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Items: 37

1.

Why Do Similarity Matching Objectives Lead to Hebbian/Anti-Hebbian Networks?

Pehlevan C, Sengupta AM, Chklovskii DB.

Neural Comput. 2018 Jan;30(1):84-124. doi: 10.1162/neco_a_01018. Epub 2017 Sep 28.

PMID:
28957017
2.

Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2.

Zepeda-Mendoza CJ, Mukhopadhyay S, Wong ES, Harder N, Splinter E, de Wit E, Eckersley-Maslin MA, Ried T, Eils R, Rohr K, Mills A, de Laat W, Flicek P, Sengupta AM, Spector DL.

BMC Genomics. 2015 Nov 21;16:982. doi: 10.1186/s12864-015-2137-5.

3.

First Passage Times, Lifetimes, and Relaxation Times of Unfolded Proteins.

Dai W, Sengupta AM, Levy RM.

Phys Rev Lett. 2015 Jul 24;115(4):048101. Epub 2015 Jul 21.

4.

Breaking an epigenetic chromatin switch: curious features of hysteresis in Saccharomyces cerevisiae telomeric silencing.

Nagaraj VH, Mukhopadhyay S, Dayarian A, Sengupta AM.

PLoS One. 2014 Dec 23;9(12):e113516. doi: 10.1371/journal.pone.0113516. eCollection 2014.

5.

Soluble production and function of vascular endothelial growth factor/basic fibroblast growth factor complex peptide.

Zhang Q, Lao X, Huang J, Zhu Z, Pang L, Tang Y, Song Q, Huang J, Deng J, Deng N, Yang Q, Sengupta AM, Xiong L.

Biotechnol Prog. 2015 Jan-Feb;31(1):194-203. doi: 10.1002/btpr.1997. Epub 2014 Oct 10. Erratum in: Biotechnol Prog. 2016 Mar;32(2):535.

PMID:
25271020
6.

The role of multiple marks in epigenetic silencing and the emergence of a stable bivalent chromatin state.

Mukhopadhyay S, Sengupta AM.

PLoS Comput Biol. 2013;9(7):e1003121. doi: 10.1371/journal.pcbi.1003121. Epub 2013 Jul 18.

7.

Titration and hysteresis in epigenetic chromatin silencing.

Dayarian A, Sengupta AM.

Phys Biol. 2013 Jun;10(3):036005. doi: 10.1088/1478-3975/10/3/036005. Epub 2013 Apr 16.

PMID:
23588040
8.

SLIQ: simple linear inequalities for efficient contig scaffolding.

Roy RS, Chen KC, Sengupta AM, Schliep A.

J Comput Biol. 2012 Oct;19(10):1162-75. doi: 10.1089/cmb.2011.0263.

PMID:
23057825
9.

Internucleosomal interactions mediated by histone tails allow distant communication in chromatin.

Kulaeva OI, Zheng G, Polikanov YS, Colasanti AV, Clauvelin N, Mukhopadhyay S, Sengupta AM, Studitsky VM, Olson WK.

J Biol Chem. 2012 Jun 8;287(24):20248-57. doi: 10.1074/jbc.M111.333104. Epub 2012 Apr 19.

10.

Theoretical analysis of the role of chromatin interactions in long-range action of enhancers and insulators.

Mukhopadhyay S, Schedl P, Studitsky VM, Sengupta AM.

Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):19919-24. doi: 10.1073/pnas.1103845108. Epub 2011 Nov 28.

11.

Statistical Mechanics of Transcription-Factor Binding Site Discovery Using Hidden Markov Models.

Mehta P, Schwab DJ, Sengupta AM.

J Stat Phys. 2011 Apr;142(6):1187-1205.

12.

Regulated antisense transcription controls expression of cell-type-specific genes in yeast.

Gelfand B, Mead J, Bruning A, Apostolopoulos N, Tadigotla V, Nagaraj V, Sengupta AM, Vershon AK.

Mol Cell Biol. 2011 Apr;31(8):1701-9. doi: 10.1128/MCB.01071-10. Epub 2011 Feb 7.

13.

Locus dependence in epigenetic chromatin silencing.

Mukhopadhyay S, Nagaraj VH, Sengupta AM.

Biosystems. 2010 Oct;102(1):49-54. doi: 10.1016/j.biosystems.2010.07.012. Epub 2010 Jul 22.

14.

SOPRA: Scaffolding algorithm for paired reads via statistical optimization.

Dayarian A, Michael TP, Sengupta AM.

BMC Bioinformatics. 2010 Jun 24;11:345. doi: 10.1186/1471-2105-11-345.

15.

OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif.

Drawid A, Gupta N, Nagaraj VH, Gélinas C, Sengupta AM.

BMC Bioinformatics. 2009 Jul 7;10:208. doi: 10.1186/1471-2105-10-208.

16.

Inheritance of epigenetic chromatin silencing.

David-Rus D, Mukhopadhyay S, Lebowitz JL, Sengupta AM.

J Theor Biol. 2009 May 7;258(1):112-20. doi: 10.1016/j.jtbi.2008.12.021. Epub 2008 Dec 31.

