Current Position of Alumini Students

Dr. Dongho-Kim : Employed in Korean pharmaceutical company, Seoul, South Korea.

Dr. Saba Haq : Assistant Professor in Capital University of Science and Technology, Islamabad, Pakistan.

Dr. Naresh Poondla : Clinical Research Scientist in Icahn School of Medicine at Mount Sinai, New York, USA.

Dr. Soumyadip Das : Management consultant at Price Waterhouse Coopers in India.

Dr. Arun Pandian Chadrasekaran : Post-doctoral Research Scientist in King Abdullah University of Science and Technology (KAUST), Saudi Arabia.

Dr. Kamini Kaushal : Post-doctoral fellowship in Heidelberg University, Germany.

Dr. Ainsley Mike Antao : Post-doctoral fellowship in Columbia University Irving Medical Center, New York, USA. 

Dr. Apoorvi Tyagi : Post doctoral fellowship in New York University, New York, USA.

Dr. Neha Sarodaya : Post-doctoral fellowship in St. Jude Children’s Research Hospital, Memphis, USA.

Dr. Janardhan Keshav Karpurkar: Post-doctoral fellowship in Boston University, Boston, USA.

Dongho- Kim, Ph.D

Publications

  1. Usp7 Regulates Glial Lineage Cell-Specific Transcription Factors by Modulating Histone H2B Monoubiquitination. Kim DH, Kim SL, Singh V*, Ramakrishna S*. International Journal of Stem Cells (IF: 2.5). 2024, 17:427-436, *(Co-Corresponding author)
  2. CRISPR/Cas9-based genome-wide screening of the deubiquitinase subfamily identifies USP3 as a protein stabilizer of REST blocking neuronal differentiation and promotes neuroblastoma tumorigenesis. Karapurkar JK, Kim MS, Colaco JC, Suresh B, Sarodaya N, Kim DH, Park CH, Hong SH, Kim KS, Ramakrishna S. Journal of Experimental Clinic and Cancer Research. 2023 42: 121. (IF: 12.65). 
  3. NFAT5 promotes in vivo development of murine melanoma metastasis. Kim DH, Kim KS*, Ramakrishna S*. Biochemical and Biophysical Research Communications, 2018, 505(3):748-754. 
  4. Transcriptional activation of LGR5 gene by an engineered CRISPR-Cas9-based system induces hepatic-specific factors. Kim DH, Kim KS*, Ramakrishna S*. Indian Journal of Biotechnology, 2018, 17:561-568. 

Patent

  1. Ramakrishna, S., Kim, K.-S, Chandrasekaran, A.P., & Kim, D.-H. (2019). Deubiquitinating enzyme gene knock-out cell line library. KR Patent, 10-2017-0,051,407.

Saba Haq, Ph.D

Publications

  1. USP19 negatively regulates p53 and promotes cervical cancer progression. Tyagi A, Karapurkar JK, Colaco JC, Sarodaya N, Antao AM, Kaushal K, Haq S, Chandrasekaran AP, Das S, Singh V, Singh V, Hong SH, Suresh B*, Kim KS*, Suresh Ramakrishna*. Molecular biotechnology (IF: 2.4). 2024, 66: 2032-2045. 
  2. CYLD destabilizes NoxO1 protein by promoting ubiquitination and regulates prostate cancer progression. Haq S*, Sarodaya N*, Karapurkar JK, Suresh B, Jo JK, Singh V, Bae YS, Kim KS and Ramakrishna S. Cancer Letters (IF: 8.67), 2022, 525: 146-157. *(Co-First author).  
  3. Genome-wide screening for deubiquitinase subfamily identifies ubiquitin-specific protease 49 as a novel regulator of odontogenesis. Kaushal K, Kim EJ, Tyagi A, Karapurkar JK, Haq S, Jung HS*, Kim KS*, Ramakrishna S*. Cell Death and Differentiation (IF: 15.8). 2022, 29: 1689-1704.
  4. Genome-scale screening of deubiquitinase subfamily identifies USP3 as a stabilizer of Cdc25A regulating cell cycle in cancer. Das S, Chandrasekaran AP, Suresh B, Haq S, Kang JH, Lee SJ, Kim J, Kim J, Lee S, Kim HH*, Kim KS* and Ramakrishna S*. Cell Death and Differentiation, 2020, 27:3004-3020.
  5. Redox regulation of DUBs and its therapeutic implications in cancer. Tyagi A, Haq S and Ramakrishna S. Redox Biology (IF: 11.79), 2021, 48: 102194. 
  6. The stability and oncogenic function of LIN28A are regulated by USP28. Haq S, Das S, Kim D, Chandrasekaran AP, Hong SH, Kim KS, Ramakrishna S. Biochim Biophy Acta Molecular Basis of Disease, 2019, 1865(3):599-610. *(Co-First author).
  7. Efficient genome editing by FACS enrichment of paired D10A Cas9 nickases coupled with fluorescent proteins. Gopalappa R, Song M, Chandrashekaran AP, Das S, Haq S and Ramakrishna. Archieves of Pharmacal research, 2018, 41(9):911-920.
  8. Scaffolding protein RanBPM and its interactions in diverse signaling pathways in health and disease. Das S, Haq S and Ramakrishna S. Discovery Medicine, 2018, 25(138):177-194.
  9. Deubiquitylating enzymes as cancer stem cell therapeutics. Haq S, Suresh B*, Ramakrishna S*. BBA reviews on Cancers, 2018, 1869: 1-10.
  10. Future application of deubiquitylating enzymes for rapid and efficient cellular reprogramming. Haq S and Ramakrishna S*. Journal of Stem Cell Research and Therapeutics, 2017, 2(6): 00083.
  11. Deubiquitylation of Deubiquitylases. Haq S and Ramakrishna S*. Open Biology, 2017, 7:170016.

Naresh Poondla, Ph.D

Publications

  1. Dual role of deubiquitinating enzyme USP19 regulates mitotic progression and tumorigenesis by stabilizing survivin. Chandrasekaran AP, Tyagi A, Poondla N, Sarodaya N, Karapurkar JK, Kaushal K, Park CH, Hong SH, Kim KS*, Ramakrishna S*. Molecular Therapy (IF: 11.45). 2022, In Press. 

