1. Micah B. Castillo, Sakuni Rankothgedera, Shiyanth Thevasagayampillai, Aaranyah Kandasamy, Jaila Lewis, Cole Woody, Martiela Vaz De Freitas, Dinler Amaral Antunes, Randa El-Zein, Preethi Gunaratne*. Identification of Immunogenic KIF5BRET Fusion Neopeptides Driving Immune Stimulation in Tumor Specific CD8+ T cells. Front. Immunol., Sec. Vaccines and Molecular Therapeutics. 29 Volume 16 - 2025 | https://doi.org/10.3389/fimmu.2025.1635810.
2. Distinct populations of vascular smooth muscle and sinoatrial progenitors are localized adjacent to proepicardium. Ming-Fu. CELL-REPORTS-D-25-05416R5
3. Erez N Baruch, Frederico O Gleber-Netto, Priyadharsini Nagarajan, Xiayu Rao, Shamima Akhter, Tuany Eichwald, Tongxin Xie, Mohammad Balood, Adebayo Adewale, Shorook Naara, Hinduja N Sathishkumar, Shajedul Islam, William McCarthy, Brandi J Mattson, Renata Ferrarotto, Michael K Wong, Michael A Davies, Sonali Jindal, Sreyashi Basu, Karine Roversi, Amin Reza Nikpoor, Maryam Ahmadi, Ali Ahmadi, Catherine Harwood, Irene Leigh, Dennis Gong, Paulino Tallón de Lara, Derrick L Tao, Tara M Davidson, Nadim J Ajami, Andrew Futreal, Kunal Rai, Veena Kochat, Micah Castillo, Preethi Gunaratne, Ryan P Goepfert, Sharia D Hernandez, Nikhil I Khushalani, Jing Wang, Stephanie S Watowich, George A Calin, Michael R Migden, Mona Yuan, Naijiang Liu, Yi Ye, William L Hwang, Paola D Vermeer, Nisha J D’Silva, Yuri L Bunimovich, Dan Yaniv, Jared K Burks, Javier Gomez, Patrick M Dougherty, Kenneth Y Tsai, James P Allison, Padmanee Sharma, Jennifer A Wargo, Jeffrey N Myers, Sebastien Talbot, Neil D Gross, Moran Amit. Cancer-induced nerve injury promotes resistance to anti-PD-1 therapy. Nature. 2025/8/20: 1-12.
4. Joy M Schmitz, Jin Ho Yoon, Bruno Kluwe-Schiavon, John A Harvin, Preethi H Gunaratne, Darrion Mouton, Kandice Motley, Erin E Fox, Jessica Vincent, Megan Tarbet, Consuelo Walss-Bass. Identifying bio-behavioural signatures of persistent opioid use risk in trauma injury patients: a protocol for a prospective cohort study. BMJ open. 2025/9/1, 15 (9), e103053.
5. Jangwook P. Jung, Oluyinka O. Olutoye II, Tanuj J. Prajati, Olivia S. Jung, Lane D. Yutzy, Kenny L. Nguyen, Stephen W. Wheat, JoAnne Huang, Benjamin W. Padon, Fayiz Faruk, Sonya S. Keswani, Phillip Kogan, Aditya Kaul, Ling Yu, Hui Li, Shiyanth Thevasagayampillai, Mary E. Guerra, Walker D. Short, Preethi H. Gunaratne, Swathi Balaji. Sustained ROS Scavenging and Pericellular Oxygenation by Lignin Composites Rescue HIF-1α and VEGF Levels to Improve Diabetic Wound Neovascularization and Healing. Acta Biomaterialia. 2025.
6. Thomas R. Kosten, Amrit Koirala, David A. Nielsen, Coreen B. Domingo, Ynhi T. Thomas, Preethi H. Gunaratne and Cristian Coarfa. Plasma microRNAs to Select Optimal Patients for Antibody Production from Anti-Addiction Vaccines. MDPI- Vaccines 2025, 13: 181.
7. Sandra L Grimm, Tia Talley, Rahul K Jangid, Amrit Koirala, Micah B Castillo, Preethi H Gunaratne, Cristian Coarfa, Cheryl L Walker. Transcriptomic and epigenomic signatures distinguish high‐and low‐risk endotypes for liver tumor development. Environmental and Molecular Mutagenesis. 2025. 65 (9): 351-359
8. Fernanda CP Mesquita, Madelyn King, Patricia Luciana da Costa Lopez, Shiyanth Thevasagayampillai, Preethi H Gunaratne, Camila Hochman-Mendez. Laminin Alpha 2 Enhances the Protective Effect of Exosomes on Human iPSC-Derived Cardiomyocytes in an In Vitro Ischemia-Reoxygenation Model. Int. J. Mol. Sci. 2024, 25(7), 3773.
9. Aniket S Joshi, Micah B Castillo, Meiricris Tomaz da Silva, Anh Tuan Vuong, Preethi H Gunaratne, Radbod Darabi, Yu Liu, Ashok Kumar. Single-nucleus transcriptomic analysis reveals the regulatory circuitry of myofiber XBP1 during regenerative myogenesis. iScience. 111372November 11, 2024
10. Aniket S Joshi, Meiricris Tomaz da Silva, Anirban Roy, Tatiana E Koike, Mingfu Wu, Micah B Castillo, Preethi H Gunaratne, Yu Liu, Takao Iwawaki, Ashok Kumar. The IRE1α/XBP1 signaling axis drives myoblast fusion in adult skeletal muscle. EMBO Rep. 2024 Aug; 25(8): 3627–3650. Published online 2024 Jul 9. doi: 10.1038/s44319-024-00197-4. PMCID: PMC11316051
11. Wang B, Reville PK, Yassouf MY, Jelloul FZ, Ly C, Desai PN, Wang Z, Borges P, Veletic I, Dasdemir E, Burks JK, Tang G, Guo S, Garza AI, Nasnas C, Vaughn NR, Baran N, Deng Q, Matthews J, Gunaratne PH, Antunes DA, Ekmekcioglu S, Sasaki K, Garcia MB, Cuglievan B, Hao D, Daver N, Green MR, Konopleva M, Futreal A, Post SM, Abbas HA. Comprehensive characterization of IFNγ signaling in acute myeloid leukemia reveals prognostic and therapeutic strategies. Nat Commun. 2024 Feb 28;15(1):1821. doi: 10.1038/s41467-024-45916-6. PubMed PMID: 38418901; PubMed Central PMCID: PMC10902356.
12. Napoli M, Deshpande AA, Chakravarti D, Rajapakshe K, Gunaratne PH, Coarfa C, Flores ER. Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses. Cancer Res Commun. 2024 Feb 1;4(2):264-278. doi: 10.1158/2767-9764.CRC-23-0358. PubMed PMID: 38165157; PubMed Central PMCID: PMC10832605.
13. Maryam Seifishahpar, Micah Castillo, Preethi Gunaratne, Naima Moustaid-Moussa, Shane Scoggin, Jung Han Kim, Kalhara Menikdiwela. Effects of Supplemental Tart Cherry and Fish Oil on Inflammation and Gut Microbiota in Diet-induced (C57BL/6J) and Genetically (TALLYHO/Jng) Obese Mice Models. Current Deveopments in Nutrion. Volume 8, Supplement 2103396July 2024.
14. Lianjie Miao, Yangyang Lu, Anika Nusrat, Luqi Zhao, Micah Castillo, Yongqi Xiao, Hongyang Guo, Yu Liu, Preethi Gunaratne, Robert J Schwartz, Alan R Burns, Ashok Kumar, C Michael DiPersio, Mingfu Wu. β1 integrins regulate cellular behaviour and cardiomyocyte organization during ventricular wall formation. Cardiovascular Research, Volume 120, Issue 11, July 2024, Pages 1279–1294.
15. Meiricris Tomaz da Silva, Aniket S Joshi, Micah B Castillo, Tatiana E Koike, Anirban Roy, Preethi H Gunaratne, Ashok Kumar. Fn14 promotes myoblast fusion during regenerative myogenesis. Life Sci Alliance. 2023 Dec; 6(12): e202302312. Published online 2023 Oct 9. doi: 10.26508/lsa.202302312. PMCID:PMC10561765
16. Erez N. Baruch, Priyadahrshini Nagarajan, Frederico O. Gleber-Netto, Xiayu Rao, Tongxin Xie, Shamima Akhter, Adebayo Adewale, Islam Shajedul, Brandi J Mattson, Renata Ferrarotto, Michael K. Wong, Michael A Davies, Sonali Jindal, Sreyashi Basu, Catherine Harwood, Irene Leigh, Nadim Ajami, Andrew Futreal, Micah Castillo, Preethi Gunaratne, Ryan P. Goepfert, Nikhil Khushalani, Jing Wang, Stephanie Watowich, George A Calin, Michael R. Migden, Paola Vermeer, Nisha D’Silva, Dan Yaniv, Jared K Burks, Javier Gomez, Patrick M Dougherty, Kenneth Y. Tsai, James P Allison, Padmanee Sharma, Jennifer Wargo, Jeffrey N. Myers, Neil D. Gross, Moran Amit. Inflammation induced by tumor-associated nerves promotes resistance to anti-PD-1 therapy in cancer patients and is targetable by interleukin-6 blockade. Version 1. Res Sq. Preprint. 2023 Jul 18. doi: 10.21203/rs.3.rs-3161761/v1. PMCID: PMC10371163.
17. Seo S, Patil SL, Ahn YO, Armetta J, Hegewisch-Solloa E, Castillo M, Guilz NC, Patel A, Corneo B, Borowiak M, Gunaratne P, Mace EM. iPSC-based modeling of helicase deficiency reveals impaired cell proliferation and increased apoptosis after NK cell lineage commitment. bioRxiv. 2023 Sep 25;. doi: 10.1101/2023.09.25.559149. PubMed PMID: 37808662; PubMed Central PMCID: PMC10557596.
18. Mistretta B, Rankothgedera S, Castillo M, Rao M, Holloway K, Bhardwaj A, El Noafal M, Albarracin C, El-Zein R, Rezaei H, Su X, Akbani R, Shao XM, Czerniecki BJ, Karchin R, Bedrosian I, Gunaratne PH*. Chimeric RNAs reveal putative neoantigen peptides for developing tumor vaccines for breast cancer. Front Immunol. 2023;14:1188831. eCollection 2023. PubMed PMID: 37744342; PubMed Central PMCID: PMC10512078. (*Corresponding Author)
19. Baruch EN, Nagarajan P, Gleber-Netto FO, Rao X, Xie T, Akhter S, Adewale A, Shajedul I, Mattson BJ, Ferrarotto R, Wong MK, Davies MA, Jindal S, Basu S, Harwood C, Leigh I, Ajami N, Futreal A, Castillo M, Gunaratne P, Goepfert RP, Khushalani N, Wang J, Watowich S, Calin GA, Migden MR, Vermeer P, D'Silva N, Yaniv D, Burks JK, Gomez J, Dougherty PM, Tsai KY, Allison JP, Sharma P, Wargo J, Myers JN, Gross ND, Amit M. Inflammation induced by tumor-associated nerves promotes resistance to anti-PD-1 therapy in cancer patients and is targetable by interleukin-6 blockade. Res Sq. 2023 Jul 18;. doi: 10.21203/rs.3.rs-3161761/v1. PubMed PMID: 37503252; PubMed Central PMCID: PMC10371163.