17.

Shape, size, and robustness: feasible regions in the parameter space of biochemical networks.

Dayarian A, Chaves M, Sontag ED, Sengupta AM.

PLoS Comput Biol. 2009 Jan;5(1):e1000256. doi: 10.1371/journal.pcbi.1000256. Epub 2009 Jan 2.

18.

Better estimation of protein-DNA interaction parameters improve prediction of functional sites.

Nagaraj VH, O'Flanagan RA, Sengupta AM.

BMC Biotechnol. 2008 Dec 23;8:94. doi: 10.1186/1472-6750-8-94.

19.

Repression of B-cell linker (BLNK) and B-cell adaptor for phosphoinositide 3-kinase (BCAP) is important for lymphocyte transformation by rel proteins.

Gupta N, Delrow J, Drawid A, Sengupta AM, Fan G, Gélinas C.

Cancer Res. 2008 Feb 1;68(3):808-14. doi: 10.1158/0008-5472.CAN-07-3169.

20.

Epigenetic chromatin silencing: bistability and front propagation.

Sedighi M, Sengupta AM.

Phys Biol. 2007 Nov 7;4(4):246-55.

21.

Quantitative modeling and data analysis of SELEX experiments.

Djordjevic M, Sengupta AM.

Phys Biol. 2005 Dec 16;3(1):13-28.

PMID:
16582458
22.

Thermodynamic and kinetic modeling of transcriptional pausing.

Tadigotla VR, O Maoiléidigh D, Sengupta AM, Epshtein V, Ebright RH, Nudler E, Ruckenstein AE.

Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4439-44. Epub 2006 Mar 13. Erratum in: Proc Natl Acad Sci U S A. 2006 May 2;103(18):7198.

23.

Stochastic evolutionary dynamics on two levels.

Traulsen A, Sengupta AM, Nowak MA.

J Theor Biol. 2005 Aug 7;235(3):393-401.

PMID:
15882701
24.

Non-additivity in protein-DNA binding.

O'Flanagan RA, Paillard G, Lavery R, Sengupta AM.

Bioinformatics. 2005 May 15;21(10):2254-63. Epub 2005 Mar 3.

PMID:
15746285
25.

Optimal path to epigenetic switching.

Roma DM, O'Flanagan RA, Ruckenstein AE, Sengupta AM, Mukhopadhyay R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Jan;71(1 Pt 1):011902. Epub 2005 Jan 11.

PMID:
15697625
26.

G-protein-coupled enzyme cascades have intrinsic properties that improve signal localization and fidelity.

Ramanathan S, Detwiler PB, Sengupta AM, Shraiman BI.

Biophys J. 2005 May;88(5):3063-71. Epub 2005 Jan 28.

27.

Repression of the yeast HO gene by the MATalpha2 and MATa1 homeodomain proteins.

Mathias JR, Hanlon SE, O'Flanagan RA, Sengupta AM, Vershon AK.

Nucleic Acids Res. 2004 Dec 14;32(22):6469-78. Print 2004.

28.

Combined analysis of expression data and transcription factor binding sites in the yeast genome.

Nagaraj VH, O'Flanagan RA, Bruning AR, Mathias JR, Vershon AK, Sengupta AM.

BMC Genomics. 2004 Aug 26;5(1):59.

29.

A biophysical approach to transcription factor binding site discovery.

Djordjevic M, Sengupta AM, Shraiman BI.

Genome Res. 2003 Nov;13(11):2381-90.

30.

Distributions of singular values for some random matrices.

Sengupta AM, Mitra PP.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1999 Sep;60(3):3389-92.

PMID:
11970154
31.

Specificity and robustness in transcription control networks.

Sengupta AM, Djordjevic M, Shraiman BI.

Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):2072-7.

32.

Communication through a diffusive medium: coherence and capacity

Moustakas AL, Baranger HU, Balents L, Sengupta AM, Simon SH.

Science. 2000 Jan 14;287(5451):287-90.

33.

Overscreened single-channel Kondo problem.

Sengupta AM, Kim YB.

Phys Rev B Condens Matter. 1996 Dec 1;54(21):14918-14921. No abstract available.

PMID:
9985536
34.

Nonequilibrium dynamics following a quench to the critical point in a semi-infinite system.

Majumdar SN, Sengupta AM.

Phys Rev Lett. 1996 Mar 25;76(13):2394-2397. No abstract available.

PMID:
10060686
35.

Non-Fermi-liquid behavior near a T=0 spin-glass transition.

Sengupta AM, Georges A.

Phys Rev B Condens Matter. 1995 Oct 1;52(14):10295-10302. No abstract available.

PMID:
9980080
36.

Solution of the Two-Impurity, Two-Channel Kondo Model.

Georges A, Sengupta AM.

Phys Rev Lett. 1995 Apr 3;74(14):2808-2811. No abstract available.

PMID:
10058023
37.

Emery-Kivelson solution of the two-channel Kondo problem.

Sengupta AM, Georges A.

Phys Rev B Condens Matter. 1994 Apr 1;49(14):10020-10022. No abstract available.

PMID:
10009815

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