  2. Chandrasekaran, A. P.,* Poondla, N.,* Ko, N.-R., Oh, S.-J., & Ramakrishna, S. (2020). YM155 sensitizes TRAIL-mediated apoptosis through cFLIP and survivin downregulation in HeLa cells. Oncology Letters. (In press)

  3. Poondla, N.,* Chandrasekaran, A. P.,* Heese, K., Kim, K.-S., & Ramakrishna, S. (2019). CRISPR-mediated upregulation of DR5 and downregulation of cFLIP synergistically sensitize HeLa cells to TRAIL-mediated apoptosis. Biochemical and Biophysical Research Communications, 512(1), 60–65.
  4. Poondla, N.,* Chandrasekaran, A. P.,* Kim, K.-S., & Ramakrishna, S. (2019). Deubiquitinating enzymes as cancer biomarkers: new therapeutic opportunities? BMB Reports, 52(3), 181–189.

Soumyadip Das, Ph.D

Publications

  1. USP19 negatively regulates p53 and promotes cervical cancer progression. Tyagi A, Karapurkar JK, Colaco JC, Sarodaya N, Antao AM, Kaushal K, Haq S, Chandrasekaran AP, Das S, Singh V, Singh V, Hong SH, Suresh B*, Kim KS*, Suresh Ramakrishna*. Molecular biotechnology (IF: 2.4). 2024, 66: 2032-2045
  2. Ubiquitin specific protease 7 deubiquitinates and regulates Aurora B-mediated cytokinesis. kaushal K, Antao AM, Das S, Kim SL, Birappa G, Rajkumar S, Gowda DAA, Ajaykumar CB, Singh V, Kim K*, Suresh B*, and Ramakrishna S*. BMB Reports (IF: 2.9). In press.
  3. CRISPR/Cas9-based genome-wide screening for deubiquitinase subfamily identifies USP1 regulating MAST1-driven cisplatin-resistance in cancer cells. Tyagi A, Kaushal K, Chandrasekaran AP, Sarodaya N, Das S, Park CH, Hong SH, Kim KS*, Ramakrishna S*. Theranostics (IF: 11.55). 2022, 12(13): 5949-5970. 
  4. USP48 governs cell cycle progression by regulating the protein level of Aurora B. Antao AM, Kaushal K, Das S, Singh V, Suresh B, Kim KS* and Ramakrishna S*. International journal of Molecular Science (IF: 5.9). 2021, 22: 8508.   
  5. Ubiquitin-specific protease 29 regulates Cdc25A-mediated tumorigenesis. Chandrasekaran AP, Woo SH, Sarodaya N, Rhie BH, Tyagi A, Das S, Suresh B, Ko NR, Oh SJ*, Kim KS* and Ramakrishna S*.  International journal of Molecular Science (IF: 5.9). 2021, 22: 5584. 

  6. HAUSP stabilizes Cdc25A and protects cervical cancer cells from DNA damage response. Das S, Chandrasekaran AP, Jo KS, Ko Na Re, Oh SJ*, Kim KS*, Ramakrishna S*. BBA Molecular Cell Research (IF: 4.1), 2020, 1867:118835. (First author)

  7. Genome-scale screening of deubiquitinase subfamily identifies USP3 as a stabilizer of Cdc25A regulating cell cycle in cancer. Das S*, Chandrasekaran AP*, Suresh B*, Haq S, Kang JH, Lee SJ, Kim J, Kim J, Lee S, Kim HH, Kim KS and Ramakrishna S. Cell Death and Differentiation, 2020, 27:3004-3020. *(Co-First author)

  8. Critical roles of deubiquitinating enzymes in the nervous system and neurodegenerative disorders. Das S, Ramakrishna S* and Kim KS*. Molecules and Cells, 2020, 43(3): 203-214. (First author).

  9. RanBPM: a potential therapeutic target for modulating diverse physiological disorders. Das S, Suresh B, Kim HH*, Ramakrishna S*. Drug Discovery Today, 2017, 22: 1816-1824. (First author)
  10. The stability and oncogenic function of LIN28A are regulated by USP28. Haq S*, Das S*, Kim D, Chandrasekaran AP, Hong SH, Kim KS, Ramakrishna S. Biochim Biophy Acta Molecular Basis of Disease, 2019, 1865(3):599-610. *(Co-First author)
  11. Efficient genome editing by FACS enrichment of paired D10A Cas9 nickases coupled with fluorescent proteins. Gopalappa R, Song M, Chandrashekaran AP, Das S, Haq S and Ramakrishna. Archieves of Pharmacal research, 2018, 41(9):911-920.
  12. Scaffolding protein RanBPM and its interactions in diverse signaling pathways in health and disease. Das S, Haq S and Ramakrishna S. Discovery Medicine, 2018, 25(138):177-194. (First author)
  13. Promising bio-composites of polypyrrole and chitosan: Surface protective and in vitro biocompatibility performance on 316L SS implants. A Kumar*, Suresh B, Das S, Obot I.B and Ramakrishna S*. Carbohydrate Polymers, 2017, 173:121-130.