20. Sandra L. Grimm, Emily F. Mendez, Laura Stertz, Thomas D. Meyer, Gabriel R. Fries, Tanmay Gandhi, Rupa Kanchi, Sudhakar Selvaraj, Antonio L. Teixeira, Thomas R. Kosten, Preethi Gunaratne, Cristian Coarfa and Consuelo Walss-Bass. MicroRNA–mRNA networks are dysregulated in opioid use disorder postmortem brain: Further evidence for opioid-induced neurovascular alterations. Front. Psychiatry, 12 January 2023. Sec. Molecular Psychiatry. Volume 13. doi.org/10.3389/fpsyt.2022.1025346
21. Donorexosomebiomarkers for Primary Graft Dysfunction in Transplants Using Ex-Vivo Lung PerfusionR Kanchi, L Chacon, E D'Silva, M Salan-Gomez, A Leon-Pena, M Castillo, P Gunaratne, C Hochman Mendez, C Coarfa, G Loor. The Journal of Heart and Lung Transplantation.April 1; 42(4): S179.
22. Nicole Prodan, Faheem Ershad, Arfaxad Reyes-Alcaraz, Luge Li, Brandon Mistretta, Lei Gonzalez, Zhoulyu Rao, Cunjiang Yu, Preethi H. Gunaratne, Na Li, Robert J. Schwartz, Bradley K. McConnell. Direct reprogramming of cardiomyocytes into cardiac Purkinje-like cells iScience. 2022 Nov 18; 25(11): 105402. Published online 2022 Oct 20. doi: 10.1016/j.isci.2022.105402. PMCID: PMC9646947
23. Jose Thaiparambil, Jianrong Dong, Sandra L Grimm, Dimuthu Perera, Chandra Shekar R Ambati, Vasanta Putluri, Matthew J Robertson, Tajhal D Patel, Brandon Mistretta, Preethi H Gunaratne, Min P Kim, Jason T Yustein, Nagireddy Putluri, Cristian Coarfa, Randa El-Zein. Integrative metabolomics and transcriptomics analysis reveals novel therapeutic vulnerabilities in lung cancer. Cancer Med. 2022 Jun 8. PMID: 35676822
24. Sarah E Woodfield, Brandon J Mistretta, Roma H Patel, Aryana M Ibarra, Kevin E Fisher, Stephen F Sarabia, Ilavarasi Gandhi, Jacquelyn Reuther, Zbigniew Starosolski, Andrew Badachhape, Jessica Epps, Barry Zorman, Aayushi P Shah, Samuel R Larson, Rohit K Srivastava, Yan Shi, Andres F Espinoza, Saiabhiroop R Govindu, Richard S Whitlock, Kimberly Holloway, Angshumoy Roy, Pavel Sumazin, Ketan B Ghaghada, Dolores Lopez-Terrada, Preethi H Gunaratne, and Sanjeev A Vasudevan. HepT1-derived murine models of high-risk hepatoblastoma display vascular invasion, metastasis, and circulating tumor cells. Biol Open. 2022 Sep 15;11(9): bio058973. doi: 10.1242/bio.058973. Epub 2022 Sep 12. PMID: 35451474
25. Yajuan Li, Zhi Tan, Yaohua Zhang, Zhao Zhang, Qingsong Hu, Ke Liang, Jun Yao, Youqiong Ye, Yi-Chuan Li, Chunlai Li, Lan Liao, Jianming Xu, Zhen Xing, Yinghong Pan, Sujash S. Chatterjee, Tina K. Nguyen, Heidi Hsiao, Sergey D. Egranov, Nagireddy Putluri, Cristian Coarfa, David H. Hawke, Preethi H. Gunaratne, Kuang-Lei Tsai, Leng Han, Mien-Chie Hung, George A. Calin, Fares Namour, Jean-Louis Guéant, Ania C. Muntau, Nenad Blau, V. Reid Sutton, Manuel Schiff, François Feillet, Shuxing Zhang, Chunru Lin, Liuqing Yang. A noncoding RNA modulator potentiates phenylalanine metabolism in mice Science. 2021 Aug 6; 373(6555): 662–673. PMCID: PMC9714245
26. Yajuan Li, Yaohua Zhang, Qingsong Hu, Sergey D. Egranov, Zhen Xing, Zhao Zhang, Ke Liang, Youqiong Ye, Yinghong Pan, Sujash S. Chatterjee, Brandon Mistretta, Tina K. Nguyen, David H. Hawke, Preethi H. Gunaratne, Mien-Chie Hung, Leng Han, Liuqing Yang, Chunru Lin. Genome Med. 2021; 13: 137. Published online 2021 Aug 28. doi: 10.1186/s13073-021-00937-4. Functional significance of gain-of-function H19 lncRNA in skeletal muscle differentiation and anti-obesity effects. PMCID:PMC8403366
27. Divya Ravirala, Brandon Mistretta, Preethi H Gunaratne, Guangsheng Pei, Zhongming Zhao, Xiaoliu Zhang. Co-delivery of novel bispecific and trispecific engagers by an amplicon vector augments the therapeutic effect of an HSV-based oncolytic virotherapy. J Immunother Cancer. 2021; 9(7): e002454. Published online 2021 Jul 6. doi: 10.1136/jitc-2021-002454. PMCID: PMC8261877
28. Stewart Fannin, Jonathan Rangel, Abiodun P. Bodurin, Tannon Yu, Brandon Mistretta, Sujina Mali, Preethi Gunaratne, Steven J. Bark, Jerry O. Ebalunode, Arshad Khan, William R. Widger, Mehmet Sen. Functional and structural characterization of Hyp730, a highly conserved and dormancy‐specific hypothetical membrane protein. Microbiologyopen. 2021 Jan; 10(1): e1154. Published online 2021 Feb 3. doi: 10.1002/mbo3.1154. PMCID: PMC7856521
29. Marco Napoli, Xiaobo Li, Hayley D. Ackerman, Avani A. Deshpande, Ivan Barannikov, Marlese A. Pisegna, Isabelle Bedrosian, Jürgen Mitsch, Philip Quinlan, Alastair Thompson, Kimal Rajapakshe, Cristian Coarfa, Preethi H. Gunaratne, Douglas C. Marchion, Anthony M. Magliocco, Kenneth Y. Tsai, Elsa R. Flores. Pan-cancer analysis reveals TAp63-regulated oncogenic lncRNAs that promote cancer progression through AKT activation. Nat Commun. 2020; 11: 5156. Published online 2020 Oct 14. doi: 10.1038/s41467-020-18973-w. PMCID: PMC7561725
30. Smith SL, Kennedy PR, Stacey KB, Worboys JD, Yarwood A, Seo S, Solloa EH, Mistretta B, Chatterjee SS, Gunaratne P, Allette K, Wang YC, Smith ML, Sebra R, Mace EM, Horowitz A, Thomson W, Martin P, Eyre S, Davis DM. Diversity of peripheral blood human NK cells identified by single-cell RNA sequencing. Blood Adv. 2020 Apr 14;4(7):1388-1406. doi: 10.1182/bloodadvances.2019000699. PMID:32271902
31. Kalhara R. Menikdiwela, Latha Ramalingam, Mostafa M. Abbas, Halima Bensmail, Shane Scoggin, Nishan S. Kalupahana, Asha Palat, Preethi Gunaratne, Naima Moustaid-Moussa. Role of microRNA 690 in Mediating Angiotensin II Effects on Inflammation and Endoplasmic Reticulum Stress. Cells. 2020 Jun; 9(6): 1327. Published online 2020 May 26. doi: 10.3390/cells9061327. PMCID:PMC7348980
32. Zhenlin Ju, Anjana Bhardwaj, Matthew D. Embury, Harpreet Singh, Preethi H. Gunaratne, Isabelle Bedrosian, Jing Wang. Integrative Analyses of Multilevel Omics Reveal Preneoplastic Breast to Possess a Molecular Landscape That is Globally Shared with Invasive Basal-Like Breast Cancer (Running Title: Molecular Landscape of Basal-Like Breast Cancer Progression) Cancers (Basel) 2020 Mar; 12(3): 722. Published online 2020 Mar 19. doi: 10.3390/cancers12030722. PMCID: PMC7140033
33. Smith SL, Kennedy PR, Stacey KB, Worboys JD, Yarwood A, Seo S, Solloa EH, Mistretta B, Chatterjee SS, Gunaratne P, Allette K, Wang YC, Smith ML, Sebra R, Mace EM, Horowitz A, Thomson W, Martin P, Eyre S, Davis DM. Diversity of peripheral blood human NK cells identified by single-cell RNA sequencing. Blood Adv. 2020 Apr 14;4(7):1388-1406. doi: 10.1182/bloodadvances.2019000699. PMID:32271902
34. Green DG, Whitener AE, Mohanty S, Mistretta B, Gunaratne P, Yeh AT, Lekven AC. Wnt signaling regulates neural plate patterning in distinct temporal phases with dynamic transcriptional outputs. Dev Biol. 2020 Mar 31. pii: S0012-1606(20)30104-4. doi: 10.1016/j.ydbio.2020.03.016. PMID: 32243887
35. Integrative Analyses of Multilevel Omics Reveal Preneoplastic Breast to Possess a Molecular Landscape That is Globally Shared with Invasive Basal-Like Breast Cancer (Running Title: Molecular Landscape of Basal-Like Breast Cancer Progression). Ju Z, Bhardwaj A, Embury MD, Singh H, Gunaratne PH, Bedrosian I, Wang J. Cancers (Basel). 2020 Mar 19;12(3). pii: E722. doi: 10.3390/cancers12030722. PMID: 32204397
36. Andrew J. Davis, Maksym Tsinkevich, Jason Rodencal, Hussein A. Abbas, Xiao-hua Su, Young-Jin Gi, Bin Fang, Kimal Rajapakshe, Cristian Coarfa, Preethi H. Gunaratne, John M. Koomen, Kenneth Y. Tsai, Elsa R. Flores. TAp63-regulated microRNAs suppress cutaneous squamous cell carcinoma through inhibition of a network of cell cycle genes. Cancer Res. 2020 Jun 15; 80(12): 2484–2497. PMCID: PMC7299759
37. Raghunathan S, Islas JF, Mistretta B, Iyer D, Shi L, Gunaratne PH, Ko G, Schwartz RJ, McConnell BK. Conversion of human cardiac progenitor cells into cardiac pacemaker-like cells. J Mol Cell Cardiol. 2020 Jan;138:12-22. doi: 10.1016/j.yjmcc.2019.09.015. Epub 2019 Oct 31. PMID: 31678351
