Publications

Goyal S, Singh P, Gupta M, Gupta S, Singh SS, Gupta AK, Gupta N.

Representations of carbon dioxide in the mosquito antennal lobe.

bioRxiv: https://www.biorxiv.org/content/10.1101/2023.03.22.533824v1 (preprint)

Singh SS, Garg S, Singh P, Gupta S, Airan A, Goyal S, Gupta N.

Plasticity and interactions in the odor responses of maxillary palps neurons in Aedes aegypti.

bioRxiv: https://www.biorxiv.org/content/10.1101/2022.10.02.510498v1 (preprint)

Mittal AM, Lin AC, Gupta N. 

Pairwise Relative Distance (PRED) is an intuitive and robust metric for assessing vector similarity and class separability. 

bioRxiv: https://doi.org/10.1101/2021.08.13.456194  (preprint)

Sun K, Ray S, Gupta N, Aldworth Z, Stopfer M (2024). 

Olfactory system structure and function in newly hatched and adult locusts. 

Scientific Reports. 14: 2608.

Singh P, Goyal S, Gupta S, Garg S, Tiwari A, Rajput V, Bates AS, Gupta AK, Gupta N (2023).

Combinatorial encoding of odors in the mosquito antennal lobe. 

Nature Communications. 14:3539.

+ Media: Twitter thread | IndiaBioscience | Biopatrika

Onkar A, Seshadri D, Rai A, Gupta AK, Gupta N, Ganesh S (2023).

Increase in brain glycogen levels ameliorates disease phenotype and rescues neurodegeneration in the Drosophila model of Huntington's disease.

Disease Models and Mechanisms.  16 (10): dmm050238. 

Keesey IW, Zhang J, Depetris-Chauvin A, Obiero GF, Gupta A, Gupta N, Knaden M, Hansson BS (2022).

Mechanisms of olfactory receptor evolution in Drosophila suzukii and the subgenus Sophophora.

iScience.  25:104212.

Gupta A, Singh SS, Mittal AM, Singh P, Goyal S, Kannan KR, Gupta AK, Gupta N (2022). 

Mosquito Olfactory Response Ensemble enables pattern discovery by curating a behavioral and electrophysiological response database. 

iScience.  25:103938.

Mittal AM, Gupta D, Singh A, Lin AC, Gupta N (2020). 

Multiple network properties overcome random connectivity to enable stereotypic sensory responses. 

Nature Communications. 11:1023. 

        + Media: TheWeek | India Alliance | Twitter thread | PTI Press Release

Dalal T, Gupta N, Haddad R (2020). 

Bilateral and unilateral odor processing and odor perception.

Communications Biology. 3:150. (Review)

Chepurwar S, Gupta A, Haddad R, Gupta N (2019).

Sequence-based prediction of olfactory receptor responses.

Chemical Senses. 44:693-703.

Singh SS, Mittal AM, Chepurwar S, Gupta N (2019).

Olfactory Systems in Insects: Similarities and Differences Between Species.

(Book Chapter) Olfactory Concepts of Insect Control - Alternative to insecticides (editor: J.F.Picimbon), pages 29-48, Springer.

Mittal AM, Singh SS, Gupta N (2018).

Sensory coding: neurons that wire together fire longer.

Current Biology. 28:R608-R610. (Dispatch).

Gupta N, Singh SS, Stopfer M (2016).

Oscillatory integration windows in neurons.

Nature Communications. 7:13808. 

Murase S, Lantz CL, Kim E, Gupta N, Higgins R, Stopfer M, Hoffman DA, Quinlan EM (2016).

Matrix Metalloproteinase-9 Regulates Neuronal Circuit Development and Excitability.

Molecular Neurobiology. 53(5): 3477-3493. PubMed.

Sanda P, Kee T, Gupta N, Stopfer M, Bazhenov M (2016).

Classification of odorants across layers in locust olfactory pathway.

Journal of Neurophysiology. 115(5):2303-16. PubMed.

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(10):e1004531. PubMed.

N. Gupta, M. Stopfer (2015).

Insect olfaction: a model system for neural circuit modeling. 

Encyclopedia of Computational Neuroscience. (Book chapter). Springer

N. Gupta, M. Stopfer (2014).

A temporal channel for information in sparse sensory coding. 

Current Biology. 24:2247-2256. PubMed  Code for classification accuracy

        + Commentary on this article by Kloppenburg and Nawrot

N. Gupta, M. Stopfer (2012).

Functional analysis of a higher olfactory center, the lateral horn.

Journal of Neuroscience. 32(24):8138–8148. PubMed 

        + Cover Article

N. Gupta, M. Stopfer (2011).

Insect olfactory coding and memory at multiple timescales.

Current Opinion in Neurobiology. 21(5):768-773. (Review). PubMed

N. Gupta, M. Stopfer (2011).

Olfactory coding: giant inhibitory neuron governs sparse odor codes.

Current Biology. 21(13):R504-6. (Dispatch). Pubmed 

Ghosh A, Cherian RC, Wagle S, Sharma P, Kannan KR, Bajpai A, Gupta N (2023).

An Unguided, Computerized Cognitive Behavioral Therapy Intervention (TreadWill) in a Lower Middle-Income Country: Pragmatic Randomized Controlled Trial.

JMIR. 25:e41005.

Ghosh A, Agnihotri J, Bhalotia S, Sati BK, Goyal L, Akash A, Tandon S, Meena K, Raj S, Azad Y, Gupta S, Gupta N (2023).

Design of serious games based on cognitive bias modification and learned helplessness paradigms for treatment of depression. 

JMIR Serious Games. 11:e37105.