Arun Pandian Chandrasekaran, Ph.D

Post-doctoral Researcher,                                                                                                                     

Publications

  1.  βTrCP1 promotes SLC35F2 protein ubiquitination and inhibits cancer progression in HeLa cells. Colaco JC, Chandrasekaran AP, Karapurkar JK, Birappa G, Rajkumar S, Gowda ADA, Suresh B, Lee J, Singh V, Hong SH*, Kim KS*, Ramakrishna S*. Biochemical and Biophysical Research Communications (IF: 2.5). 2023, 682: 27-38. (Co-first author). 
  2. USP19 negatively regulates p53 and promotes cervical cancer progression. Tyagi A, Karapurkar JK, Colaco JC, Sarodaya N, Antao AM, Kaushal K, Haq S, Chandrasekaran AP, Das S, Singh V, Singh V, Hong SH, Suresh B*, Kim KS*, Suresh Ramakrishna*. Molecular biotechnology (IF: 2.4). 2024, 66: 2032-2045
  3. E3 Ubiquitin ligase APC/Cdh1 regulates SLC35F2 protein turnover and inhibits cancer progression in HeLa cells. Colaco JC*, Chandrasekaran AP*, Karapurkar JK, Gowda ADA, Birappa G, Rajkumar S, Suresh B, Ko N, Hong SH, Oh SJ, Kim KS, Ramakrishna S. BBA-General Subjects. 2023, In Press. (Co-first author)
  4. The role of the CRISPR-Cas system in cancer drug development: Mechanisms of action and therapy. Chandrasekaran AP*, Karapurkar JK*, Chung HY, Ramakrishna S. Biotechnology Journal (IF: 4.67). 2022,17(7): e2100468. (Co- First author).  
  5. Dual role of deubiquitinating enzyme USP19 regulates mitotic progression and tumorigenesis by stabilizing survivin. Chandrasekaran AP*, Tyagi A*, Poondla N, Sarodaya N, Karapurkar JK, Kaushal K, Park CH, Hong SH, Kim KS*, Ramakrishna S*. Molecular Therapy (IF: 11.45). 2022, In Press. (Co-First author). 
  6. USP32 conferes cancer cell resistance to YM155 via promoting ER-associated degradation of solute carrier protein SLC35F2. Chandrasekaran AP, Kaushal K, Park CH, Kim KS and Ramakrishna S. Theranostics (IF: 11.6). 2021, 11:9752-9771. (First author).  
  7. CRISPR/Cas9-based genome-wide screening for deubiquitinase subfamily identifies USP1 regulating MAST1-driven cisplatin-resistance in cancer cells. Tyagi A, Kaushal K, Chandrasekaran AP, Sarodaya N, Das S, Park CH, Hong SH, Kim KS*, Ramakrishna S*. Theranostics (IF: 11.55). 2022, 12(13): 5949-5970. 
  8. Smart vitamin micelles as cancer nanomedicines for enhanced intracellular delivery of doxorubicin. Ko NR, Lee SJ, Chandrasekaran AP, Tyagi A, Ramakrishna S, Kim SY, Kim DW, Pack CG and Oh SJ. International Journal of Molecular Sciences (IF: 5.9). 2021, 22,20, 11298. (Co-author).
  9. Ubiquitin-specific protease 29 regulates Cdc25A-mediated tumorigenesis. Chandrasekaran AP, Woo SH, Sarodaya N, Rhie BH, Tyagi A, Das S, Suresh B, Ko NR, Oh SJ, Kim KS and Ramakrishna S.  International journal of Molecular Science (IF: 4.5). 2021, 22: 5584. (First author).
  10. Ubiquitin specific protease 29 functions as an Oncogene promoting tumorigenesis in colorectal carcinoma. Chandrasekaran AP, Suresh B, Sarodaya N, Ko NR, Oh SH, Kim KS, Ramakrishna S. Cancers (IF: 6.1). 2021, In press. (First author).
  11. Tyagi, A., Sarodaya, N., Kaushal, K., Chandrasekaran, A. P., Antao, A. M., Suresh, B., Rhie, B.-H., Kim K.-S., & Ramakrishna, S. (2020). E3 Ubiquitin Ligase APC/CCdh1 Regulation of Phenylalanine Hydroxylase Stability and Function. International Journal of Molecular Sciences, 21, 9076. (IF: 4.556). (Co-authors).
  12. Das S, Chandrasekaran AP, Jo KS, Ko Na Re, Oh SJ, Kim KS, Ramakrishna S (2020). HAUSP stabilizes Cdc25A and protects cervical cancer cells from DNA damage response. BBA Molecular Cell Research (IF: 4.1),  2020, 1867:118835. (Co-authors).
  13. Chandrasekaran, A. P.,* Poondla, N.,* Ko, N.-R., Oh, S.-J., & Ramakrishna, S. (2020). YM155 sensitizes TRAIL-mediated apoptosis through cFLIP and survivin downregulation in HeLa cells. Oncology Letters. 2020, 20:72 (*Equal co-first authors).
  14. Das, S.,* Chandrasekaran, A. P.,* Suresh, B.,* Haq, S., Kang, J.-H., Lee, S.-J., Kim, J., Kim, J., Lee, S., Kim, H. H., Kim, K.-S., & Ramakrishna, S. (2020). Genome-scale screening of deubiquitinase subfamily identifies USP3 as a stabilizer of Cdc25A regulating cell cycle in cancer. Cell Death & Differentiation. (*Equal co-first authors).
  15. Poondla, N.,* Chandrasekaran, A. P.,* Heese, K., Kim, K.-S., & Ramakrishna, S. (2019). CRISPR-mediated upregulation of DR5 and downregulation of cFLIP synergistically sensitize HeLa cells to TRAIL-mediated apoptosis. Biochemical and Biophysical Research Communications, 512(1), 60–65. (*Equal co-first authors).
  16. Poondla, N.,* Chandrasekaran, A. P.,* Kim, K.-S., & Ramakrishna, S. (2019). Deubiquitinating enzymes as cancer biomarkers: new therapeutic opportunities? BMB Reports, 52(3), 181–189. (*Equal co-first authors).

  17. Different methods of delivering CRISPR/Cas9 into cells. Chandrasekaran AP, Song M, Kye-Seong Kim* and Ramakrishna S*. Progress in Molecular Biology and Translational Science (IF: 2.98), 2018, 159:157-176. *(Co-First author).

  18. Haq, S., Das, S., Kim, D.-H., Chandrasekaran, A. P., Hong, S.-H., Kim, K.-S., & Ramakrishna, S. (2019). The stability and oncogenic function of LIN28A are regulated by USP28. Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease, 1865(3), 599–610.

  19. Gopalappa, R., Song, M., Chandrasekaran, A. P., Das, S., Haq, S., Koh, H. C., & Ramakrishna, S. (2018). Efficient genome editing by FACS enrichment of paired D10A Cas9 nickases coupled with fluorescent proteins. Archives of Pharmacal Research. 41(9), 911-920.
  20. Chandrasekaran, A.P., Song, M., & Ramakrishna, S. (2017). Genome editing: a robust technology for human stem cells. Cellular and Molecular Life Sciences, 74(18), 3335-3346. (First author).
  21. Chandrasekaran, A.P.,* Suresh, B.,* Kim, H. H., Kim, K.-S., & Ramakrishna, S. (2017). Concise Review: Fate Determination of Stem Cells by Deubiquitinating Enzymes. Stem Cells, 35(1), 9-16. (*Equal co-first authors).

