydrolysis at one of the two sites in ABC transporters initiates transport related conformational transitions

    Article • Biochimica et Biophysica Acta (BBA) - Biomembranes, December 2011, Elsevier

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  21. Debio 0507 primarily forms diaminocyclohexane-Pt-d(GpG) and -d(ApG) DNA adducts in HCT116 cells

    Article • Cancer Chemotherapy and Pharmacology, October 2011, Springer Science + Business Media

    Dr Srinivas Ramachandran

  22. Faculty Opinions recommendation of α-Synuclein occurs physiologically as a helically folded tetramer that resists aggregation.

    Article • September 2011, F1000Research

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  23. Flanking Bases Influence the Nature of DNA Distortion by Platinum 1,2-Intrastrand (GG) Cross-Links

    Article • PLoS ONE, August 2011, PLOS

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  24. Faculty Opinions recommendation of The crystal structure of a voltage-gated sodium channel.

    Article • July 2011, F1000Research

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  25. Gaia: automated quality assessment of protein structure models

    Article • Bioinformatics, June 2011, Oxford University Press (OUP)

    Dr Srinivas Ramachandran

  26. Faculty Opinions recommendation of Genetic selection designed to stabilize proteins uncovers a chaperone called Spy.

    Article • May 2011, F1000Research

    Dr Srinivas Ramachandran

  27. Faculty Opinions recommendation of Structure of a nanobody-stabilized active state of the β(2) adrenoceptor.

    Article • February 2011, F1000Research

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  28. Thermodynamic Stability of Histone H3 is a Necessary but not Sufficient Driving Force for its Evolutionary Conservation

    Article • Biophysical Journal, February 2011, Elsevier

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  29. Thermodynamic Stability of Histone H3 Is a Necessary but not Sufficient Driving Force for its Evolutionary Conservation

    Article • PLoS Computational Biology, January 2011, PLOS

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  30. Automated minimization of steric clashes in protein structures

    Article • Proteins Structure Function and Bioinformatics, November 2010, Wiley

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  31. Faculty Opinions recommendation of Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T.

    Article • September 2010, F1000Research

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  32. Faculty Opinions recommendation of Protein interface conservation across structure space.

    Article • June 2010, F1000Research

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  33. Abstract 3504: Debio 0507 primarily forms diaminocyclohexane-d(GpG) and -d(ApG) DNA adducts in HCT116 cells

    Article • Cancer Research, April 2010, American Association for Cancer Research (AACR)

    Dr Srinivas Ramachandran

  34. A Structural Model of the Pore-Forming Region of the Skeletal Muscle Ryanodine Receptor (RyR1)

    Article • PLoS Computational Biology, April 2009, PLOS

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  35. Structural basis for the sequence-dependent effects of platinum-DNA adducts

    Article • Nucleic Acids Research, March 2009, Oxford University Press (OUP)

    Dr Srinivas Ramachandran

  36. Solution Structure of the DNA Damage Lesion 8-Oxoguanosine from Ultraviolet Resonance Raman Spectroscopy

    Article • The Journal of Physical Chemistry A, February 2009, American Chemical Society (ACS)

    Dr Srinivas Ramachandran, Namrata Jayanth

  37. Ryanodine Receptor Pore Structure and Function

    Article • Biophysical Journal, February 2009, Elsevier

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  38. Differences in Conformation and Conformational Dynamics Between Cisplatin and Oxaliplatin DNA Adducts

    Article • January 2009, Springer Science + Business Media

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran

  39. Thermodynamics of calmodulin binding to cardiac and skeletal muscle ryanodine receptor ion channels

    Article • Proteins Structure Function and Bioinformatics, July 2008, Wiley

    Professor Nikolay V Dokholyan, Dr Srinivas Ramachandran