38. Patil SL, Palat A, Pan Y, Rajapakshe K, Mirchandani R, Bondesson M, Yustein JT, Coarfa C, Gunaratne PH.* MicroRNA-509-3p inhibits cellular migration, invasion, and proliferation, and sensitizes osteosarcoma to cisplatin. Sci Rep. 2019 Dec 13;9(1):19089. doi: 10.1038/s41598-019-55170-2. PMID: 31836741. Corresponding Author*
39. Havis S, Bodunrin A, Rangel J, Zimmerer R, Murphy J, Storey JD, Duong TD, Mistretta B, Gunaratne P, Widger WR, Bark SJ. A Universal Stress Protein that Controls Bacterial Stress Survival in Micrococcus luteus. J Bacteriol. 2019 Sep 23. pii: JB.00497-19. doi: 10.1128/JB.00497-19. PMID: 31548273
40. Hu Q, Ye Y, Chan LC, Li Y, Liang K, Lin A, Egranov SD, Zhang Y, Xia W, Gong J, Pan Y, Chatterjee SS, Yao J, Evans KW, Nguyen TK, Park PK, Liu J, Coarfa C, Donepudi SR, Putluri V, Putluri N, Sreekumar A, Ambati CR, Hawke DH, Marks JR, Gunaratne PH, Caudle AS, Sahin AA, Hortobagyi GN, Meric-Bernstam F, Chen L, Yu D, Hung MC, Curran MA, Han L, Lin C, Yang L. Oncogenic lncRNA downregulates cancer cell antigen presentation and intrinsic tumor suppression. Nat Immunol. 2019 Jun 3. doi: 10.1038/s41590-019-0400-7. PMID:31160797
41. Maria Moreno-Villanueva, Ye Zhang, Alan Feiveson, Brandon Mistretta, Yinghong Pan, Sujash Chatterjee, Winston Wu, Ryan Clanton, Mayra, Nelman-Gonzalez, Stephanie Krieger, Preethi Gunarantne, Brian Crucian, Honglu Wu. Single-cell RNA-sequencing identifies activation of TP53 and STAT1 pathways in human T lymphocyte subpopulations in response to ex vivo radiation exposure. Int. J. Mol. Sci. 2019, ijms-487137
42. Gunaratne PH*, Pan Y, Rao AK, Lin C, Hernandez-Herrera A, Liang K, Rait AS, Venkatanarayan A, Benham AL, Rubab F, Kim SS, Rajapakshe K, Chan CK, Mangala LS, Lopez-Berestein G, Sood AK, Rowat AC, Coarfa C, Pirollo KF, Flores ER, Chang EH*. Activating p53 family member TAp63: A novel therapeutic strategy for targeting p53-altered tumors. Cancer. 2019 Apr 23. doi: 10.1002/cncr.32053. PMID: 31012964. Corresponding Authors*
43. Chen C, Meng Q, Xia Y, Ding C, Wang L, Dai R, Cheng L, Gunaratne P, Gibbs RA, Min S, Coarfa C, Reid JG, Zhang C, Jiao C, Jiang Y, Giase G, Thomas A, Fitzgerald D, Brunetti T, Shieh A, Xia C, Wang Y, Wang Y, Badner JA, Gershon ES, White KP, Liu C. The transcription factor POU3F2 regulates a gene coexpression network in brain tissue from patients with psychiatric disorders.Sci Transl Med.2018 Dec 13. pii: eaat8178. doi: 10.1126/scitranslmed.aat8178. PMID:30545964
44. Korkut A, Zaidi S, Kanchi RS, Rao S, Gough NR, Schultz A, Li X, Lorenzi PL, Berger AC, Robertson G, Kwong LN, Datto M, Roszik J, Ling S, Ravikumar V, Manyam G, Rao A, Shelley S, Liu Y, Ju Z, Hansel D, de Velasco G, Pennathur A, Andersen JB, O'Rourke CJ, Ohshiro K, Jogunoori W, Nguyen BN, Li S, Osmanbeyoglu HU, Ajani JA, Mani SA, Houseman A, Wiznerowicz M, Chen J, Gu S, Ma W, Zhang J, Tong P, Cherniack AD, Deng C, Resar L, The Cancer Genome Atlas Research Network, Weinstein JN, Mishra L, Akbani R. A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily. Cell Syst. 2018 Sep 14. pii: S2405-4712(18)30357-0. PMID: 30268436
45. Hoang J, Park CS, Lee HJ, Marquez MD, Zenasni O, Gunaratne PH, Lee TR. Quaternary Ammonium-Terminated Films Formed from Mixed Bidentate Adsorbates Provide a High-Capacity Platform for Oligonucleotide Delivery. ACS Appl Mater Interfaces. 2018 Oct 18. PMID: 30335936
46. Pahlavani M, Wijayatunga NN, Kalupahana NS, Ramalingam L, Gunaratne PH, Coarfa C, Rajapakshe K, Kottapalli P, Moustaid-Moussa N. Transcriptomic and MicroRNA analyses of gene networks regulated by eicosapentaenoic acid in brown adipose tissue of diet-induced obese mice. Biochim Biophys Acta Mol Cell Biol Lipids. 2018 Sep 24. pii: S1388-1981(18)30284-1. PMID: 30261280
47. Chen L, Youssef Y, Robinson C, Ernst GF, Carson MY, Young KA, Scoville SD, Zhang X, Harris R, Sekhri P, Mansour AG, Chan WK, Nalin AP, Mao HC, Hughes T, Mace EM, Pan Y, Rustagi N, Chatterjee SS, Gunaratne PH, Behbehani GK, Mundy-Bosse BL, Caligiuri MA, Freud AG. CD56 Expression Marks Human Group 2 Innate Lymphoid Cell Divergence from a Shared NK Cell and Group 3 Innate Lymphoid Cell Developmental Pathway. Immunity. 2018 Sep 18;49(3):464-476.e4. PMID: 30193847
48. Berger AC, Korkut A, Kanchi RS, Hegde AM, Lenoir W, Liu W, Liu Y, Fan H, Shen H, Ravikumar V, Rao A, Schultz A, Li X, Sumazin P, Williams C, Mestdagh P, Gunaratne PH, Yau C, Bowlby R, Robertson AG, Tiezzi DG, Wang C, Cherniack AD, Godwin AK, Kuderer NM, Rader JS, Zuna RE, Sood AK, Lazar AJ, Ojesina AI, Adebamowo C, Adebamowo SN, Baggerly KA, Chen TW, Chiu HS, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CS, Song Q, Vellano CP, Wentzensen N; Cancer Genome Atlas Research Network, Weinstein JN, Mills GB, Levine DA, Akbani R. A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer Cell. 2018 Apr 1. pii: S1535-6108(18)30119-3. doi: 10.1016/j.ccell.2018.03.014. [Epub ahead of print] PMID: 29622464
49. Chiu HS, Somvanshi S, Patel E, Chen TW, Singh VP, Zorman B, Patil SL, Pan Y, Chatterjee SS; Cancer Genome Atlas Research Network, Sood AK, Gunaratne PH, Sumazin P. Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context. Cell Rep. 2018 Apr 3;23(1):297-312.e12. doi: 10.1016/j.celrep.2018.03.064. PMID: 29617668
50. Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK; Cancer Genome Atlas Research Network, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Rep. 2018 Apr 3;23(1):194-212.e6. doi: 10.1016/j.celrep.2018.03.063. PMID: 29617660
51. Wijayatunga NN, Pahlavani M, Kalupahana NS, Kottapalli KR, Gunaratne PH, Coarfa C, Ramalingam L, Moustaid-Moussa N. An integrative transcriptomic approach to identify depot differences in genes and microRNAs in adipose tissues from high fat fed mice. Oncotarget. 2018 Jan 13;9(10):9246-9261. doi: 10.18632/oncotarget.24226. eCollection 2018 Feb 6. PMID:29507687
52. Abbas H, Bao Bui NH, Rajapakshe K, Wong J, Gunaratne P, Tsai KY, Coarfa C, Flores ER. Distinct TP63 isoform-driven transcriptional signatures predict tumor progression and clinical outcomes. Cancer Res. 2017 Nov 27. pii: canres.1803.2017. doi: 10.1158/0008-5472.CAN-17-1803. PMID:29180475
53. Fujita J, Freire P, Coarfa C, Benham AL, Gunaratne P, Schneider MD, Dejosez M, Zwaka TP. Ronin Governs Early Heart Development by Controlling Core Gene Expression Programs. Cell Rep. 2017 Nov 7;21(6):1562-1573. doi: 10.1016/j.celrep.2017.10.036. PMID:29117561
54. Shakiba A, Patil SL, Zenasni O, Schmitt ME, Gunaratne PH, Lee TR. DNA Loading and Release Using Custom-Tailored Poly(l-lysine) Surfaces. ACS Appl Mater Interfaces. 2017 Jul 19;9(28):23370-23378. doi: 10.1021/acsami.7b05024. Epub 2017 Jul 10. PMID: 28636320
55. Bhardwaj A, Singh H, Rajapakshe K, Tachibana K, Ganesan N, Pan Y, Gunaratne PH, Coarfa C, Bedrosian I. Regulation of miRNA-29c and its downstream pathways in preneoplastic progression of triple-negative breast cancer. Oncotarget. 2017 Jan 30. doi: 10.18632/oncotarget.14902. PMID: 28160548
56. Su X, Napoli M, Abbas HA, Venkatanarayan A, Bui NH, Coarfa C, Gi YJ, Kittrell F, Gunaratne PH, Medina D, Rosen JM, Behbod F, Flores ER. TAp63 suppresses mammary tumorigenesis through regulation of the Hippo pathway. Oncogene. 2016 Nov 21. doi: 10.1038/onc.2016.388. PMID: 27869165
57. Chan CK, Pan Y, Nyberg K, Marra MA, Lim EL, Jones SJ, Maar D, Gibb EA, Gunaratne PH, Robertson AG, Rowat AC. Tumour-suppressor microRNAs regulate ovarian cancer cell physical properties and invasive behaviour. Open Biol. 2016 Nov;6(11). pii: 160275. PMID: 27906134
58. Chitsazzadeh V, Coarfa C, Drummond JA, Nguyen T, Joseph A, Chilukuri S, Charpiot E, Adelmann CH, Ching G, Nguyen TN, Nicholas C, Thomas VD, Migden M, MacFarlane D, Thompson E, Shen J, Takata Y, McNiece K, Polansky MA, Abbas HA, Rajapakshe K, Gower A, Spira A, Covington KR, Xiao W, Gunaratne P, Pickering C, Frederick M, Myers JN, Shen L, Yao H, Su X, Rapini RP, Wheeler DA, Hawk ET, Flores ER, Tsai KY. Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates. Nat Commun. 2016 Aug 30;7:12601. doi: 10.1038/ncomms12601. PMID: 27574101