Book Chapter

  1. Chandrasekaran, A.P., Song, M., Kim, K.-S., & Ramakrishna, S. (2018). Different Methods of Delivering CRISPR/Cas9 Into Cells. Progress in Molecular Biology and Translational Science. 159, 157-176. (First author).

Patent

  1. Ramakrishna, S., Kim, K.-S, Chandrasekaran, A.P., & Kim, D.-H. (2019). Deubiquitinating enzyme gene knock-out cell line library. KR Patent, 10-2017-0,051,407.

Kamini Kaushal, Ph.D                                                                                                                                            

Publications

13. USP19 negatively regulates p53 and promotes cervical cancer progression. Tyagi A, Karapurkar JK, Colaco JC, Sarodaya N, Antao AM, Kaushal K, Haq S, Chandrasekaran AP, Das S, Singh V, Singh V, Hong SH, Suresh B*, Kim KS*, Suresh Ramakrishna*. Molecular biotechnology (IF: 2.4). 2024, 66: 2032-2045.

12. The Role of Deubiquitinating Enzymes in Primary Bone Cancer. Colaco JC, Suresh B, Kaushal K, Singh V*, Ramakrishna S*. Molecular Biotechnology (IF: 2.4). 2024, In press.

11. Ubiquitin specific protease 7 deubiquitinates and regulates Aurora B-mediated cytokinesis. Kaushal K, Antao AM, Das S, Kim SL, Birappa G, Rajkumar S, Gowda DAA, Ajaykumar CB, Singh V, Kim K*, Suresh B*, and Ramakrishna S*. BMB Reports (IF: 2.9). In press (First author)

10. CRISPR/Cas9-based genome-wide screening for deubiquitinase subfamily identifies USP1 regulating MAST1-driven cisplatin-resistance in cancer cells. Tyagi A*, Kaushal K*, Chandrasekaran AP, Sarodaya N, Das S, Park CH, Hong SH, Kim KS, Ramakrishna S. Theranostics (IF: 11.55). 2022, 12(13): 5949-5970. *(Co-First author). 

9. Dual role of deubiquitinating enzyme USP19 regulates mitotic progression and tumorigenesis by stabilizing survivin. Chandrasekaran AP, Tyagi A, Poondla N, Sarodaya N, Karapurkar JK, Kaushal K, Park CH, Hong SH, Kim KS*, Ramakrishna S*. Molecular Therapy (IF: 11.45). 2022, In Press.  

8. Genome-wide screening for deubiquitinase subfamily identifies ubiquitin-specific protease 49 as a novel regulator of odontogenesis. Kaushal K*, Kim EJ*, Tyagi A*, Karapurkar JK, Haq S, Jung HS, Kim KS, Ramakrishna S. Cell Death and Differentiation (IF: 15.8). 2022, 29: 1689-1704. *(Co-First author). 

7. Genome-wide CRISPR/Cas9-based screening for Deubiquitinase subfamily identifies ubiquitin-specific protease 11 as a novel regulator of osteogenic differentiation. Kaushal K*, Tyagi A*, Karapurkar JK, Kim EJ, Tanguturi P, Kim KS, Jung HS, Ramakrishna S. International Journal of Molecular Science (IF: 6.02). 2022. 23(2): 856. *(Co-First author). 

6. USP32 conferes cancer cell resistance to YM155 via promoting ER-associated degradation of solute carrier protein SLC35F2. Chandrasekaran AP, Kaushal K, Park CH, Kim KS and Ramakrishna S. Theranostics (IF: 11.6). 2021, 11:9752-9771. (co-author).  

5. USP48 governs cell cycle progression by regulating the protein level of Aurora B. Antao AM*, Kaushal K*, Das S, Singh V, Suresh B, Kim KS and Ramakrishna S. International journal of Molecular Science (IF: 5.9). 2021, 22: 8508. *(Co-First author).  

4. Deubiquitinating enzyme-mediated signaling networks in cancer stem cells. Kaushal K* and Ramakrishna S. Cancers (IF: 6.1), 2020, 12:3253.(*First authors).

3. E3 Ubiquitin ligase APC/C Cdh1 negatively regulates FAH protein stability by promoting its polyubiquitination. Kaushal K*, Woo SH*, Tyagi A, Kim DH, Suresh B, Kim KS, Ramkrishna S. International Journal of Molecular Science (IF: 4.5), 2020, 21:8719. (*Equal co-first authors).

2. E3 Ubiquitin ligase APC/C Cdh1 regulation of phenylalanine hydroxylase stability and function. Tyagi A, Sarodaya N, Kaushal K, Chandrasekaran AP, Antao AM, Suresh B, Rhie BH, Kim KS*, Ramakrishna S*. International Journal of Molecular Science (IF: 4.5), 2020, 21: 9076. *(Co-author).

1. Deubiquitinating enzymes in cancer stem cells: functions and targeted inhibition for cancer therapy. Kaushal K*, Antao AM*, Kim KS, Ramakrishna S.Drug Discov Today. 2018; 23(12):1974-1982. (*Equal co-first authors).

 

Ainsley Mike Antao, Ph.D

Publications

1. Ubiquitin specific protease 7 deubiquitinates and regulates Aurora B-mediated cytokinesis. kaushal K, Antao AM, Das S, Kim SL, Birappa G, Rajkumar S, Gowda DAA, Ajaykumar CB, Singh V, Kim K*, Suresh B*, and Ramakrishna S*. BMB Reports (IF: 2.9). In press. (Co-First author).

2. An Efficient Endothelial Cell Differentiation Protocol Using Bioactive Lipid O-Cyclic Phytosphingosine-1-Phosphate in Human Embryonic Stem Cells. Jo KS, Jo WJ, Antao AM, Karapurkar JK, Park YJ, Choi MJ, Ramakrishna S*, Kim KS*. International Journal of Stem Cells (IF: 2.5). 2024, In press. *(Co-Corresponding author).

