Cancer cells forgo translating mRNA transcribed from genes of nonspecialized tasks

Mahmoud Ahmed, Trang Minh Pham, Hyun Joon Kim, Deok Ryong Kim

FEBS Open Bio, n/a

Regulation of Cell Cycle Progression through RB Phosphorylation by Nilotinib and AT-9283 in Human Melanoma A375P Cells

Trang Minh Pham, Mahmoud Ahmed, Trang Huyen Lai, Md Entaz Bahar, Jin Seok Hwang, Rizi Firman Maulidi, Quang Nhat Ngo, Deok Ryong Kim

International Journal of Molecular Sciences, vol. 25, 2024

Editorial: Opportunities and challenges in reusing public genomics data

Mahmoud Ahmed, Deok Ryong Kim

Frontiers in Pharmacology, vol. 14, 2023

Manipulating RKIP reverses the metastatic potential of breast cancer cells

Trang Huyen Lai, Mahmoud Ahmed, Jin Seok Hwang, Md Entaz Bahar, Trang Minh Pham, Jinsung Yang, Wanil Kim, Rizi Firman Maulidi, Dong-Kun Lee, Dong-Hee Kim, Hyun Joon Kim, Deok Ryong Kim

Frontiers in Oncology, vol. 13, 2023

Validating a re-implementation of an algorithm to integrate transcriptome and ChIP-seq data

Mahmoud Ahmed, Deok Ryong Kim

PeerJ, vol. 11, 2023 Oct, pp. e16318

Maximizing the utility of public data

Mahmoud Ahmed, Hyun Joon Kim, Deok Ryong Kim

Frontiers in Genetics, vol. 14, Frontiers Media SA, 2023 Mar

Tissue-specific gene expression in obese hyperglycemic mice

Mahmoud Ahmed, Omar Elashkar, Jong Youl Lee, Eun Ae Jeong, Kyung Eun Kim, Gu Seob Roh, Deok Ryong Kim

All Life, vol. 15(1), Taylor & Francis, 2022, pp. 555-561

Disruption of cancer cell functions by task-specific drug perturbations

Mahmoud Ahmed, Deok Ryong Kim

Frontiers in Pharmacology, vol. 13, 2022

Meta-analysis of the Effect of Orlistat on The Body Mass Index in Obese Subjects

Gyeonghwa Jeong, Dongwoo Han, Mahmoud Ahmed, Deok Ryong Kim

medRxiv, Cold Spring Harbor Laboratory Press, 2022

Re-implementation of an algorithm to integrate transcriptome and ChIP-seq data

Mahmoud Ahmed, Deok Ryong Kim

bioRxiv, Cold Spring Harbor Laboratory, 2022 Nov 25

Hierarchical Regulation of Autophagy During Adipocyte Differentiation

Mahmoud Ahmed, Trang Huyen Lai, Trang Minh Pham, Sahib Zada, Omar Elashkar, Jin Seok Hwang, Deok Ryong Kim

PLoS ONE, vol. 17(1), 2022 6, pp. e0250865

LINPS: a database for cancer-cell-specific perturbations of biological networks

Mahmoud Ahmed, Deok Ryong Kim

Database, issue 2021, 2021

target: an R package to predict combined function of transcription factors

Mahmoud Ahmed, Deok Ryong Kim

F1000Research, vol. 10, 2021

A functional network model of the metastasis suppressor RKIP and its regulators in breast cancer cells

Mahmoud Ahmed, Trang Huyen Lai, Deok Ryong Kim

Cancers, vol. 13(23), 2021

A Small Fraction of Progenitors Differentiate Into Mature Adipocytes by Escaping the Constraints on the Cell Structure.

Mahmoud Ahmed, Trang Huyen Lai, Deok Ryong Kim

Frontiers in Cell and Developmental Biology, vol. 9, 2021 Sep 11

Cross talk between autophagy and oncogenic signaling pathways and implications for cancer therapy.