59. Shen X, Soibam B, Benham A, Xu X, Chopra M, Peng X, Yu W, Bao W, Liang R, Azares A, Liu P, Gunaratne PH, Mercola M, Cooney AJ, Schwartz RJ, Liu Y. miR-322/-503 cluster is expressed in the earliest cardiac progenitor cells and drives cardiomyocyte specification. Proc Natl Acad Sci U S A. 2016 Aug 10. pii: 201608256. PMID: 27512039
60. Liu Y, Chen L, Diaz AD, Benham A, Xu X, Wijaya CS, Fa'ak F, Luo W, Soibam B, Azares A, Yu W, Lyu Q, Stewart MD, Gunaratne P, Cooney A, McConnell BK, Schwartz RJ. Mesp1 Marked Cardiac Progenitor Cells Repair Infarcted Mouse Hearts. Sci Rep. 2016 Aug 19;6:31457. doi: 10.1038/srep31457. PMID: 27538477
61. Basu-Roy U, Han E, Rattanakorn K, Gadi A, Verma N, Maurizi G, Gunaratne PH, Coarfa C, Kennedy OD, Garabedian MJ, Basilico C, Mansukhani A. PPARγ agonists promote differentiation of cancer stem cells by restraining YAP transcriptional activity. Oncotarget. 2016 Aug 12. doi: 10.18632/oncotarget.11273. PMID: 27528232
62. Napoli M, Venkatanarayan A, Raulji P, Meyers BA, Norton W, Mangala LS, Sood AK, Rodriguez-Aguayo C, Lopez-Berestein G, Vin H, Duvic M, Tetzlaff MB, Curry JL, Rook AH, Abbas HA, Coarfa C, Gunaratne PH, Tsai KY, Flores ER. ΔNp63/DGCR8-Dependent MicroRNAs Mediate Therapeutic Efficacy of HDAC Inhibitors in Cancer. Cancer Cell. 2016 Jun 13;29(6):874-888. doi: 10.1016/j.ccell.2016.04.016. PMID: 27300436
63. O'Brien R, Tran SL, Maritz M, Liu B, Kong CF, Purgato S, Yang C, Murray J, Russel AJ, Flemming CL, von Jonquieres G, Pickett HA, London WB, Haber M, Gunaratne PH, Norris MD, Perrini G, Fletcher JI, MacKenzie KL. MYC-driven neuroblastomas are addicted to a telomerase-independent function of dyskerin. Cancer Res. 2016 Apr 13. pii: canres.0879.2015. PMID: 27197171
64. Pan Y, Robertson G, Pedersen L, Lim E, Hernandez-Herrera A, Rowat AC, Patil SL, Chan CK, Wen Y, Zhang X, Basu-Roy U, Mansukhani A, Chu A, Sipahimalani P, Bowlby R, Brooks D, Thiessen N, Coarfa C, Ma Y, Moore RA, Schein JE, Mungall AJ, Liu J, Pecot CV, Sood AK, Jones SJ, Marra MA, Gunaratne PH. miR-509-3p is clinically significant and strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer. Oncotarget. 2016 Mar 27. doi: 10.18632/oncotarget.8412. PMID: 27036018
65. Saurabh Agarwal, Rajib Ghosh, Zaowen Chen, Anna Lakoma, Preethi H. Gunaratne, Eugene S. Kim, Jason M. Shohet. Transmembrane adaptor protein PAG1 is a novel tumor suppressor in neuroblastoma. Oncotarget 2016. Mar 16. doi: 10.18632/oncotarget.8116. PMID: 26993602
66. Thomas AL, Coarfa C, Qian J, Wilkerson JJ, Rajapakshe K, Krett NL, Gunaratne PH, Rosen ST. Identification of potential glucocorticoid receptor therapeutic targets in multiple myeloma. Nucl Recept Signal. 2015 Dec 22;13:e006. doi: 10.1621/nrs.13006. eCollection 2015. PMID: 26715915
67. Liu C, Lou CH, Shah V, Ritter R, Talley J, Soibam B, Benham A, Zhu H, Perez E, Shieh YE, Gunaratne PH, Sater AK. Identification of microRNAs and microRNA Targets in Xenopus gastrulae: The role of miR-26 in the regulation of Smad1. Dev Biol. 2015 Nov 5. pii: S0012-1606(15)30277-3. doi: 10.1016/j.ydbio.2015.11.005. PMID: 26548531
68. Jonsson P, Coarfa C, Mesmar F, Raz T, Rajapakshe K, Thompson JF, Gunaratne PH, Williams C. Single-molecule sequencing reveals estrogen-regulated clinically relevant lncRNAs in breast cancer. Mol Endocrinol. 2015 Oct 1:me20151153. PMID: 26426411
69. Venkatanarayan A, Raulji P, Norton W, Chakravarti D, Coarfa C, Su X, Sandur SK, Ramirez MS, Lee J, Kingsley CV, Sananikone EF, Rajapakshe K, Naff K, Parker-Thornburg J, Bankson JA, Tsai KY, Gunaratne PH, Flores ER. IAPP-driven metabolic reprogramming induces regression of p53-deficient tumours in vivo. Nature. 2015 Jan 29;517(7536):626-30. doi: 10.1038/nature13910. Epub 2014 Nov 17. PMID: 25409149
70. Bhardwaj A, Ganesan N, Tachibana K, Rajapakshe K, Albarracin CT, Gunaratne PH, Coarfa C, Bedrosian. Annexin A1 Preferentially Predicts Poor Prognosis of Basal-Like Breast Cancer Patients by Activating mTOR-S6 Signaling. PLoS One. 2015 May 22;10(5):e0127678. doi: 10.1371/journal.pone.0127678. eCollection 2015. PMID: 26000884
71. Menon DU, Coarfa C, Xiao W, Gunaratne PH, Meller VH. siRNAs from an X-linked satellite repeat promote X-chromosome recognition in Drosophila melanogaster. Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):16460-5. doi: 10.1073/pnas.1410534111. Epub 2014 Nov 3. PMID: 25368194
72. Yu Z, Kim J, He L, Creighton CJ, Gunaratne PH, Hawkins SM, Matzuk MM. Functional analysis of miR-34c as a putative tumor suppressor in high-grade serous ovarian cancer. Biol Reprod. 2014 Nov;91(5):113. doi: 10.1095/biolreprod.114.121988. Epub 2014 Oct 1. PMID: 25273528
73. Davis CF, Ricketts CJ, Wang M, Yang L, Cherniack AD, Shen H, Buhay C, Kang H, Kim SC, Fahey CC, Hacker KE, Bhanot G, Gordenin DA, Chu A, Gunaratne PH, Biehl M, Seth S, Kaipparettu BA, Bristow CA, Donehower LA, Wallen EM, Smith AB, Tickoo SK, Tamboli P, Reuter V, Schmidt LS, Hsieh JJ, Choueiri TK, Hakimi AA; Cancer Genome Atlas Research Network, Chin L, Meyerson M, Kucherlapati R, Park WY, Robertson AG, Laird PW, Henske EP, Kwiatkowski DJ, Park PJ, Morgan M, Shuch B, Muzny D, Wheeler DA, Linehan WM, Gibbs RA, Rathmell WK, Creighton CJ. The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell. 2014 Sep 8;26(3):319-30. doi: 10.1016/j.ccr.2014.07.014. Epub 2014 Aug 21. PMID: 25155756
74. Bliss-Moreau M, Coarfa C, Gunaratne PH, Guitart J, Krett NL, Rosen ST. J Invest Dermatol. Identification of p38β as a therapeutic target for the treatment of Sézary syndrome. 2015 Feb;135(2):599-608. doi: 10.1038/jid.2014.367. Epub 2014 Aug 22. PMID: 25148579
75. Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, Leiserson MD, Niu B, McLellan MD, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, Chu A, Margolin AA, Van't Veer LJ, Lopez-Bigas N, Laird PW, Raphael BJ, Ding L, Robertson AG, Byers LA, Mills GB, Weinstein JN, Van Waes C, Chen Z, Collisson EA; Cancer Genome Atlas Research Network, Benz CC, Perou CM, Stuart JM. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell. 2014 Aug 14;158(4):929-44. doi: 10.1016/j.cell.2014.06.049. Epub 2014 Aug 7. PMID: 25109877
76. Boele J, Persson H, Shin JW, Ishizu Y, Newie IS, Søkilde R, Hawkins SM, Coarfa C, Ikeda K, Takayama K, Horie-Inoue K, Ando Y, Burroughs AM, Sasaki C, Suzuki C, Sakai M, Aoki S, Ogawa A, Hasegawa A, Lizio M, Kaida K, Teusink B, Carninci P, Suzuki H, Inoue S, Gunaratne PH, Rovira C, Hayashizaki Y, de Hoon MJ. PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease. Proc Natl Acad Sci U S A. 2014 Aug 5;111(31):11467-72. doi: 10.1073/pnas.1317751111. Epub 2014 Jul 21. PMID: 25049417
77. Marmoset Genome Sequencing and Analysis Consortium. The common marmoset genome provides insight into primate biology and evolution. Nat Genet. 2014 Aug;46(8):850-7. doi: 10.1038/ng.3042. Epub 2014 Jul 20. PMID: 25038751
78. Chakravarti D, Su X, Cho MS, Bui NH, Coarfa C, Venkatanarayan A, Benham AL, Flores González RE, Alana J, Xiao W, Leung ML, Vin H, Chan IL, Aquino A, Müller N, Wang H, Cooney AJ, Parker-Thornburg J, Tsai KY, Gunaratne PH, Flores ER. Induced multipotency in adult keratinocytes through down-regulation of ΔNp63 or DGCR8. Proc Natl Acad Sci U S A. 2014 Feb 4;111(5):E572-81. doi: 10.1073/pnas.1319743111. Epub 2014 Jan 21. PMID: 24449888
79. Cheng JC, McBrayer SK, Coarfa C, Dalva-Aydemir S, Gunaratne PH, Carpten JD, Keats JK, Rosen ST, Shanmugam M. Expression and phosphorylation of the AS160_v2 splice variant supports GLUT4 activation and the Warburg effect in multiple myeloma. Cancer Metab. 2013 May 29;1(1):14. doi: 10.1186/2049-3002-1-14. PMID: 24280290
80. Jeong M, Sun D, Luo M, Huang Y, Challen GA, Rodriguez B, Zhang X, Chavez L, Wang H, Hannah R, Kim SB, Yang L, Ko M, Chen R, Göttgens B, Lee JS, Gunaratne P, Godley LA, Darlington GJ, Rao A, Li W, Goodell MA. Large conserved domains of low DNA methylation maintained by Dnmt3a. Nat Genet. 2014 Jan;46(1):17-23. doi: 10.1038/ng.2836. Epub 2013 Nov 24. PMID: 24270360
81. Hamilton MP, Rajapakshe K, Hartig SM, Reva B, McLellan MD, Kandoth C, Ding L, Zack TI, Gunaratne PH, Wheeler DA, Coarfa C, McGuire SE. Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif. Nat Commun. 2013;4:2730. doi: 10.1038/ncomms3730. PMID: 24220575