3. USP19 negatively regulates p53 and promotes cervical cancer progression. Tyagi A, Karapurkar JK, Colaco JC, Sarodaya N, Antao AM, Kaushal K, Haq S, Chandrasekaran AP, Das S, Singh V, Singh V, Hong SH, Suresh B*, Kim KS*, Suresh Ramakrishna*. *(Co-Corresponding author). Molecular biotechnology (IF: 2.4). 2024, 66: 2032-2045

4. USP48 governs cell cycle progression by regulating the protein level of Aurora B. Antao AM, Kaushal K, Das S, Singh V, Suresh B, Kim KS and Ramakrishna S. International journal of Molecular Science (IF: 5.9). 2021, 22: 8508. *(Co-First author).  

5. Bioactive lipid O-cyclic phytosphingosine-1-phosphate promotes differentiation of Human embryonic stem cells into cardiomyocytes via ALK3/BMPR signaling. Jang JH, Kim MS, Antao AM, Jo WJ, Kim HJ, Kim SJ, Choi MJ, Ramakrishna S* and Kim KS*. International journal of Molecular Science (IF: 5.9). 2021, 22: 7015.  

6. Ubiquitin-specific Protease 3 deubiquitinates and stabilizes Oct4 protein in human embryonic stem cells. Rhie BH, Antao AM, Karapurkar JK, Kim MS, Jo WJ, Ramakrishna S* and Kim KS*. International journal of Molecular Science (IF: 5.9). 2021, 22: 5584. 

7. CRISPR-Cas9 based genome editing for defective gene correction in humans and other mammals. Karapurkar JK, Antao AM, Kim KS  and Ramakrishna S. Progress in Molecular Biology and Translational Science (IF: 4.07). 2021, In Press. *(Co-First author).  

8. The role of NKX3.1 in cancers and stemness. Antao AM, Ramakrishna S  and Kim KS. International Journal of stem cells (IF: 2.5), 2021, In Press. *(First author).

9. E3 Ubiquitin ligase APC/C Cdh1 regulation of phenylalanine hydroxylase stability and function. Tyagi A, Sarodaya N, Kaushal K, Chandrasekaran AP, Antao AM, Suresh B, Rhie BH, Kim KS*, Ramakrishna S*. International Journal of Molecular Science (IF: 4.5), 2020, 21: 9076. 

10. Disease modeling and stem cell immunoengineering in regenerative medicine using CRISPR/Cas9 systems. Antao AM, Karapurkar JK, Lee DR, Kim KS, Ramakrishna S. Computational and Structural Biotechnology Journal. (IF: 6.01) 2020, 18:3649-3665. *(Co-First author).

11. Advances in deubiquitinating enzyme inhibition and applications in cancer therapeutics. Antao AM, Tyagi A, Kim KS and Ramakrishna S. Cancers (IF: 6.1), 2020, 12:1579 *(Co-First author).

12. Deubiquitinating enzymes in cancer stem cells: functions and targeted inhibition for cancer therapy. Kaushal K, Antao AM, Kim KS* and Ramakrishna S*. Drug Discovery Today (IF: 6.84), 2018, 23(12):1974-1982. *(Co-First author)

 

Apoorvi Tyagi, Ph.D

Email: apoorvityagi09@gmail.com

Research Interest: Role of deubiquitinating enzymes in Cancer biology; Stem cell and differentiation; Bioinformatics; Neurology

Publications

15. USP28 promotes tumorigenesis and cisplatin resistance by deubiquitinating MAST1 protein in cancer cells. Karapurkar JK, Colaco JC, Suresh B, Tyagi A, Woo SH, Jo WJ, Ko N, Singh V, Hong SH, Oh SJ*, Kim KS*, Ramakrishna S*. Cellular and Molecular Life Sciences (IF: 8.0). 2024, 81:145.

14. USP19 negatively regulates p53 and promotes cervical cancer progression. Tyagi A, Karapurkar JK, Colaco JC, Sarodaya N, Antao AM, Kaushal K, Haq S, Chandrasekaran AP, Das S, Singh V, Singh V, Hong SH, Suresh B*, Kim KS*, Suresh Ramakrishna*. Molecular biotechnology (IF: 2.4). 2024, 66: 2032-2045. (First author).

13. Human pluripotent stem cell-derived macrophages and macrophage-derived exosomes: Therapeutic potential in pulmonary fibrosis. Rasaei R*, Tyagi A*, Rasaei S,  Lee SJ, Yang SR, Kim KS, Ramakrishna S, Hong SH. Stem Cell Research and Therapy (IF: 6.832). 2022, 13: 433. *(Co-First author).

12. Deubiquitinase USP19 stabilizes and promotes enzymatic activity of phenylalanine hydroxylase variants. Sarodaya N*, Tyagi A*, Kim HJ, Kang JS, Singh V, Hong SH, Kim WJ, Kim KS, Ramakrishna S. Scientific Reports (IF: 4.37). 2022, 12:14243. *(Co-First author).

11. CRISPR/Cas9-based genome-wide screening for deubiquitinase subfamily identifies USP1 regulating MAST1-driven cisplatin-resistance in cancer cells. Tyagi A*, Kaushal K*, Chandrasekaran AP, Sarodaya N, Das S, Park CH, Hong SH, Kim KS, Ramakrishna S. Theranostics (IF: 11.55). 2022, 12(13): 5949-5970. *(Co-First author). 

10. Dual role of deubiquitinating enzyme USP19 regulates mitotic progression and tumorigenesis by stabilizing survivin. Chandrasekaran AP*, Tyagi A*, Poondla N, Sarodaya N, Karapurkar JK, Kaushal K, Park CH, Hong SH, Kim KS, Ramakrishna S. Molecular Therapy (IF: 11.45). 2022, In Press. *(Co-First author). 

9. Deubiquitinase USP19 enhances phenylalanine hydroxylase protein stability and its enzymatic activity. Sarodaya N*, Tyagi A*, Kim HJ, Colaco JC, Kang JS, Kim WJ, Kim KS, Ramakrishna S. Cell Biology and Toxicology. (IF: 6.69), 2022, In Press. *(Co-First author). 

