Nguyen NDH, Pham NT, Tran DT, Wei L, Malik A*, Manavalan B. xBitterT5: an explainable transformer-based framework with multimodal inputs for identifying bitter-taste peptides. J Cheminform. 2025;17(1):127. doi: 10.1186/s13321-025-01078-1.
Firoz A, Malik A, Mahajan N, Phan LT, Ali HSHM, Kim CB, Manavalan B. TP-ML: A Machine-Learning-Based Tool to Identify Threonine Proteases Using Sequence-Derived Optimal Features. IEEE Transactions on Computational Biology and Bioinformatics. 2025;22(3):984-996. doi: 10.1109/TCBBIO.2025.3540588.
Ghosh A, Rathore A, Gaba S, Kamli MR, Maigoro AY, Kwon HW, Mahajan N, Kim CB*, Malik A*. The Chinese mitten crab (Eriocheir sinensis) and its microbiome: A Review. Aquaculture. 2025;595(1):741518. doi: 10.1016/j.aquaculture.2024.741518.
Pham NT, Rakkiyapan R, Park J, Malik A*, Manavalan B*. H2Opred: A Robust and Efficient Hybrid Deep Learning Model for Predicting 2'-OM-Methylation Sites in Human RNA. Brief Bioinform. 2023 Nov 22;25(1):bbad476. doi: 10.1093/bib/bbad476.
Malik A, Kamli MR, Sabir JSM, Le PT, Kim CB, Manavalan B. RDR100: an effective computational method for identifying Kruppel-like factors. Current Bioinformatics. 2023 Oct 16;19(6):584-599. http://dx.doi.org/10.2174/1574893618666230905102407.
Choi TJ, Malik A, Han SM, Kim CB. Differences in alternative splicing events in the adaptive strategies of two Daphnia galeata genotypes induced by fish kairomones. BMC Genomics. 2024 Jul 26;25(1):725. doi: 10.1186/s12864-024-10643-1. PMID: 39060996.
Malik A, Kamli MR, Sabir JSM, Rather IA, Phan LT, Kim CB, Manavalan B. APLpred: A machine learning-based tool for accurate prediction and characterization of asparagine peptide lyases using sequence-derived optimal features. Methods. 2024 Jun 27:S1046-2023(24)00133-6. doi: 10.1016/j.ymeth.2024.05.014. Epub ahead of print. PMID: 38944134.
An HE, Mun MH, Malik A, Kim CB. Development of a two-layer machine learning model for the forensic application of legal and illegal poppy classification based on sequence data. Forensic Sci Int Genet. 2024 May 22;71:103061. doi: 10.1016/j.fsigen.2024.103061.
An H-E, Malik A*, Lee J, Mun M-H, Lee KH, Yoo HY, Kim C-B*. Comparison of Bacterial Community Composition in Gut of Chinese Mitten Crabs from Three Distinct Rivers in Korea. Fishes. 2024; 9(4):144. https://doi.org/10.3390/fishes9040144
Choi TJ, Han SM, Malik A, Kim CB. Comparative transcriptome analysis of two Daphnia galeata genotypes displaying contrasting phenotypic variation induced by fish kairomones in the same environment of the Han River, Korea. BMC Genomics. 2023 Oct 2;24(1):580. doi: 10.1186/s12864-023-09701-x.
Firoz A, Malik A*, Ali HM, Akhter Y, Manavalan B*, Kim CB*. PRR-HyPred: A two-layer hybrid framework to predict pattern recognition receptors and their families by employing sequence encoded optimal features. Int J Biol Macromol. 2023 Apr 15;234:123622. doi: 10.1016/j.ijbiomac.2023.123622.
Malik A, Shoombuatong W, Kim CB, Manavalan B. GPApred: The first computational predictor for identifying proteins with LPXTG-like motif using sequence-based optimal features. Int J Biol Macromol. 2023 Feb 28;229:529-538. doi: 10.1016/j.ijbiomac.2022.12.315.
Rasool Kamli M, Malik A, S M Sabir J, Ahmad Rather I, Kim CB. Insights into the biodegradation and heavy metal resistance potential of the genus Brevibacillus through comparative genome analyses. Gene. 2022 Dec 20;846:146853. doi: 10.1016/j.gene.2022.146853
Malik A*, Mahajan N, Dar TA, Kim CB. C10Pred: A First Machine Learning Based Tool to Predict C10 Family Cysteine Peptidases Using Sequence-Derived Features. Int J Mol Sci. 2022 Aug 23;23(17):9518. doi: 10.3390/ijms23179518.
Choi TJ, Malik A, An HE, Kim JI, Dinh Do T, Kim CB. Seasonal Diversity of Microeukaryotes in the Han River, Korea Through 18S rRNA Gene Metabarcoding. Evol Bioinform Online. 2022 Jan 25;18:11769343221074688. doi: 10.1177/11769343221074688.
Malik A, Subramaniyam S, Kim CB, Manavalan B. SortPred: The first machine learning based predictor to identify bacterial sortases and their classes using sequence-derived information. Comput Struct Biotechnol J. 2021 Dec 14;20:165-174. doi: 10.1016/j.csbj.2021.12.014.