82. Pan Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. Nat Genet. 2013 Oct;45(10):1113-20. doi: 10.1038/ng.2764. PMID: 24071849
83. Tennakoon JB, Wang H, Coarfa C, Cooney AJ, Gunaratne PH. Chromatin changes in dicer-deficient mouse embryonic stem cells in response to retinoic acid induced differentiation. PLoS One. 2013 Sep 9;8(9):e74556. doi: 10.1371/journal.pone.0074556. eCollection 2013. PMID: 24040281
84. Seo E, Basu-Roy U, Gunaratne PH, Coarfa C, Lim DS, Basilico C, Mansukhani A. SOX2 regulates YAP1 to maintain stemness and determine cell fate in the osteo-adipo lineage. Cell Rep. 2013 Jun 27;3(6):2075-87. doi: 10.1016/j.celrep.2013.05.029. Epub 2013 Jun 20. PMID: 23791527
85. Cancer Genome Atlas Research Network. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013 Jul 4;499(7456):43-9. doi: 10.1038/nature12222. Epub 2013 Jun 23. PMID: 23792563
86. Hsu DM, Agarwal S, Benham A, Coarfa C, Trahan DN, Chen Z, Stowers PN, Courtney AN, Lakoma A, Barbieri E, Metelitsa LS, Gunaratne P, Kim ES, Shohet JM. G-CSF receptor positive neuroblastoma subpopulations are enriched in chemotherapy-resistant or relapsed tumors and are highly tumorigenic. Cancer Res. 2013 Jul 1;73(13):4134-46. doi: 10.1158/0008-5472.CAN-12-4056. Epub 2013 May 16. PMID: 23687340
87. Mach CM, Kim J, Soibam B, Creighton CJ, Hawkins SM, Zighelboim I, Goodfellow P, Gunaratne PH, Odunsi K, Salem PA, Anderson ML. Novel MicroRNAs regulating proliferation and apoptosis in uterine papillary serous carcinomas. Cancer Lett. 2013 Jul 28;335(2):314-22. doi: 10.1016/j.canlet.2013.02.043. Epub 2013 Feb 26. PMID: 23454583
88. Munch EM, Harris RA, Mohammad M, Benham AL, Pejerrey SM, Showalter L, Hu M, Shope CD, Maningat PD, Gunaratne PH, Haymond M, Aagaard K. Transcriptome profiling of microRNA by Next-Gen deep sequencing reveals known and novel miRNA species in the lipid fraction of human breast milk. PLoS One. 2013;8(2):e50564. doi: 10.1371/journal.pone.0050564. Epub 2013 Feb 13. PMID: 23418415
89. Plé H, Landry P, Benham A, Coarfa C, Gunaratne PH, Provost P. The repertoire and features of human platelet microRNAs. PLoS One. 2012;7(12):e50746. doi: 10.1371/journal.pone.0050746. Epub 2012 Dec 4. PMID: 23226537
90. Ghosh R, Singh LC, Shohet JM, Gunaratne PH. A gold nanoparticle platform for the delivery of functional microRNAs into cancer cells. Biomaterials. 2013 Jan;34(3):807-16. doi: 10.1016/j.biomaterials.2012.10.023. Epub 2012 Oct 27. PMID: 23111335
91. Donehower LA, Creighton CJ, Schultz N, Shinbrot E, Chang K, Gunaratne PH, Muzny D, Sander C, Hamilton SR, Gibbs RA, Wheeler D. MLH1-silenced and non-silenced subgroups of hypermutated colorectal carcinomas have distinct mutational landscapes. J Pathol. 2013 Jan;229(1):99-110. doi: 10.1002/path.4087. PMID: 22899370
92. Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 Jul 18;487(7407):330-7. doi: 10.1038/nature11252. PMID: 22810696
93. Hawkins SM, Andreu-Vieyra CV, Kim TH, Jeong JW, Hodgson MC, Chen R, Creighton CJ, Lydon JP, Gunaratne PH, DeMayo FJ, Matzuk MM. Dysregulation of uterine signaling pathways in progesterone receptor-Cre knockout of dicer. Mol Endocrinol. 2012 Sep;26(9):1552-66. doi: 10.1210/me.2012-1042. Epub 2012 Jul 13. PMID: 22798293
94. Wang Y, Brahmakshatriya V, Lupiani B, Reddy SM, Soibam B, Benham AL, Gunaratne P, Liu HC, Trakooljul N, Ing N, Okimoto R, Zhou H. Integrated analysis of microRNA expression and mRNA transcriptome in lungs of avian influenza virus infected broilers. BMC Genomics. 2012 Jun 22;13:278. doi: 10.1186/1471-2164-13-278. PMID: 22726614
95. Plante I, Plé H, Landry P, Gunaratne PH, Provost P. Modulation of microRNA Activity by Semi-microRNAs. Front Genet. 2012 Jun 4;3:99. doi: 10.3389/fgene.2012.00099. eCollection 2012. PMID: 22675332
96. Creighton CJ, Hernandez-Herrera A, Jacobsen A, Levine DA, Mankoo P, Schultz N, Du Y, Zhang Y, Larsson E, Sheridan R, Xiao W, Spellman PT, Getz G, Wheeler DA, Perou CM, Gibbs RA, Sander C, Hayes DN, Gunaratne PH; Cancer Genome Atlas Research Network. Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma. PLoS One. 2012;7(3):e34546. doi: 10.1371/journal.pone.0034546. Epub 2012 Mar 29. PMID: 22479643
97. Luo Z, Xu X, Gu P, Lonard D, Gunaratne PH, Cooney AJ, Azencott R. miRNA regulatory circuits in ES cells differentiation: a chemical kinetics modeling approach. PLoS One. 2011;6(10):e23263. doi: 10.1371/journal.pone.0023263. Epub 2011 Oct 19. PMID: 22039400
98. Tessel MA, Benham AL, Krett NL, Rosen ST, Gunaratne PH. Role for microRNAs in regulating glucocorticoid response and resistance in multiple myeloma. Horm Cancer. 2011 Jun;2(3):182-9. doi: 10.1007/s12672-011-0072-8. PMID: 21761344
99. Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 29;474(7353):609-15. doi: 10.1038/nature10166. Erratum in: Nature. 2012 Oct 11;490(7419):298. PMID: 21720365
100. 100.Gunaratne PH, Lin YC, Benham AL, Drnevich J, Coarfa C, Tennakoon JB, Creighton CJ, Kim JH, Milosavljevic A, Watson M, Griffiths-Jones S, Clayton DF. Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain. BMC Genomics. 2011 May 31;12(1):277. doi: 10.1186/1471-2164-12-277. PMID: 21627805
101. 101.Shohet JM, Ghosh R, Coarfa C, Ludwig A, Benham AL, Chen Z, Patterson DM, Barbieri E, Mestdagh P, Sikorski DN, Milosavljevic A, Kim ES, Gunaratne PH. A genome-wide search for promoters that respond to increased MYCN reveals both new oncogenic and tumor suppressor microRNAs associated with aggressive neuroblastoma. Cancer Res. 2011 Jun 1;71(11):3841-51. doi: 10.1158/0008-5472.CAN-10-4391. Epub 2011 Apr 15. PMID: 21498633
102. 102.Hawkins SM, Creighton CJ, Han DY, Zariff A, Anderson ML, Gunaratne PH, Matzuk MM. Functional microRNA involved in endometriosis.  Mol Endocrinol. 2011 May;25(5):821-32. doi: 10.1210/me.2010-0371. Epub 2011 Mar 24. PMID: 21436257
103. 103.Mullany LK, Fan HY, Liu Z, White LD, Marshall A, Gunaratne P, Anderson ML, Creighton CJ, Xin L, Deavers M, Wong KK, Richards JS. Molecular and functional characteristics of ovarian surface epithelial cells transformed by KrasG12D and loss of Pten in a mouse model in vivo. Oncogene. 2011 Aug 11;30(32):3522-36. doi: 10.1038/onc.2011.70. Epub 2011 Mar 21. PMID: 21423204
104. 104.Zhang L, Sullivan PS, Goodman JC, Gunaratne PH, Marchetti D. MicroRNA-1258 suppresses breast cancer brain metastasis by targeting heparanase. Cancer Res. 2011 Feb 1;71(3):645-54. doi: 10.1158/0008-5472.CAN-10-1910. Epub 2011 Jan 25. PMID: 21266359
105. 105.Buchold GM, Coarfa C, Kim J, Milosavljevic A, Gunaratne PH, Matzuk MM. Analysis of microRNA expression in the prepubertal testis. PLoS One. 2010 Dec 29;5(12):e15317. doi: 10.1371/journal.pone.0015317. PMID: 21206922
106. 106.Gunaratne GH, Gunaratne PH, Seemann L, Török A. Using effective subnetworks to predict selected properties of gene networks. PLoS One. 2010 Oct 8;5(10):e13080. doi: 10.1371/journal.pone.0013080. PMID: 20949025
107. 107.Polikepahad S, Knight JM, Naghavi AO, Oplt T, Creighton CJ, Shaw C, Benham AL, Kim J, Soibam B, Harris RA, Coarfa C, Zariff A, Milosavljevic A, Batts LM, Kheradmand F, Gunaratne PH, Corry DB. Proinflammatory role for let-7 microRNAS in experimental asthma. J Biol Chem. 2010 Sep 24;285(39):30139-49. doi: 10.1074/jbc.M110.145698. Epub 2010 Jul 14. PMID: 20630862
108. 108.Dejosez M, Levine SS, Frampton GM, Whyte WA, Stratton SA, Barton MC, Gunaratne PH, Young RA, Zwaka TP. Ronin/Hcf-1 binds to a hyperconserved enhancer element and regulates genes involved in the growth of embryonic stem cells. Genes Dev. 2010 Jul 15;24(14):1479-84. doi: 10.1101/gad.1935210. Epub 2010 Jun 25. PMID: 20581084
109. 109.Zhu H, Gunaratne PH, Roman GW, Gunaratne GH. A theory for the arrangement of sensory organs in Drosophila. Chaos. 2010 Mar;20(1):013132. doi: 10.1063/1.3368727. PMID: 20370287
110. 110.Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backström N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Völker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK. The genome of a songbird. Nature. 2010 Apr 1;464(7289):757-62. doi: 10.1038/nature08819. PMID: 20360741