8. Genome-wide screening for deubiquitinase subfamily identifies ubiquitin-specific protease 49 as a novel regulator of odontogenesis. Kaushal K*, Kim EJ*, Tyagi A*, Karapurkar JK, Haq S, Jung HS, Kim KS, Ramakrishna S. Cell Death and Differentiation (IF: 15.8). 2022, 29: 1689-1704. *(Co-Frist author). 

7. Genome-wide CRISPR/Cas9-based screening for Deubiquitinase subfamily identifies ubiquitin-specific protease 11 as a novel regulator of osteogenic differentiation. Kaushal K*, Tyagi A*, Karapurkar JK, Kim EJ, Tanguturi P, Kim KS, Jung HS, Ramakrishna S. International Journal of Molecular Science (IF: 6.02). 2022. 23(2): 856. *(Co-First author). 

6. Redox regulation of DUBs and its therapeutic implications in cancer. Tyagi A, Haq S and Ramakrishna S. Redox Biology (IF: 11.79), 2021, 48: 102194. (First author).  

5. Smart vitamin micelles as cancer nanomedicines for enhanced intracellular delivery of doxorubicin. Ko NR, Lee SJ, Chandrasekaran AP, Tyagi A, Ramakrishna S, Kim SY, Kim DW, Pack CG and Oh SJ. International Journal of Molecular Sciences (IF: 5.9). 2021, 22,20, 11298.

4. Ubiquitin-specific protease 29 regulates Cdc25A-mediated tumorigenesis. Chandrasekaran AP, Woo SH, Sarodaya N, Rhie BH, Tyagi A, Das S, Suresh B, Ko NR, Oh SJ, Kim KS and Ramakrishna S.  International journal of Molecular Science (IF: 4.5). 2021, 22: 5584. (Co-authors).

3. E3 Ubiquitin ligase APC/C Cdh1 regulation of phenylalanine hydroxylase stability and function. Tyagi A*, Sarodaya N*, Kaushal K, Chandrasekaran AP, Antao AM, Suresh B, Rhie BH, Kim KS, Ramakrishna S. International Journal of Molecular Science (IF: 4.5), 2020, 21: 9076. (*Equal co-first authors).

2. E3 Ubiquitin ligase APC/C Cdh1 negatively regulates FAH protein stability by promoting its polyubiquitination. Kaushal K, Woo SH, Tyagi A, Kim DH, Suresh B, Kim KS, Ramkrishna S. International Journal of Molecular Science (IF: 4.5), 2020, 21:8719. (Co-authors).

1. Advances in deubiquitinating enzyme inhibition and applications in cancer therapeutics. Antao AM*, Tyagi A*, Kim KS and Ramakrishna S.Cancer (Basel), 2020; In Press (*Equal co-first authors).

Neha Sarodaya, Ph.D 

Email: neyha19@gmail.com

Research Interest: Cancer Biology, Genome editing, Post translational modification, in vivo studies, Drug discovery, stem cell Biology

Publications

13. CRISPR/Cas9-based genome-wide screening of the deubiquitinase subfamily identifies USP3 as a protein stabilizer of REST blocking neuronal differentiation and promotes neuroblastoma tumorigenesis. Karapurkar JK, Kim MS, Colaco JC, Suresh B, Sarodaya N, Kim DH, Park CH, Hong SH, Kim KS*, Ramakrishna S*. Journal of Experimental Clinic and Cancer Research. 2023 42: 121. (IF: 12.65).

12. USP19 negatively regulates p53 and promotes cervical cancer progression. Tyagi A, Karapurkar JK, Colaco JC, Sarodaya N, Antao AM, Kaushal K, Haq S, Chandrasekaran AP, Das S, Singh V, Singh V, Hong SH, Suresh B*, Kim KS*, Suresh Ramakrishna*. Molecular biotechnology (IF: 2.4). 2024, 66: 2032-2045.

11. Deubiquitinase USP19 stabilizes and promotes enzymatic activity of phenylalanine hydroxylase variants. Sarodaya N*, Tyagi A*, Kim HJ, Kang JS, Singh V, Hong SH, Kim WJ, Kim KS, Ramakrishna S. Scientific Reports (IF: 4.37). 2022, 12:14243. *(Co-First author).

10. CRISPR/Cas9-based genome-wide screening for deubiquitinase subfamily identifies USP1 regulating MAST1-driven cisplatin-resistance in cancer cells. Tyagi A, Kaushal K, Chandrasekaran AP, Sarodaya N, Das S, Park CH, Hong SH, Kim KS*, Ramakrishna S*. Theranostics (IF: 11.55). 2022, 12(13): 5949-5970. 

9. Dual role of deubiquitinating enzyme USP19 regulates mitotic progression and tumorigenesis by stabilizing survivin. Chandrasekaran AP, Tyagi A, Poondla N, Sarodaya N, Karapurkar JK, Kaushal K, Park CH, Hong SH, Kim KS*, Ramakrishna S*. Molecular Therapy (IF: 11.45). 2022, In Press. 

8. Deubiquitinase USP19 enhances phenylalanine hydroxylase protein stability and its enzymatic activity. Sarodaya N*, Tyagi A*, Kim HJ, Colaco JC, Kang JS, Kim WJ, Kim KS, Ramakrishna S. Cell Biology and Toxicology. (IF: 6.69), 2022, In Press. *(Co-First author). 

7. CYLD destabilizes NoxO1 protein by promoting ubiquitination and regulates prostate cancer progression. *Haq S, *Sarodaya N, Karapurkar JK, Suresh B, Jo JK, Singh V, Bae YS, Kim KS and Ramakrishna S. Cancer Letters (IF: 8.67), 2022, 525: 146-157. *(Co-First author).  

6.  Ubiquitin-specific protease 29 regulates Cdc25A-mediated tumorigenesis. Chandrasekaran AP, Woo SH, Sarodaya N, Rhie BH, Tyagi A, Das S, Suresh B, Ko NR, Oh SJ, Kim KS and Ramakrishna S.  International journal of Molecular Science (IF: 4.5). 2021, 22: 5584. (Co-authors).

5. Ubiquitin specific protease 29 functions as an Oncogene promoting tumorigenesis in colorectal carcinoma. Chandrasekaran AP, Suresh B, Sarodaya N, Ko NR, Oh SH, Kim KS, Ramakrishna S. Cancers (IF: 6.1). 2021, In press. (Co-authors).  