Wei L, He W, Malik A, Su R, Cui L, Manavalan B. Computational prediction and interpretation of cell-specific replication origin sites from multiple eukaryotes by exploiting stacking framework. Brief Bioinform. 2021 Jul 20;22(4):bbaa275. doi: 10.1093/bib/bbaa275.
Kamli MR, Alzahrani NAY, Hajrah NH, Sabir JSM, Malik A*. Genome-Driven Discovery of Enzymes with Industrial Implications from the Genus Aneurinibacillus. Microorganisms. 2021 Feb 26;9(3):499. doi: 10.3390/microorganisms9030499.
Malik A*, Kim CB*. Role of Transportome in the Gills of Chinese Mitten Crabs in Response to Salinity Change: A Meta-Analysis of RNA-Seq Datasets. Biology (Basel). 2021 Jan 8;10(1):39. doi: 10.3390/biology10010039.
Malik A, Kim YR, Jang IH, Hwang S, Oh DC, Kim SB. Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium. BMC Genomics. 2020 Feb 3;21(1):118. doi: 10.1186/s12864-020-6468-5.
Malik A, Kim YR, Kim SB. Genome Mining of the Genus Streptacidiphilus for Biosynthetic and Biodegradation Potential. Genes (Basel). 2020 Oct 3;11(10):1166. doi: 10.3390/genes11101166.
Yun BR, Malik A, Kim SB. Genome based characterization of Kitasatospora sp. MMS16-BH015, a multiple heavy metal resistant soil actinobacterium with high antimicrobial potential. Gene. 2020 Apr 5;733:144379. doi: 10.1016/j.gene.2020.144379.
Roh SG, Lee C, Kim MK, Kang HJ, Kim YS, Kim MJ, Malik A, Kim SB. Nocardioides euryhalodurans sp. nov., Nocardioides seonyuensis sp. nov. and Nocardioides eburneiflavus sp. nov., isolated from soil. Int J Syst Evol Microbiol. 2020 Apr;70(4):2682-2689. doi: 10.1099/ijsem.0.004095.
Malik A, Kim SB. A comprehensive in silico analysis of sortase superfamily. J Microbiol. 2019 Jun;57(6):431-443. doi: 10.1007/s12275-019-8545-5.
Boopathi V, Subramaniyam S, Malik A, Lee G, Manavalan B, Yang DC. mACPpred: A Support Vector Machine-Based Meta-Predictor for Identification of Anticancer Peptides. Int J Mol Sci. 2019 Apr 22;20(8):1964. doi: 10.3390/ijms20081964.
Lee EJ, Jan AT, Baig MH, Ahmad K, Malik A, Rabbani G, Kim T, Lee IK, Lee YH, Park SY, Choi I. Fibromodulin and regulation of the intricate balance between myoblast differentiation to myocytes or adipocyte-like cells. FASEB J. 2018 Feb;32(2):768-781. doi: 10.1096/fj.201700665R.
Sheikh IA, Malik A, AlBasri SFM, Beg MA. In silico identification of genes involved in chronic metabolic acidosis. Life Sci. 2018 Jan 1;192:246-252. doi: 10.1016/j.lfs.2017.11.014.
Firoz A, Malik A*, Singh SK, Jha V, Ali A. Identification of hub glycogenes and their nsSNP analysis from mouse RNA-Seq data. Gene. 2015 Dec 15;574(2):235-46. doi: 10.1016/j.gene.2015.08.012.
Tayubi IA, Firoz A, Barukab OM, Malik A. Identification of hub genes and their SNP analysis in West Nile virus infection for designing therapeutic methodologies using RNA-Seq data. Genes Genom. 2015;37:679–691. https://doi.org/10.1007/s13258-015-0297-y
Malik A, Lee EJ, Jan AT, Ahmad S, Cho KH, Kim J, Choi I. Network Analysis for the Identification of Differentially Expressed Hub Genes Using Myogenin Knock-down Muscle Satellite Cells. PLoS One. 2015 Jul 22;10(7):e0133597. doi: 10.1371/journal.pone.0133597.
Pokharel S, Kamli MR, Mir BA, Malik A, Lee EJ, Choi I. Expression of Transthyretin during bovine myogenic satellite cell differentiation. In Vitro Cell Dev Biol Anim. 2014 Sep;50(8):756-65. doi: 10.1007/s11626-014-9757-y.
Firoz A, Malik A*, Singh SK, Jha V, Ali A. Comparative Analysis of Glycogene Expression in Different Mouse Tissues Using RNA-Seq Data. Int J Genomics. 2014;2014:837365. doi: 10.1155/2014/837365.
Malik A, Lee J, Lee J. Community-based network study of protein-carbohydrate interactions in plant lectins using glycan array data. PLoS One. 2014 Apr 22;9(4):e95480. doi: 10.1371/journal.pone.0095480.