Sahib Zada, Jin Seok Hwang, Mahmoud Ahmed, Trang Huyen Lai, Trang Minh Pham, Omar Elashkar, Deok Ryong Kim

Biochimica et Biophysica Acta, vol. 1876(1), 2021 Apr 13, pp. 188565-188565

Transcriptional Repression of Raf Kinase Inhibitory Protein Gene by Metadherin during Cancer Progression.

Trang Huyen Lai, Mahmoud Ahmed, Jin Seok Hwang, Sahib Zada, Trang Minh Pham, Omar Elashkar, Deok Ryong Kim

International Journal of Molecular Sciences, vol. 22(6), 2021 Feb 17

Anti-cancer effect of RKIP via modulating autophagy during metastasis

Mahmoud Ahmed, Deok Ryong KIm

Prognostic and Therapeutic Applications of RKIP in Cancer, Benjamin Bonavida, Stavroula Baritaki, chapter 15, 1st ed., vol. 1, Academic Press, 2020, pp. 277-293

Integrating binding and expression data to predict transcription factors combined function

Mahmoud Ahmed, Do Sik Min, Deok Ryong Kim

BMC Genomics, vol. 21(1), 2020, p. 610

Curated gene expression dataset of differentiating 3T3-L1 adipocytes under pharmacological and genetic perturbations

Mahmoud Ahmed, Do Sik Min, Deok Ryong Kim

Adipocyte, vol. 9(1), 2020, pp. 600-608

cRegulome: an R package for accessing microRNA and transcription factor-gene expression correlations in cancer.

Mahmoud Ahmed, Deok Ryong Kim

PeerJ, vol. 7, 2019, pp. e6509

Modelling the gene expression and the DNA-binding in the 3T3-L1 differentiating adipocytes.

Mahmoud Ahmed, Deok Ryong Kim

Adipocyte, vol. 8(1), 2019, pp. 401-411

Transcriptional Regulation of Autophagy Genes via Stage-Specific Activation of CEBPB and PPARG during Adipogenesis: A Systematic Study Using Public Gene Expression and Transcription Factor Binding Datasets

Mahmoud Ahmed, Trang Huyen Lai, Jin Seok Hwang, Sahib Zada, Trang Minh Pham, Deok Ryong Kim

Cells, vol. 8(11), 2019 Sep 25

colocr: an R package for conducting co-localization analysis on fluorescence microscopy images.

Mahmoud Ahmed, Trang Huyen Lai, Deok Ryong Kim

PeerJ, vol. 7, 2019 Jun 4

Functional Linkage of RKIP to the Epithelial to Mesenchymal Transition and Autophagy during the Development of Prostate Cancer.

Mahmoud Ahmed, Trang Huyen Lai, Sahib Zada, Jin Seok Hwang, Trang Minh Pham, Miyong Yun, Deok Ryong Kim

Cancers, vol. 10(8), 2018 Jul 16

Co-Expression Network Analysis of AMPK and Autophagy Gene Products during Adipocyte Differentiation

Mahmoud Ahmed, Jin Seok Hwang, Trang Huyen Lai, Sahib Zada, Huynh Quoc Nguyen, Trang Min Pham, Miyong Yun, Deok Ryong Kim

International Journal of Molecular Sciences, vol. 19(6), 2018 May 19

pcr: an R package for quality assessment, analysis and testing of qPCR data

Mahmoud Ahmed, Deok Ryong Kim

PeerJ, vol. 6, 2018 Feb 16

Systematic characterization of autophagy-related genes during the adipocyte differentiation using public-access data.

Mahmoud Ahmed, Huynh Quoc Nguyen, Jin Seok Hwang, Sahib Zada, Trang Huyen Lai, Sang Soo Kang, Deok Ryong Kim

Oncotarget, vol. 9(21), 2018 Jan 15, pp. 15526-15541

miRCancerdb: a database for correlation analysis between microRNA and gene expression in cancer.

Mahmoud Ahmed, Huynh Nguyen, Trang Lai, Deok Ryong Kim

BMC Research Notes, vol. 11(1), 2018 Jan 7, pp. 103-103