4. E3 Ubiquitin ligase APC/C Cdh1 regulation of phenylalanine hydroxylase stability and function. Tyagi A*, Sarodaya N*, Kaushal K, Chandrasekaran AP, Antao AM, Suresh B, Rhie BH, Kim KS, Ramakrishna S. International Journal of Molecular Science (IF: 4.5), 2020, 21: 9076. (*Equal co-first authors).

3.  Importance of Deubiquitination in Macrophage-Mediated Viral Response and Inflammation. Rasaei R*, Sarodaya N*, Kim KS, Ramakrishna S, Hong SH. International Journal of Molecular Science. (IF: 4.5). 2020, 21:8090. (*Equal co-first authors).

2. Protein degradation and the pathologic basis of Phenylketonuria and hereditary tyrosinemia. Sarodaya N, Suresh B, Kim K and Ramakrishna S. International Journal of Molecular Science (IF: 4.5), 2020, 21(14): 4996. (First author).

1. The Role of Deubiquitinating Enzymes in Hematopoiesis and Hematological Malignancies. Sarodaya N*, Karapurkar J*, Kim KS, Hong SH, Ramakrishna S. Cancers (Basel). 2020;12(5):1103. (*Equal co-first authors).

Janardhan Keshav Karapurkar , Ph.D

Post-Doc                                                                                                                                                 

Email: kalpesh25021992@gmail.com

Research Interest: Cancer biology, Genome Editing, Hybridoma technology, In vivo studies, Immunology, Stem cell technology

Chapter

1. CRISPR-Cas9 based genome editing for defective gene correction in humans and other mammals. Karapurkar JK*, Antao AM*, Kim KS  and Ramakrishna S *. Progress in Molecular Biology and Translational Science (IF: 4.07). 2021, In Press. (*Equal co-first authors).

Research Publications

19. Loss of Ubiquitin-specific protease 11 mitigates pulmonary fibrosis in human pluripotent stem cell-derived alveolar organoids. Rajkumar S, Jung JH, Kim JY, Karapurkar JK, Birappa G, Gowda DAA, Ajaykumar CB, Perumalsamy H, Suresh B, Kim KS*, Hong SH*, Ramakrishna S*. International Journal of Stem Cells (IF: 2.5). 2025. In press

18. AXL kinase inhibitor exhibits antitumor activity by inducing apoptotic cell death in triple-negative breast cancer cells. Woo SH, Kim DH, Karapurkar JK, Kim SJ, Jang HY, Jang JY, Han BW, Kim JS, Park YJ, Choi MJ, Ramakrishna S* and Kim KS*. BBA-Molecular Cell Research (IF: 4.6). 2025, 1872: 119928.

17. Targeting USP11 counteracts SFTPC-I73T-associated pulmonary fibrosis in hiPSCs-derived alveolar organoids and in vivo models. Karapurkar JK, Rajkumar S, Jung JH, Kim JY, Birappa G, Gowda DAA, Colaco JC, Suresh B, Choi JY, Woo SH, Jo WJ, Lee JH, Kim KS*, Hong SH* and  Ramakrishna S*. Theranostics. 2025, 15:4526-4549. (IF: 12.4) (First author)

16. USP28 promotes tumorigenesis and cisplatin resistance by deubiquitinating MAST1 protein in cancer cells. Karapurkar JK, Colaco JC, Suresh B, Tyagi A, Woo SH, Jo WJ, Ko N, Singh V, Hong SH, Oh SJ*, Kim KS*, Ramakrishna S*. Cellular and Molecular Life Sciences (IF: 8.0). 2024, 81:145 (First author).

15. An Efficient Endothelial Cell Differentiation Protocol Using Bioactive Lipid O-Cyclic Phytosphingosine-1-Phosphate in Human Embryonic Stem Cells. Jo KS, Jo WJ, Antao AM, Karapurkar JK, Park YJ, Choi MJ, Ramakrishna S*, Kim KS*. International Journal of Stem Cells (IF: 2.5). 2024, In press.

14. βTrCP1 promotes SLC35F2 protein ubiquitination and inhibits cancer progression in HeLa cells. Colaco JC, Chandrasekaran AP, Karapurkar JK, Birappa G, Rajkumar S, Gowda ADA, Suresh B, Lee J, Singh V, Hong SH*, Kim KS*, Ramakrishna S*. Biochemical and Biophysical Research Communications (IF: 2.5). 2023, 682: 27-38. 

13. E3 Ubiquitin ligase APC/Cdh1 regulates SLC35F2 protein turnover and inhibits cancer progression in HeLa cells. Colaco JC, Chandrasekaran AP, Karapurkar JK, Gowda ADA, Birappa G, Rajkumar S, Suresh B, Ko N, Hong SH, Oh SJ, Kim KS, Ramakrishna S. BBA-General Subjects. 2023, In Press.   

12. CRISPR/Cas9-based genome-wide screening of the deubiquitinase subfamily identifies USP3 as a protein stabilizer of REST blocking neuronal differentiation and promotes neuroblastoma tumorigenesis. Karapurkar JK, Kim MS, Colaco JC, Suresh B, Sarodaya N, Kim DH, Park CH, Hong SH, Kim KS, Ramakrishna S. Journal of Experimental Clinic and Cancer Research. 2023 42: 121. (IF: 12.65). (Co-First author).

11. USP19 negatively regulates p53 and promotes cervical cancer progression. Tyagi A, Karapurkar JK, Colaco JC, Sarodaya N, Antao AM, Kaushal K, Haq S, Chandrasekaran AP, Das S, Singh V, Singh V, Hong SH, Suresh B*, Kim KS*, Suresh Ramakrishna*. *(Co-First author). Molecular biotechnology. In Press

10. Phage Engineering and phage-assisted CRISPR-Cas delivery to combat mutidrug-resistant pathoges. Khambhati K, Bhattacharjee G, Gohil N, Dhanoa GK, Sagona AP, Mani I, Bui NL, Chu DT, Karapurkar JK, Jang SH, Chung HY, Maurya R, Alzahrani KJ, Ramakrishna S, Singh V. Bioengineering and Translational Medicine. (IF: 10.6), 2022. 8: e13381.