111. 111.Creighton CJ, Benham AL, Zhu H, Khan MF, Reid JG, Nagaraja AK, Fountain MD, Dziadek O, Han D, Ma L, Kim J, Hawkins SM, Anderson ML, Matzuk MM, Gunaratne PH. Discovery of novel microRNAs in female reproductive tract using next generation sequencing. PLoS One. 2010 Mar 10;5(3):e9637. doi: 10.1371/journal.pone.0009637. PMID: 20224791
112. 112.Creighton CJ, Fountain MD, Yu Z, Nagaraja AK, Zhu H, Khan M, Olokpa E, Zariff A, Gunaratne PH, Matzuk MM, Anderson ML. profiling uncovers a p53-associated role for microRNA-31 in inhibiting the proliferation of serous ovarian carcinomas and other cancers. Cancer Res. 2010 Mar 1;70(5):1906-15. doi: 10.1158/0008-5472.CAN-09-3875. Epub 2010 Feb 23. PMID: 20179198
113. 113.Greene SB, Gunaratne PH, Hammond SM, Rosen JM. A putative role for microRNA-205 in mammary epithelial cell progenitors. J Cell Sci. 2010 Feb 15;123(Pt 4):606-18. doi: 10.1242/jcs.056812. Epub 2010 Jan 26. PMID: 20103531
114. 114.Nagaraja AK, Creighton CJ, Yu Z, Zhu H, Gunaratne PH, Reid JG, Olokpa E, Itamochi H, Ueno NT, Hawkins SM, Anderson ML, Matzuk MM. A link between mir-100 and FRAP1/mTOR in clear cell ovarian cancer. Mol Endocrinol. 2010 Feb;24(2):447-63. doi: 10.1210/me.2009-0295. Epub 2010 Jan 15. PMID: 20081105
115. 115.Wang Y, Brahmakshatriya V, Zhu H, Lupiani B, Reddy SM, Yoon BJ, Gunaratne PH, Kim JH, Chen R, Wang J, Zhou H. Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach. BMC Genomics. 2009 Nov 5;10:512. doi: 10.1186/1471-2164-10-512. Erratum in: BMC Genomics. 2010;11:373. PMID: 19891781
116. 116.MGC Project Team, Temple G, Gerhard DS, Rasooly R, Feingold EA, Good PJ, Robinson C, Mandich A, Derge JG, Lewis J, Shoaf D, Collins FS, Jang W, Wagner L, Shenmen CM, Misquitta L, Schaefer CF, Buetow KH, Bonner TI, Yankie L, Ward M, Phan L, Astashyn A, Brown G, Farrell C, Hart J, Landrum M, Maidak BL, Murphy M, Murphy T, Rajput B, Riddick L, Webb D, Weber J, Wu W, Pruitt KD, Maglott D, Siepel A, Brejova B, Diekhans M, Harte R, Baertsch R, Kent J, Haussler D, Brent M, Langton L, Comstock CL, Stevens M, Wei C, van Baren MJ, Salehi-Ashtiani K, Murray RR, Ghamsari L, Mello E, Lin C, Pennacchio C, Schreiber K, Shapiro N, Marsh A, Pardes E, Moore T, Lebeau A, Muratet M, Simmons B, Kloske D, Sieja S, Hudson J, Sethupathy P, Brownstein M, Bhat N, Lazar J, Jacob H, Gruber CE, Smith MR, McPherson J, Garcia AM, Gunaratne PH, Wu J, Muzny D, Gibbs RA, Young AC, Bouffard GG, Blakesley RW, Mullikin J, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Hirst M, Zeng T, Tse K, Moksa M, Deng M, Ma K, Mah D, Pang J, Taylor G, Chuah E, Deng A, Fichter K, Go A, Lee S, Wang J, Griffith M, Morin R, Moore RA, Mayo M, Munro S, Wagner S, Jones SJ, Holt RA, Marra MA, Lu S, Yang S, Hartigan J, Graf M, Wagner R, Letovksy S, Pulido JC, Robison K, Esposito D, Hartley J, Wall VE, Hopkins RF, Ohara O, Wiemann S. The completion of the Mammalian Gene Collection (MGC). Genome Res. 2009 Dec;19(12):2324-33. doi: 10.1101/gr.095976.109. Epub 2009 Sep 18. PMID: 19767417
117. 117.Wang X, Sutton VR, Eble TN, Lewis RA, Gunaratne P, Patel A, Van den Veyver IB. A genome-wide screen for copy number alterations in Aicardi syndrome. Am J Med Genet. 2009 Oct;149A(10):2113-21. doi: 10.1002/ajmg.a.32976. PMID: 19760649
118. 118.Ma L, Buchold GM, Greenbaum MP, Roy A, Burns KH, Zhu H, Han DY, Harris RA, Coarfa C, Gunaratne PH, Yan W, Matzuk MM GASZ is essential for male meiosis and suppression of retrotransposon expression in the male germline. PLoS Genet. 2009 Sep;5(9):e1000635. doi: 10.1371/journal.pgen.1000635. Epub 2009 Sep 4. Erratum in: PLoS Genet. 2009 Dec;5(12). doi: 10.1371/annotation/20bf08d1-07e9-451e-b079-166832ebe158. PMID: 19730684
119. 119.López-Terrada D, Gunaratne PH, Adesina AM, Pulliam J, Hoang DM, Nguyen Y, Mistretta TA, Margolin J, Finegold MJ. Histologic subtypes of hepatoblastoma are characterized by differential canonical Wnt and Notch pathway activation in DLK+ precursors. Hum Pathol. 2009 Jun;40(6):783-94. doi: 10.1016/j.humpath.2008.07.022. Epub 2009 Feb 5. PMID: 19200579
120. 120.Adesina AM, Lopez-Terrada D, Wong KK, Gunaratne P, Nguyen Y, Pulliam J, Margolin J, Finegold MJ. Gene expression profiling reveals signatures characterizing histologic subtypes of hepatoblastoma and global deregulation in cell growth and survival pathways. Hum Pathol. 2009 Jun;40(6):843-53. doi: 10.1016/j.humpath.2008.10.022. Epub 2009 Feb 5. PMID: 19200578
121. 121.Creighton CJ, Nagaraja AK, Hanash SM, Matzuk MM, Gunaratne PH. A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions. RNA. 2008 Nov;14(11):2290-6. doi: 10.1261/rna.1188208. Epub 2008 Sep 23. PMID: 18812437
122. 122.Nagaraja AK, Andreu-Vieyra C, Franco HL, Ma L, Chen R, Han DY, Zhu H, Agno JE, Gunaratne PH, DeMayo FJ, Matzuk MM. Deletion of Dicer in somatic cells of the female reproductive tract causes sterility. Mol Endocrinol. 2008 Oct;22(10):2336-52. doi: 10.1210/me.2008-0142. Epub 2008 Aug 7. PMID: 18687735
123. 123.Reid JG, Nagaraja AK, Lynn FC, Drabek RB, Muzny DM, Shaw CA, Weiss MK, Naghavi AO, Khan M, Zhu H, Tennakoon J, Gunaratne GH, Corry DB, Miller J, McManus MT, German MS, Gibbs RA, Matzuk MM, Gunaratne PH. Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes. Genome Res. 2008 Oct;18(10):1571-81. doi: 10.1101/gr.078246.108. Epub 2008 Jul 9. PMID: 18614752
124. 124.Gu P, Reid JG, Gao X, Shaw CA, Creighton C, Tran PL, Zhou X, Drabek RB, Steffen DL, Hoang DM, Weiss MK, Naghavi AO, El-daye J, Khan MF, Legge GB, Wheeler DA, Gibbs RA, Miller JN, Cooney AJ, Gunaratne PH. Novel microRNA candidates and miRNA-mRNA pairs in embryonic stem (ES) cells. PLoS One. 2008 Jul 2;3(7):e2548. doi: 10.1371/journal.pone.0002548. PMID: 18648548
125. 125.Muzny DM, Scherer SE, Kaul R, Wang J, Yu J, Sudbrak R, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZM, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavljevic A, Miner GR, Morgan MB, Nazareth LV, Scott G, Sodergren E, Song XZ, Steffen D, Wei S, Wheeler DA, Wright MW, Worley KC, Yuan Y, Zhang Z, Adams CQ, Ansari-Lari MA, Ayele M, Brown MJ, Chen G, Chen Z, Clendenning J, Clerc-Blankenburg KP, Chen R, Chen Z, Davis C, Delgado O, Dinh HH, Dong W, Draper H, Ernst S, Fu G, Gonzalez-Garay ML, Garcia DK, Gillett W, Gu J, Hao B, Haugen E, Havlak P, He X, Hennig S, Hu S, Huang W, Jackson LR, Jacob LS, Kelly SH, Kube M, Levy R, Li Z, Liu B, Liu J, Liu W, Lu J, Maheshwari M, Nguyen BV, Okwuonu GO, Palmeiri A, Pasternak S, Perez LM, Phelps KA, Plopper FJ, Qiang B, Raymond C, Rodriguez R, Saenphimmachak C, Santibanez J, Shen H, Shen Y, Subramanian S, Tabor PE, Verduzco D, Waldron L, Wang J, Wang J, Wang Q, Williams GA, Wong GK, Yao Z, Zhang J, Zhang X, Zhao G, Zhou J, Zhou Y, Nelson D, Lehrach H, Reinhardt R, Naylor SL, Yang H, Olson M, Weinstock G, Gibbs RA. The DNA sequence, annotation and analysis of human chromosome 3. Nature. 2006 Apr 27;440(7088):1194-8. PMID: 16641997
126. 126.Scherer SE, Muzny DM, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZM, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavljevic A, Miner GR, Montgomery KT, Morgan MB, Nazareth LV, Scott G, Sodergren E, Song XZ, Steffen D, Lovering RC, Wheeler DA, Worley KC, Yuan Y, Zhang Z, Adams CQ, Ansari-Lari MA, Ayele M, Brown MJ, Chen G, Chen Z, Clerc-Blankenburg KP, Davis C, Delgado O, Dinh HH, Draper H, Gonzalez-Garay ML, Havlak P, Jackson LR, Jacob LS, Kelly SH, Li L, Li Z, Liu J, Liu W, Lu J, Maheshwari M, Nguyen BV, Okwuonu GO, Pasternak S, Perez LM, Plopper FJ, Santibanez J, Shen H, Tabor PE, Verduzco D, Waldron L, Wang Q, Williams GA, Zhang J, Zhou J, Allen CC, Amin AG, Anyalebechi V, Bailey M, Barbaria JA, Bimage KE, Bryant NP, Burch PE, Burkett CE, Burrell KL, Calderon E, Cardenas V, Carter K, Casias K, Cavazos I, Cavazos SR, Ceasar H, Chacko J, Chan SN, Chavez D, Christopoulos C, Chu J, Cockrell R, Cox CD, Dang M, Dathorne SR, David R, Davis CM, Davy-Carroll L, Deshazo DR, Donlin JE, D'Souza L, Eaves KA, Egan A, Emery-Cohen AJ, Escotto M, Flagg N, Forbes LD, Gabisi AM, Garza M, Hamilton C, Henderson N, Hernandez O, Hines S, Hogues ME, Huang M, Idlebird DG, Johnson R, Jolivet A, Jones S, Kagan R, King LM, Leal B, Lebow H, Lee S, LeVan JM, Lewis LC, London P, Lorensuhewa LM, Loulseged H, Lovett DA, Lucier A, Lucier RL, Ma J, Madu RC, Mapua P, Martindale AD, Martinez E, Massey E, Mawhiney S, Meador MG, Mendez S, Mercado C, Mercado IC, Merritt CE, Miner ZL, Minja E, Mitchell T, Mohabbat F, Mohabbat K, Montgomery B, Moore N, Morris S, Munidasa M, Ngo RN, Nguyen NB, Nickerson E, Nwaokelemeh OO, Nwokenkwo S, Obregon M, Oguh M, Oragunye N, Oviedo RJ, Parish BJ, Parker DN, Parrish J, Parks KL, Paul HA, Payton BA, Perez A, Perrin W, Pickens A, Primus EL, Pu LL, Puazo M, Quiles MM, Quiroz JB, Rabata D, Reeves K, Ruiz SJ, Shao H, Sisson I, Sonaike T, Sorelle RP, Sutton AE, Svatek AF, Svetz LA, Tamerisa KS, Taylor TR, Teague B, Thomas N, Thorn RD, Trejos ZY, Trevino BK, Ukegbu ON, Urban JB, Vasquez LI, Vera VA, Villasana DM, Wang L, Ward-Moore S, Warren JT, Wei X, White F, Williamson AL, Wleczyk R, Wooden HS, Wooden SH, Yen J, Yoon L, Yoon V, Zorrilla SE, Nelson D, Kucherlapati R, Weinstock G, Gibbs RA; Baylor College of Medicine Human Genome Sequencing Center Sequence Production Team. The finished DNA sequence of human chromosome 12. Nature. 2006 Mar 16;440(7082):346-51. PMID: 16541075