Wagle S, Ghosh A, Karthic P, Ghosh A, Pervaiz T, Kapoor R, Patil K, Gupta N (2021). 

Development and testing of a game-based digital intervention for working memory training in autism spectrum disorder. 

Scientific Reports. 11:13800. 

N. Gupta, Y. Jang, S. Mednick, D.E. Huber (2012).

The road not taken: Creative solutions require avoidance of high frequency responses.

Psychological Science. 23(3):288-94. PubMed

        + Press Release

N. Gupta, A.R. Aron (2011).

Urges for food and money spill over into motor system excitability before action is taken.

European Journal of Neuroscience. 33(1):183-8. PubMed

        + Featured Article

        + Commentary on this article by Alonso-Alonso.

S. Bonissone, N. Gupta, M. Romine, R.A. Bradshaw, P.A. Pevzner (2013).

N-terminal protein processing: A comparative proteogenomic analysis.

Molecular and Cellular Proteomics. 12:14–28. PubMed

N. Gupta, M. Stopfer (2011).

Negative results need airing too. 

Nature. 470(7332):39. PubMed 

(This is a brief correspondence letter concerning the debate raised by the publication of a parapsychology paper)

N. Gupta, N. Bandeira, U. Keich, P.A. Pevzner (2011).

Target-Decoy Approach and False Discovery Rate: When Things May Go Wrong.

Journal of the American Society for Mass Spectrometry. 22(7):1111-20. PubMed

        + Published as a "Critical Insight"

N. Gupta, S. Bark, W.D. Lu, L. Taupenot, D. O'Connor, P.A. Pevzner, V. Hook (2010).

Mass Spectrometry-Based Neuropeptidomics of Human Secretory Vesicles from Adrenal Medullary Pheochromocytoma Reveals Novel Peptide Products of Prohormone Processing.

Journal of Proteome Research. 9(10):5065-75. PubMed

N. Gupta, K. K. Hixson, D. E. Culley, R. D. Smith, P. A. Pevzner (2010).

Analyzing protease specificity and detecting in vivo proteolytic events using tandem mass-spectrometry.

Proteomics. 10(15):2833-44. PubMed

V. Hook, S. Bark, N. Gupta, M. Lortie, W.D. Lu, N. Bandeira, L. Funkelstein, J. Wegrzyn, D.T. O’Connor, P.A. Pevzner (2010).

Neuropeptidomic Components Generated by Proteomic Functions in Secretory Vesicles for Neuroendocrine Cell-Cell Communication.

AAPS Journal. 12(4):635-45. (Review) PubMed

N. Gupta, P.A. Pevzner (2009).

False discovery rates of protein identifications: a strike against the two-peptide rule.

Journal of Proteome Research. 8(9):4173-81. PubMed

+ Commentary on this article by Katie Cottingham

S. Kim, N. Gupta, N. Bandeira, P.A. Pevzner (2009).  

Spectral Dictionaries: Integrating De Novo Peptide Sequencing with Database Search of Tandem Mass Spectra. 

Molecular and Cellular Proteomics. 8(1):53-69. PubMed

B. Dost, T. Shlomi, N. Gupta, E. Ruppin, V. Bafna, R. Sharan (2008). 

QNet: a tool for querying protein interaction networks. 

Journal of Computational Biology . 15(7):913-25. Pubmed.  (Also published in the proceedings of RECOMB 2007)

N. Gupta, J. Benhamida, V. Bhargava, D. Goodman, E. Kain, I. Kerman, N. Nguyen, N. Ollikainen, J. Rodriguez, J. Wang, M.S. Lipton, M. Romine, V. Bafna, R.D. Smith, P.A. Pevzner (2008).  

Comparative Proteogenomics: Combining Mass Spectrometry and Comparative Genomics to Analyze Multiple Genomes. 

Genome Research. 18:1133-1142.  PubMed

+ Included in Research Highlights of Nature Reviews Genetics 

+ Presented in a talk by Nitin Gupta at the conference ASMS 2008

+ Press releases on undergraduate participation:  UCSD | HHMI

S. Kim, N. Gupta, P.A. Pevzner (2008). 

Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. 

Journal of Proteome Research. 7(8): 3354 - 3363. PubMed

J. Rodriguez, N. Gupta, R.D. Smith and P.A. Pevzner (2008). 

Does trypsin cut before Proline? 

Journal of Proteome Research. 7(1):300-5. PubMed

N. Gupta, S. Tanner, N. Jaitly, J.N. Adkins, M. Lipton, R. Edwards, M. Romine, A. Osterman, V. Bafna, R.D. Smith, P.A. Pevzner (2007).  

Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. 

Genome Research. 17(9):1362-77. PubMed

+ Research highlight at Pacific Northwest National Labs [link].

K. Gaurav, N. Gupta and R. Sowdhamini (2005). 

FASSM: Enhanced Function Association in whole genome analysis using Sequence and Structural Motifs. 

In Silico Biology. 5:0040. PubMed

N. Gupta, N. Mangal, S. Biswas (2005). 

Evolution and similarity evaluation of protein structures in contact map space. 

Proteins: Structure, Function and Bioinformatics. 59(2):196-204. PubMed

A. Bhaduri, G. Pugalenthi, N. Gupta, R. Sowdhamini (2004). 

iMOT: an interactive package for the selection of spatially interacting motifs. 

Nucleic Acids Research. 32:W602-W605. PubMed

N. Gupta, A. Irback (2004). 

Coupled folding-binding versus docking: A lattice model study.

Journal of Chemical Physics. 120:3983-3989. PubMed

S. Kim, N. Gupta, P.A. Pevzner (2014).

Method for identifying peptides using tandem mass spectra by dynamically determining the number of peptide reconstructions required. 

US Patent 8,639,447.