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Items: 1 to 20 of 65


A Comparison of Shallow and Deep Learning Methods for Predicting Cognitive Performance of Stroke Patients From MRI Lesion Images.

Chauhan S, Vig L, De Filippo De Grazia M, Corbetta M, Ahmad S, Zorzi M.

Front Neuroinform. 2019 Jul 31;13:53. doi: 10.3389/fninf.2019.00053. eCollection 2019.


Enabling full-length evolutionary profiles based deep convolutional neural network for predicting DNA-binding proteins from sequence.

Chauhan S, Ahmad S.

Proteins. 2019 Jun 22. doi: 10.1002/prot.25763. [Epub ahead of print]


ECG anomaly class identification using LSTM and error profile modeling.

Chauhan S, Vig L, Ahmad S.

Comput Biol Med. 2019 Jun;109:14-21. doi: 10.1016/j.compbiomed.2019.04.009. Epub 2019 Apr 16.


APBioNet's annual International Conference on Bioinformatics (InCoB) returns to India in 2018.

Ahmad S, Gromiha MM, Raghava GPS, Schönbach C, Ranganathan S.

BMC Genomics. 2019 Apr 18;19(Suppl 9):266. doi: 10.1186/s12864-019-5582-8.


Deciphering RNA-Recognition Patterns of Intrinsically Disordered Proteins.

Srivastava A, Ahmad S, Gromiha MM.

Int J Mol Sci. 2018 May 29;19(6). pii: E1595. doi: 10.3390/ijms19061595.


Integrating sequence and gene expression information predicts genome-wide DNA-binding proteins and suggests a cooperative mechanism.

Ahmad S, Prathipati P, Tripathi LP, Chen YA, Arya A, Murakami Y, Mizuguchi K.

Nucleic Acids Res. 2018 Jan 9;46(1):54-70. doi: 10.1093/nar/gkx1166.


Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences.

Andrabi M, Hutchins AP, Miranda-Saavedra D, Kono H, Nussinov R, Mizuguchi K, Ahmad S.

Sci Rep. 2017 Jun 22;7(1):4071. doi: 10.1038/s41598-017-03199-6.


Improved pose and affinity predictions using different protocols tailored on the basis of data availability.

Prathipati P, Nagao C, Ahmad S, Mizuguchi K.

J Comput Aided Mol Des. 2016 Sep;30(9):817-828. Epub 2016 Oct 6.


Profiles of microRNA networks in intestinal epithelial cells in a mouse model of colitis.

Lee J, Park EJ, Yuki Y, Ahmad S, Mizuguchi K, Ishii KJ, Shimaoka M, Kiyono H.

Sci Rep. 2015 Dec 9;5:18174. doi: 10.1038/srep18174.


RNA polymerase III regulates cytosolic RNA:DNA hybrids and intracellular microRNA expression.

Koo CX, Kobiyama K, Shen YJ, LeBert N, Ahmad S, Khatoo M, Aoshi T, Gasser S, Ishii KJ.

J Biol Chem. 2015 Mar 20;290(12):7463-73. doi: 10.1074/jbc.M115.636365. Epub 2015 Jan 26.


Brefeldin A-inhibited guanine nucleotide-exchange protein 3 (BIG3) is predicted to interact with its partner through an ARM-type α-helical structure.

Chen YA, Murakami Y, Ahmad S, Yoshimaru T, Katagiri T, Mizuguchi K.

BMC Res Notes. 2014 Jul 6;7:435. doi: 10.1186/1756-0500-7-435.


Integrated pathway clusters with coherent biological themes for target prioritisation.

Chen YA, Tripathi LP, Dessailly BH, Nyström-Persson J, Ahmad S, Mizuguchi K.

PLoS One. 2014 Jun 11;9(6):e99030. doi: 10.1371/journal.pone.0099030. eCollection 2014.


Conformational changes in DNA-binding proteins: relationships with precomplex features and contributions to specificity and stability.

Andrabi M, Mizuguchi K, Ahmad S.

Proteins. 2014 May;82(5):841-57. doi: 10.1002/prot.24462. Epub 2013 Nov 22.


Deconstructing RNA: optical measurement of composition and structure.

Hobro AJ, Standley DM, Ahmad S, Smith NI.

Phys Chem Chem Phys. 2013 Aug 21;15(31):13199-208. doi: 10.1039/c3cp52406j.


Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins.

Nagarajan R, Ahmad S, Gromiha MM.

Nucleic Acids Res. 2013 Sep;41(16):7606-14. doi: 10.1093/nar/gkt544. Epub 2013 Jun 20.


Prediction and experimental validation of a putative non-consensus binding site for transcription factor STAT3 in serum amyloid A gene promoter.

Tiwari P, Tripathi LP, Nishikawa-Matsumura T, Ahmad S, Song SN, Isobe T, Mizuguchi K, Yoshizaki K.

Biochim Biophys Acta. 2013 Jun;1830(6):3650-5. doi: 10.1016/j.bbagen.2013.01.024. Epub 2013 Feb 5.


Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions.

Hutchins AP, Diez D, Takahashi Y, Ahmad S, Jauch R, Tremblay ML, Miranda-Saavedra D.

Nucleic Acids Res. 2013 Feb 1;41(4):2155-70. doi: 10.1093/nar/gks1300. Epub 2013 Jan 7.


Prediction of dinucleotide-specific RNA-binding sites in proteins.

Fernandez M, Kumagai Y, Standley DM, Sarai A, Mizuguchi K, Ahmad S.

BMC Bioinformatics. 2011;12 Suppl 13:S5. doi: 10.1186/1471-2105-12-S13-S5. Epub 2011 Nov 30.


Functional residues in proteins.

Ahmad S, Wang JY, Ahmad Z, Ahmad F.

J Amino Acids. 2011;2011:606354. doi: 10.4061/2011/606354. Epub 2011 Nov 3. No abstract available.


Partner-aware prediction of interacting residues in protein-protein complexes from sequence data.

Ahmad S, Mizuguchi K.

PLoS One. 2011;6(12):e29104. doi: 10.1371/journal.pone.0029104. Epub 2011 Dec 14.

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