127. 127.Bowman TV, McCooey AJ, Merchant AA, Ramos CA, Fonseca P, Poindexter A, Bradfute SB, Oliveira DM, Green R, Zheng Y, Jackson KA, Chambers SM, McKinney-Freeman SL, Norwood KG, Darlington G, Gunaratne PH, Steffen D, Goodell MA. Differential mRNA processing in hematopoietic stem cells. Stem Cells. 2006 Mar;24(3):662-70. Epub 2005 Dec 22. PMID: 16373690
128. 128.Al-Lamki Z, Wali YA, Wasifuddin SM, Zachariah M, Al-Mjeni R, Li C, Muralitharan S, Al-Kharusi K, Gunaratne P, Peterson L, Gibbs R, Gingras MC, Margolin JF. Identification of prognosis markers in pediatric high-risk acute lymphoblastic leukemia. Pediatr Hematol Oncol. 2005 Oct-Nov;22(7):629-43. PMID: 16166056
129. 129.Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K, Muzny D, Platzer M, Howell GR, Burrows C, Bird CP, Frankish A, Lovell FL, Howe KL, Ashurst JL, Fulton RS, Sudbrak R, Wen G, Jones MC, Hurles ME, Andrews TD, Scott CE, Searle S, Ramser J, Whittaker A, Deadman R, Carter NP, Hunt SE, Chen R, Cree A, Gunaratne P, Havlak P, Hodgson A, Metzker ML, Richards S, Scott G, Steffen D, Sodergren E, Wheeler DA, Worley KC, Ainscough R, Ambrose KD, Ansari-Lari MA, Aradhya S, Ashwell RI, Babbage AK, Bagguley CL, Ballabio A, Banerjee R, Barker GE, Barlow KF, Barrett IP, Bates KN, Beare DM, Beasley H, Beasley O, Beck A, Bethel G, Blechschmidt K, Brady N, Bray-Allen S, Bridgeman AM, Brown AJ, Brown MJ, Bonnin D, Bruford EA, Buhay C, Burch P, Burford D, Burgess J, Burrill W, Burton J, Bye JM, Carder C, Carrel L, Chako J, Chapman JC, Chavez D, Chen E, Chen G, Chen Y, Chen Z, Chinault C, Ciccodicola A, Clark SY, Clarke G, Clee CM, Clegg S, Clerc-Blankenburg K, Clifford K, Cobley V, Cole CG, Conquer JS, Corby N, Connor RE, David R, Davies J, Davis C, Davis J, Delgado O, Deshazo D, Dhami P, Ding Y, Dinh H, Dodsworth S, Draper H, Dugan-Rocha S, Dunham A, Dunn M, Durbin KJ, Dutta I, Eades T, Ellwood M, Emery-Cohen A, Errington H, Evans KL, Faulkner L, Francis F, Frankland J, Fraser AE, Galgoczy P, Gilbert J, Gill R, Glöckner G, Gregory SG, Gribble S, Griffiths C, Grocock R, Gu Y, Gwilliam R, Hamilton C, Hart EA, Hawes A, Heath PD, Heitmann K, Hennig S, Hernandez J, Hinzmann B, Ho S, Hoffs M, Howden PJ, Huckle EJ, Hume J, Hunt PJ, Hunt AR, Isherwood J, Jacob L, Johnson D, Jones S, de Jong PJ, Joseph SS, Keenan S, Kelly S, Kershaw JK, Khan Z, Kioschis P, Klages S, Knights AJ, Kosiura A, Kovar-Smith C, Laird GK, Langford C, Lawlor S, Leversha M, Lewis L, Liu W, Lloyd C, Lloyd DM, Loulseged H, Loveland JE, Lovell JD, Lozado R, Lu J, Lyne R, Ma J, Maheshwari M, Matthews LH, McDowall J, McLaren S, McMurray A, Meidl P, Meitinger T, Milne S, Miner G, Mistry SL, Morgan M, Morris S, Müller I, Mullikin JC, Nguyen N, Nordsiek G, Nyakatura G, O'Dell CN, Okwuonu G, Palmer S, Pandian R, Parker D, Parrish J, Pasternak S, Patel D, Pearce AV, Pearson DM, Pelan SE, Perez L, Porter KM, Ramsey Y, Reichwald K, Rhodes S, Ridler KA, Schlessinger D, Schueler MG, Sehra HK, Shaw-Smith C, Shen H, Sheridan EM, Shownkeen R, Skuce CD, Smith ML, Sotheran EC, Steingruber HE, Steward CA, Storey R, Swann RM, Swarbreck D, Tabor PE, Taudien S, Taylor T, Teague B, Thomas K, Thorpe A, Timms K, Tracey A, Trevanion S, Tromans AC, d'Urso M, Verduzco D, Villasana D, Waldron L, Wall M, Wang Q, Warren J, Warry GL, Wei X, West A, Whitehead SL, Whiteley MN, Wilkinson JE, Willey DL, Williams G, Williams L, Williamson A, Williamson H, Wilming L, Woodmansey RL, Wray PW, Yen J, Zhang J, Zhou J, Zoghbi H, Zorilla S, Buck D, Reinhardt R, Poustka A, Rosenthal A, Lehrach H, Meindl A, Minx PJ, Hillier LW, Willard HF, Wilson RK, Waterston RH, Rice CM, Vaudin M, Coulson A, Nelson DL, Weinstock G, Sulston JE, Durbin R, Hubbard T, Gibbs RA, Beck S, Rogers J, Bentley DR. The DNA sequence of the human X chromosome. Nature. 2005 Mar 17;434(7031):325-37. PMID: 15772651
130. 130.Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J; MGC Project Team. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004 Oct;14(10B):2121-7. Erratum in: Genome Res. 2006 Jun;16(6):804. Morrin, Ryan [corrected to Morin, Ryan]. PMID: 15489334
131. 131.Wu JQ, Garcia AM, Hulyk S, Sneed A, Kowis C, Yuan Y, Steffen D, McPherson JD, Gunaratne PH, Gibbs RA. Large-scale RT-PCR recovery of full-length cDNA clones. Biotechniques. 2004 Apr;36(4):690-6, 698-700. PMID: 15088387
132. 132.Novel potential ALL low-risk markers revealed by gene expression profiling with new high-throughput SSH-CCS-PCR. Qiu J, Gunaratne P, Peterson LE, Khurana D, Walsham N, Loulseged H, Karni RJ, Roussel E, Gibbs RA, Margolin JF, Gingras MC. Leukemia. 2003 Sep;17(9):1891-900. PMID: 12970791
133. 133.Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, Collins FS, Wagner L, Shenmen CM, Schuler GD, Altschul SF, Zeeberg B, Buetow KH, Schaefer CF, Bhat NK, Hopkins RF, Jordan H, Moore T, Max SI, Wang J, Hsieh F, Diatchenko L, Marusina K, Farmer AA, Rubin GM, Hong L, Stapleton M, Soares MB, Bonaldo MF, Casavant TL, Scheetz TE, Brownstein MJ, Usdin TB, Toshiyuki S, Carninci P, Prange C, Raha SS, Loquellano NA, Peters GJ, Abramson RD, Mullahy SJ, Bosak SA, McEwan PJ, McKernan KJ, Malek JA, Gunaratne PH, Richards S, Worley KC, Hale S, Garcia AM, Gay LJ, Hulyk SW, Villalon DK, Muzny DM, Sodergren EJ, Lu X, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madan A, Young AC, Shevchenko Y, Bouffard GG, Blakesley RW, Touchman JW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Krzywinski MI, Skalska U, Smailus DE, Schnerch A, Schein JE, Jones SJ, Marra MA; Mammalian Gene Collection Program Team. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11. PMID: 12477932
134. Gunaratne PH, Richards CS. Estimated contribution of known ataxia genes in ataxia patients undergoing DNA testing. Genet Test. 1997-1998;1(4):275-8. PMID: 10464657
135. Roa BB, Greenberg F, Gunaratne P, Sauer CM, Lubinsky MS, Kozma C, Meck JM, Magenis RE, Shaffer LG, Lupski JR. Duplication of the PMP22 gene in 17p partial trisomy patients with Charcot-Marie-Tooth type-1 neuropathy. Hum Genet. 1996 May;97(5):642-9. PMID: 8655146
136. Gunaratne PH, Nakao M, Ledbetter DH, Sutcliffe JS, Chinault AC. Tissue-specific and allele-specific replication timing control in the imprinted human Prader-Willi syndrome region. Genes Dev. 1995 Apr 1;9(7):808-20. PMID: 7705658
137. Virta-Pearlman VJ, Gunaratne PH, Chinault AC. Analysis of a replication initiation sequence from the adenosine deaminase region of the mouse genome. Mol Cell Biol. 1993 Oct;13(10):5931-42. PMID: 8413198
138. Mansukhani A, Gunaratne PH, Sherwood PW, Sneath BJ, Goldberg ML. Nucleotide sequence and structural analysis of the zeste locus of Drosophila melanogaster. Mol Gen Genet. 1988 Jan;211(1):121-8. PMID: 3125410
139. 139.Gunaratne PH, Mansukhani A, Lipari SE, Liou HC, Martindale DW, Goldberg ML. Molecular cloning, germ-line transformation, and transcriptional analysis of the zeste locus of Drosophila melanogaster. Proc Natl Acad Sci U S A. 1986 Feb;83(3):701-5. PMID: 3080747