9. Dual role of deubiquitinating enzyme USP19 regulates mitotic progression and tumorigenesis by stabilizing survivin. Chandrasekaran AP, Tyagi A, Poondla N, Sarodaya N, Karapurkar JK, Kaushal K, Park CH, Hong SH, Kim KS*, Ramakrishna S*. Molecular Therapy (IF: 11.45). 2022, 30: 3414-3429. 

8. Genome-wide screening for deubiquitinase subfamily identifies ubiquitin-specific protease 49 as a novel regulator of odontogenesis. Kaushal K, Kim EJ, Tyagi A, Karapurkar JK, Haq S, Jung HS*, Kim KS*, Ramakrishna S*. Cell Death and Differentiation (IF: 15.8). 2022, 29: 1689-1704. 

7. Current approaches in CRISPR-Cas9 mediated gene editing for biomedical and therapeutic applications. Bhattacharjee G, Gohil N, Khambhati K, Mani I, Maurya R, Karapurkar JK, Gohil J, Chu DT, Vu-Thi H, Alzahrani KJ, Show PL, Rawal RM, Ramakrishna S*, Singh V*. Journal of Controlled Release, (IF: 11.47), 2022, 343:703-723. 

6. The role of the CRISPR-Cas system in cancer drug development: Mechanisms of action and therapy. Chandrasekaran AP*, Karapurkar JK*, Chung HY, Ramakrishna S. Biotechnology Journal (IF: 4.67). 2022,17(7): e2100468. (Co-First author).  

5. Genome-wide CRISPR/Cas9-based screening for Deubiquitinase subfamily identifies ubiquitin-specific protease 11 as a novel regulator of osteogenic differentiation. Kaushal K, Tyagi A, Karapurkar JK, Kim EJ, Tanguturi P, Kim KS*, Jung HS*, Ramakrishna S*. International Journal of Molecular Science (IF: 6.02). 2022. 23(2): 856. 

4. CYLD destabilizes NoxO1 protein by promoting ubiquitination and regulates prostate cancer progression. Haq S, Sarodaya N, Karapurkar JK, Suresh B, Jo JK, Singh V, Bae YS, *Kim KS and *Ramakrishna S. Cancer Letters (IF: 8.67), 2022, 525: 146-157.  

3. Ubiquitin-specific Protease 3 deubiquitinates and stabilizes Oct4 protein in human embryonic stem cells. Rhie BH, Antao AM, Karapurkar JK, Kim MS, Jo WJ, Ramakrishna S and Kim KS. International journal of Molecular Science (IF: 4.5). 2021, 22: 5584. (Co-authors). 

2. Disease modeling and stem cell immunoengineering in regenerative medicine using CRISPR/Cas9 systems. Antao AM*, Karapurkar JK*, Lee DR, Kim KS, Ramakrishna S. Computational and Structural Biotechnology Journal. (IF: 6.01) 2020, 18:3649-3665. (*Equal co-first authors). 

1. The Role of Deubiquitinating Enzymes in Hematopoiesis and Hematological Malignancies. Sarodaya N*, Karapurkar J*, Kim KS, Hong SH, Ramakrishna S. Cancers (Basel). 2020;12(5):E1103. (*Equal co-first authors).

Jencia Carminha Colaco, Ph.D

Email: jencia.c@gmail.com

Research Interest: Cancer Biology, Drug Discovery, Post-translational modification, Genome Editing. 

Publications

7. Targeting USP11 counteracts SFTPC-I73T-associated pulmonary fibrosis in hiPSCs-derived alveolar organoids and in vivo models. Karapurkar JK, Rajkumar S, Jung JH, Kim JY, Birappa G, Gowda DAA, Colaco JC, Suresh B, Choi JY, Woo SH, Jo WJ, Lee JH, Kim KS*, Hong SH* and  Ramakrishna S*. Theranostics. 2025, 15:4526-4549. (IF: 12.4).

6. USP28 promotes tumorigenesis and cisplatin resistance by deubiquitinating MAST1 protein in cancer cells. Karapurkar JK, Colaco JC, Suresh B, Tyagi A, Woo SH, Jo WJ, Ko N, Singh V, Hong SH, Oh SJ*, Kim KS*, Ramakrishna S*. Cellular and Molecular Life Sciences (IF: 8.0). 2024, 81:145 

5. The Role of Deubiquitinating Enzymes in Primary Bone Cancer. Colaco JC, Suresh B, Kaushal K, Singh V*, Ramakrishna S*. Molecular Biotechnology (IF: 2.4). 2024, In press, (First author)

4. βTrCP1 promotes SLC35F2 protein ubiquitination and inhibits cancer progression in HeLa cells. Colaco JC, Chandrasekaran AP, Karapurkar JK, Birappa G, Rajkumar S, Gowda ADA, Suresh B, Lee J, Singh V, Hong SH*, Kim KS*, Ramakrishna S*. Biochemical and Biophysical Research Communications (IF: 2.5). 2023, 682: 27-38. (First author)

3. E3 Ubiquitin ligase APC/Cdh1 regulates SLC35F2 protein turnover and inhibits cancer progression in HeLa cells. Colaco JC*, Chandrasekaran AP*, Karapurkar JK, Gowda ADA, Birappa G, Rajkumar S, Suresh B, Ko N, Hong SH, Oh SJ, Kim KS, Ramakrishna S. BBA-General Subjects. 2023, In Press. (Co-first author)

2. USP19 negatively regulates p53 and promotes cervical cancer progression. Tyagi A*, Karapurkar JK*, Colaco JC*, Sarodaya N, Antao AM, Kaushal K, Haq S, Chandrasekaran AP, Das S, Singh V, Singh V, Hong SH, Suresh B, Kim KS, Suresh Ramakrishna.  Molecular biotechnology. In Press. *(Co-First author).

1. Deubiquitinase USP19 enhances phenylalanine hydroxylase protein stability and its enzymatic activity. Sarodaya N, Tyagi A, Kim HJ, Colaco JC, Kang JS, Kim WJ, Kim KS, Ramakrishna S. Cell Biology and Toxicology. (IF: 6.69), 2022, In Press.