Lee EJ, Malik A, Pokharel S, Ahmad S, Mir BA, Cho KH, Kim J, Kong JC, Lee DM, Chung KY, Kim SH, Choi I. Identification of genes differentially expressed in myogenin knock-down bovine muscle satellite cells during differentiation through RNA sequencing analysis. PLoS One. 2014 Mar 19;9(3):e92447. doi: 10.1371/journal.pone.0092447.
Lee EJ, Kamli MR, Pokharel S, Malik A, Tareq KM, Roouf Bhat A, Park HB, Lee YS, Kim S, Yang B, Chung KY, Choi I. Expressed sequence tags for bovine muscle satellite cells, myotube formed-cells and adipocyte-like cells. PLoS One. 2013 Nov 5;8(11):e79780. doi: 10.1371/journal.pone.0079780.
Singh SK, Malik A, Firoz A, Jha V. CDKD: a clinical database of kidney diseases. BMC Nephrol. 2012 Apr 27;13:23. doi: 10.1186/1471-2369-13-23.
Firoz A, Malik A*, Joplin KH, Ahmad Z, Jha V, Ahmad S*. Residue propensities, discrimination and binding site prediction of adenine and guanine phosphates. BMC Biochem. 2011 May 13;12:20. doi: 10.1186/1471-2091-12-20.
Malik A*, Firoz A, Jha V, Sunderasan E, Ahmad S. Modeling the three-dimensional structures of an unbound single-chain variable fragment (scFv) and its hypothetical complex with a Corynespora cassiicola toxin, cassiicolin. J Mol Model. 2010 Dec;16(12):1883-93. doi: 10.1007/s00894-010-0680-1.
Firoz A, Malik A, Afzal O, Jha V. ContPro: A web tool for calculating amino acid contact distances in protein from 3D -structures at different distance threshold. Bioinformation. 2010 Jul 6;5(2):55-7. doi: 10.6026/97320630005055.
Malik A*, Firoz A, Jha V, Ahmad S. PROCARB: A Database of Known and Modelled Carbohydrate-Binding Protein Structures with Sequence-Based Prediction Tools. Adv Bioinformatics. 2010;2010:436036. doi: 10.1155/2010/436036.
Malik A, Arif SA, Ahmad S, Sunderasan E. A molecular and in silico characterization of Hev b 4, a glycosylated latex allergen. Int J Biol Macromol. 2008 Mar 1;42(2):185-90. doi: 10.1016/j.ijbiomac.2007.11.004.
Malik A, Ahmad S. Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network. BMC Struct Biol. 2007 Jan 3;7:1. doi: 10.1186/1472-6807-7-1.
Malik A, Singh H, Andrabi M, Husain SA, Ahmad S. Databases and QSAR for cancer research. Cancer Inform. 2007 Feb 15;2:99-111.
Hakeem KR, Malik A, Vardar-Sukan F, Ozturk M. Plant bioinformatics: Decoding the phyta. 2015. Springer, New York, U. S. A. https://doi.org/10.1007/978-3-319-67156-7.
Malik A, Dar TA. The Glycome: Understanding the Diversity and Complexity of Glycobiology. 2021. Apple Academic Press, New York, U. S. A. https://doi.org/10.1201/9781003145394.
Malik A, Baig MH, Manavalan B. Protein-Carbohydrate Interactions. In: Encyclopedia of Bioinformatics and Computational Biology. Ranganathan S, Gribskov M, Nakai K, Schönbach C. (Eds); Elsevier, Oxford, UK, 2019; Volume 3, pp. 666–677. https://doi.org/10.1016/B978-0-12-809633-8.20661-4.
Malik A, Sjaugi MF. Primer on Linux. In: Bioinformatics: A Practical Handbook of Next Generation Sequencing and Its Applications. Low L, Tammi M. (Eds); World Scientific, 2017; pp. 23-47. https://doi.org/10.1142/9789813144750_0002.
Malik A, Hakeem KR. Decoding the Plastid Genome. In: Plant bioinformatics: Decoding the phyta. Hakeem KR, Malik A, Vardar-Sukan F, Ozturk M. (Eds); Springer, 2015; New York, U. S. A, 2015; pp. 279-302. https://doi.org/10.1007/978-3-319-67156-7_19.
Malik A. Genomics Resources for Plants. In: Plant Omics: Trends and Applications. Hakeem KR, Tombuloğlu H, Tombuloğlu G. (Eds); Springer, 2016; pp. 29-57. https://doi.org/10.1007/978-3-319-31703-8.
Tayubi IA, Firoz A, Malik A. Protein Misfolding and Amyloid Formation in Alzheimer’s Disease. In: Proteostasis and Chaperone Surveillance. Singh LR, Dar TA, Ahmad P. (Eds); Springer, New Delhi, 2015; pp. 119-135. https://doi.org/10.1007/978-81-322-2467-9_7.
A Malik, A Firoz, O Afzal, V Jha, I Choi. Protein Structure Databases and 3D Structure Prediction Tools. In: Advances in Protein Chemistry. Ashraf GM, Sheikh IA. (Eds); Omics Group, 2014; https://www.academia.edu/9023816/2_Advances_in_protein_chemistry.