Honors & Awards

2014 McNair Foundation Award
2012 McNair Foundation Award
2011 Virginia & L. E. Simmons Family Foundation Award (joint award with Jason Shohet and Xiabo Zhou)
2011 Cullen Foundation Award
2010 Baylor Partnership Fund Raising Featured Beneficiary Award (joint award with Matthew Anderson and Martin Matzuk)
2004-2006 Moran Foundation Award (joint award with Dolores Lopez Terrada)
1989 Leukemia Research Foundation Fellowship Award
1988 Northwestern Memorial Galter Fellowship Award
1986 Amoco Research Award, Chicago

Organizations, Outreach, Boards, Memberships

Co-Founder/Chief Scientific Officer – NEXTmiRNA Technologies

National Consortia

• NCI – TCGA PanCancer Consortium – 2016-2019
  • Leader Long non-coding RNA Group
• NCI/NHGRI –The Cancer Genome Atlas (TCGA) Consortium 2009-present
  • Leader microRNA Analysis Groups – Ovarian, Colorectal, Kidney cancers
• NHGRI – Marmoset Genome Consortium – 2010-2013
  • Leader microRNA Analysis Group
• NHGRI – Zebrafinch Genome Consortium 2009
  • Leader microRNA Analysis Group
• NIDDK – Stem Cell Genome Anatomy Project (SCGAP) Consortium 2003-2005
• NHGRI/NCI – Mammalian Gene Collection (MGC) Consortium 2002-2005
  • Leader Baylor Human Genome Sequencing Center-Gene sequencing Group
  • Led Baylor Team to make the largest single contribution to the NCI- Mammalian Gene Collection in Phase I
• NHGRI – The International Human Genome Project Consortium 1999-2003
  • Human Chromosomes 3, 12 and X

Editorial Boards

2011-2019 Review Editor, Frontiers in Non-coding RNA Journal

Manuscript Review

Nature Reviews, Nature Protocols, Proc. Natl. Acad. Sci. (PNAS), Molecular Cell, Genome Research, Cancer Research, Clinical Cancer Research, Oncotarget, Nucleic Acids Research, PLoS ONE, BMC Genomics, BMC Bioinformatics, Briefings in Bioinformatics, British Journal of Cancer, Genome Biology, Molecular Carcinogenesis, Molecular Cancer Therapeutics, Frontiers in Non- coding RNA, Genomics, Genome Medicine, Gene Expression Patterns (GEP), Elsevier, Cell Research, Toxicology & Applied Pharmacology (TAAP), Journal of Theoretical Biology, Pancreas Journal

A.12. Expert Peer Reviewer – Grants & Programs

• 2020-2023 - KTH (Royal Institute of Technology in Stockholm), Sweden RAE-2020-2023
• 2020-2022 - Research Foundation Flanders (FWO), Belgium
• 2020-2021 - Department of Defense (DOD) – Peer Reviewed Medical Research Program (PRMRP)
• 2015, 2021 - Swiss National Science Foundation (SNF)
• 2017-2021 - Florida Department of Health (F-DOH)
• 2020 - Department of Defense (DOD)
  Peer Reviewed Medical Research Program (PRMRP) COVID-T-2
• 2020 - Department of Defense (DOD)
  Breast Cancer Research Program – Nanotechnology Panel (BCRP-NT)
• 2017-2019 - Pennsylvania Department of Health (PA-DOH)
• 2017-2018 - Expert Peer Review U.S. FDA Research Program
• 2016 - NCI-2016/05 ZCA1 SRB-J (M2) R–Special Emphasis Panel/Scientific Review Group
  Provocative Question 6, “What are the underlying molecular mechanisms that are responsible for the functional differences between benign proliferative diseases and premalignant states”
• 2015 - NCI-ZCA1 SRB-J (M2) S–Special Emphasis Panel/Scientific Review Group Pennsylvania Department of Health (PA DOH) Scientific Review Group
• 2011/2012 - NIH-ZRG1GGG-H30S–Special Emphasis Panel/Scientific Review Group
  NIH-ZRG1 GGG-H31S – High-end Instrumentation Grants
  NHMRC-National Health and Medical Research Council- Australia
• 2012 - Duncan Family Institute (DFI) Seed Funding Research Program
• 2011 - Czech Science Foundation
• 2011 - Netherlands-Research Foundation Flanders (FWO)
• 2010 - NIH–CNIHR–AdHoc
  Cancer Research UK
• 2009-2010 - US-Israel Binational Science Foundation
• 2010 - Israel Science Foundation

Patents - Inventor/Co-Inventor

1. Provisional Application: UH ID No. 2021-002|Attorney Docket No. 23853-P162V1 Discovery and use of immunogenic peptides for the treatment and prevention of cancers
2. Provisional Application: UH ID No. 2021-002|Attorney Docket No. 2019-058 (T-11416-
   P)
   Systems and methods for analytic mapping of the metageomic and hydrocarbon footprints of geologic subzones
3. U.S. Patent Appl. No. 13/136,498; PCT patent # PCT/US2011/001356
   Interior Functionalized Hyperbranched Dendron-Conjugated Nanoparticles and uses Thereof
4. U.S. Patent Appl. No. 13/319,446. CLFR.P0342US miRNA Expression in Allergic Disease
5. U.S. Patent Appl. No. 13/437,128; PCT patent PCT/US2012/31809 microRNA-29a,b,c as a sensitizing agent for chemotherapy
6. Issued: U.S. Patent Appl. No. 13/437,251; PCT patent PCT/US2012/31822 microRNA-130a,b as a tumor suppressor of cancer
7. Issued: U.S. Patent Appl. No. 13/453,553; PCT patent PCT/US2012/34655 microRNA-140-5p as a tumor suppressor of cancer
8. U.S. Patent Appl. No. 13/501,806; PCT patent PCT/US2012/34655 microRNA miRNA-31 as a therapeutic approach for the treatment of cancer
9. BLG# 11-052: MicroRNAs sensitize ovarian cancers to platinum chemotherapy
10. Provisional patent application for UHID-2021-002-Immunogenic Peptides for the
    Treatment and Prevention of Cancer-Winstead Ref. No. 23853-P162V1
11. UHID 2020-060; Appl No. 63/063,815; A Dual Viral Infection|Host Response detection Test Kit: Winstead Ref. 23853-P161V1
12. UHID 2329-51 (2019-058) Systems and Methods for Analytic Mapping of the Metageomic and Hydrocarbon Footprints of Geologic Subzones. Chevron Corporation.

New Company Formation

• 2019: Co-Founder, CEO and CSO, GeOME Analytics
• 2014: Founder and Chief Scientific Officer (CSO) NEXTmiRNA Technologies (http://www.nextmirna.com/)

B.2. Trainees

Faculty

• 2019-2022: Kimberly Holloway, Ph.D. (UH-Sequencing Core – Project Manager)
  • Associate Director, Translational Oncology, Iterion Therapeutics
• 2019-2021: Jignesh Chandana, M.S. (UH-Sequencing Core - Automation/Clinical Sequencing Specialist)
  • Lead Lab Automation Developer-Invitae
• 2016–2018: Sujash Chaterjee, Ph.D. (Research Assistant Professor)
  • Lead-Product Marketing and Commercialization, Genomics, NA at QIAGEN
  • Global Cancer Research Lead, Illumina
• 2017: Navin Rustagi, Ph.D. (Research Assistant Professor)
  • Data Scientist at McKinsey & Company
• 2015–2016: Utpal Pandya, Ph.D. (Research Assistant Professor)
• 2011–2013: Weiming Xiao, Ph.D. (Research Assistant Professor)
  • Co-founder and Chief Scientist at Shenzhen Lucky Source Investment Management Corporation.

Postdoctoral

• 2022-Present: Partha Bhagavatula, Ph.D. (UH-Sequencing Core, Senior Data Analytst)
• 2013–2018: Yinghong Pan, Ph.D. (Research Associate)
  • Project Manager, Genome Center, University of Pittsburgh Medical College (UPMC)
  • Sr. Application Scientist at PerkinElmer, Inc.
• 2009–2013: Lalithya Jayarathne, Ph.D. (Research Associate)
• 2007: Rafal Drabek, Ph.D. (Postdoctoral Fellow)

Graduate Students

• 2020-Present: Micah Castillo, Ph.D. Candidate, Biochemistry
• 2019-Present: Sakuni Rankothgedera, Ph.D. Candidate, Biochemistry
• 2021-Present: Aaranya Kandasamy, Ph.D. Candidate, Biochemistry
• 2021-Present: Shiyanth Thevasagayampillai, Ph.D. Candidate, Biochemistry
• 2021-Present: Dilshan Adhikari, Ph.D. Candidate, Biochemistry
• 2016–2020: Asha Palat: Ph.D. Candidate, Molecular & Cellular Biology
  • McCammon Fellowship 2019
  • Technical Support Scientist, Novogene America
  • Post Doctoral Fellow, UH-Sequencing Core, Houston, TX
  • Brandon Mistretta, Ph.D. Candidate, Biochemistry
  • McCammon Fellowship 2020
  • Field Application Scientist, 10X Genomics
• 2016–2019: Jason Hoggard, Ph.D. Candidate, Biochemistry
  • McCammon Fellowship, 2018
  • Post Doctoral Fellow, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
  • Postdoctoral Research Fellow, Division of Congenital Heart Surgery, Texas Children’s Hospital, Houston, TX
• 2012–2017: Ian Wilson. M.Sc. Candidate, Biochemistry
  • M.Sc. (2020)
  • Sagar Patil: Ph.D. Candidate, Biochemistry
  • Harwood Fellowship 2016
  • Postdoctoral Fellow, Columbia University, New York, NY
  • Lead Researcher at St. Jude Children's Research Hospital
  • Project Manager, GlaxoSmithKline (GSK) -Philadelphia
• 2012–2017: Johnson Hoang: Ph.D Candidate, Biochemistry
  
  • Ph.D., SCYM (ASCP),
• 2009–2014: Anadulce Hernandez-Herrera, Ph.D. Biochemistry (Contactyn-Fellowship)
  
  • Lester and Sue Smith Breast Center, Biobank Research Coordinator,
  • Baylor College of Medicine – 2017
  • Clinical Trials Team, UCSF, San Francisco, CA; Breast Center
• 2008–2012: Rajib Ghosh, Ph.D. Molecular & Cellular Biology
  
  • Post Doctoral Fellow – Johns Hopkins University, MD
  • Research Assistant Professor, University of West Virginia, VA
  • Senior Scientist at Abcam
  • Principal Scientist, Bristol Myers Squibb
• 2007–2011: Jayantha Tennakoon, Ph.D. Molecular & Cellular Biology
  
  • Healthcare Consulting Firm, Chicago, IL
• 2007–2011: Ashley Benham-Duret, Ph.D. Biochemistry
  
  • Post Doctoral Fellow – Texas Heart Institute, Houston
  • Senior Scientist, 10X Genomics
  • Sales Executive II
• 2007–2008: Arash Naghavi-M.SC., Molecular & Cellular Biology
  • MD program UTMB, Radiology Fellow-Moffit Cancer Center, Radiation Oncologist, FL

• Southeastern Association of Shared Resources (SEASR) - Keynote Session 3
• QIAGEN - Innovation Forum 2022
• UH Biology Student Plays Key Role in Groundbreaking Cancer Discovery
• UH Biology Student Receives Two of the Nation’s Most Prestigious Academic Awards
• UH student plays key role in groundbreaking cancer discovery
• Sophomore Earns Research and Community Service Fellowships