Publications and Presentations

PUBLICATIONS  | Peer-reviewed journal papers  

               (# = Corresponding author,    * = equal contribution)

 

Mittal AM, Singh SS, Gupta N# (2018). Sensory coding: neurons that wire together fire longer.

Current Biology. 28:R608-R610. 

Gupta N#, Swikriti Saran Singh, Stopfer M(2016). Oscillatory integration windows in neurons.

Nature Communications 7:13808. doi:10.1038/ncomms13808

Sanda P, Kee T, Gupta N, Stopfer M, Bazhenov M (2016). Classification of odorants across layers in locust olfactory pathway.

Journal of Neurophysiology.  DOI: jn.00921.2015

Murase S, Lantz C, Kim E, Gupta N, Higgins R, Stopfer M, Hoffman D, Quinlan E (2015). Matrix Metalloproteinase-9 regulates neuronal circuit development and excitability.

Molecular Neurobiology. DOI: 10.1007/s12035-015-9295-y

Kee T, Sanda P, Gupta N, Stopfer M, Bazhenov M (2015). Feed-Forward versus Feedback Inhibition in a Basic Olfactory Circuit.

PLoS Computational Biology 11:e1004531.

Gupta N#, Stopfer M# (2014). A temporal channel for information in sparse sensory coding.

Current Biology 24:2247-2256.

Bonissone S, Gupta N, Romine M, Bradshaw RA, Pevzner PA (2013). N-terminal protein processing: a comparative proteogenomic analysis.

Molecular & Cellular Proteomics 12:14–28.

Gupta N, Stopfer M (2012). Functional analysis of a higher olfactory center, the lateral horn.

Journal of Neuroscience 32:8138–8148. (Cover Article)

Gupta N, Jang Y, Mednick SC, Huber DE (2012). The road not taken: creative solutions require avoidance of high-frequency responses.

Psychological Science 23:288–294.

Gupta N, Aron AR (2011). Urges for food and money spill over into motor system excitability before action is taken.

 European Journal of Neuroscience 33:183–188. (Featured Article)

Gupta N, Bandeira N, Keich U, Pevzner PA (2011). Target-decoy approach and false discovery rate: when things may go wrong.

 Journal of the American Society for Mass Spectrometry 22:1111–1120.

Gupta N*, Bark SJ*, Lu WD, Taupenot L, O’Connor DT, Pevzner P, Hook V (2010). Mass spectrometry-based neuropeptidomics of secretory vesicles from human adrenal medullary pheochromocytoma reveals novel peptide products of prohormone processing.

Journal of Proteome Research 9:5065–5075.

Gupta N#, Hixson KK, Culley DE, Smith RD, Pevzner PA (2010). Analyzing protease specificity and detecting in vivo proteolytic events using tandem mass spectrometry.

Proteomics 10:2833–2844.

Kim S, Gupta N, Bandeira N, Pevzner PA (2009). Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra.

Molecular & Cellular Proteomics 8:53–69.

Gupta N#, Pevzner PA (2009). False discovery rates of protein identifications: a strike against the two-peptide rule.

Journal of Proteome Research 8:4173–4181. (Featured Article)

14. Kim S, Gupta N, Pevzner PA (2008). Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases.

Journal of Proteome Research 7:3354–3363.

Gupta N#, Benhamida J, Bhargava V, Goodman D, Kain E, Kerman I, Nguyen N, Ollikainen N, Rodriguez J, Wang J, Lipton MS, Romine M, Bafna V, Smith RD, Pevzner PA (2008). Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes.

Genome Research 18:1133–1142. (Highlighted in Nature Reviews Genetics)

Rodriguez J, Gupta N#, Smith RD, Pevzner PA (2008). Does trypsin cut before proline?

Journal of Proteome Research 7:300–305.

Dost B, Shlomi T, Gupta N, Ruppin E, Bafna V, Sharan R (2008). QNet: a tool for querying protein interaction networks.

Journal of Computational Biology 15:913–925.

Gupta N#,*, Tanner S*, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA (2007) Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation.

Genome Research 17:1362–1377.

Gaurav K, Gupta N, Sowdhamini R (2005). FASSM: enhanced function association in whole genome analysis using sequence and structural motifs.

In Silico Biology 5:425–438.

Gupta N#, Mangal N, Biswas S (2005). Evolution and similarity evaluation of protein structures in contact map space.

Proteins 59:196–204.

Bhaduri A, Pugalenthi G, Gupta N, Sowdhamini R (2004).  iMOT: an interactive package for the selection of spatially interacting motifs.

Nucleic Acids Research 32:W602–5.

Gupta N#, Irback A# (2004). Coupled folding-binding versus docking: a lattice model study.

Journal of Chemical Physics 120:3983–3989.

 

 

PUBLICATIONS  | Reviews, book chapters, comments (# = Corresponding author, *  = equal contribution)

Gupta N, Stopfer M (2014). Insect olfaction: a model system for neural circuit modeling.

Encyclopedia of Computational Neuroscience. Springer. (Book chapter)

Gupta N#, Stopfer M (2011). Negative results need airing too.

Nature 470:39. (Correspondence letter)

Gupta N, Stopfer M (2011). Olfactory coding: giant inhibitory neuron governs sparse odor.

Current Biology 21:R504–6. (Invited mini-review, “Dispatch”)

Gupta N, Stopfer M (2011). Insect olfactory coding and memory at multiple timescales.

Current Opinion in Neurobiology 21:768–773. (Peer-reviewed review article)

Hook V, Bark S, Gupta N, Lortie M, Lu WD, Bandeira N, Funkelstein L, Wegrzyn J, O’Connor DT, Pevzner P (2010). Neuropeptidomic components generated by proteomic functions in secretory vesicles for cell-cell communication.

The AAPS journal 12:635–645. (Peer-reviewed review article)