Photo of Ioannis S Vlachos,  PhD

Ioannis S Vlachos, PhD

Beth Israel Deaconess Medical Center

Beth Israel Deaconess Medical Center
Phone: (617) 667-4143

Ioannis S Vlachos, PhD

Beth Israel Deaconess Medical Center


  • Assistant Professor, Pathology, Harvard Medical School
  • Co-Director of the Bionformatics Program, Cancer Research Institute, Beth Israel Deaconess Medical Center
  • Director of the Bioinformatics Unit, Non-Coding RNA Precision Diagnostics and Therapeutics Core, Beth Israel Deaconess Medical Center


Research Abstract

Our group focuses on developing, implementing, and integrating new technologies and methods that can help us provide direct answers to pressing questions in cancer research. We utilize extensively whole genome approaches, single cell assays, and spatial transcriptomics and proteomics to understand the mechanisms of tumor immune evasion or the prioritization of novel biomarkers and therapeutics. We employ artificial intelligence/machine learning technologies to transform these findings into optimized methods for patient stratification and management and to inform clinical decision making.

We are also intensely exploring the regulatory dark matter comprising the 98% of our genome. Non-coding mutations or RNAs such as long non-coding RNAs and microRNAs are an untapped resource for novel therapeutic targets and effective biomarkers. We are developing methods to concurrently interrogate coding and non-coding gene expression or mutations, epigenetic information, and immunomic data, in order to inform basic and translational research, as well as clinical decision making.

Our “Whole Genome and Beyond” approach aims to maximize the layers of information that are extracted and exploited from a single patient sample. To this end, we are extensively employing bulk, single cell, and spatial transcriptomic technologies to characterize cellular transcriptional programs and cell-cell communication, as well as how they are derailed in disease. This approach permits us to identify and prioritize novel biomarkers or therapeutic targets, regardless of their coding potential.

With the creation of the Spatial Technologies Unit ( and the Precision RNA Medicine Core, Harvard Medical School Initiative for RNA Medicine, we provide access to technologies we develop in the lab to the research community.


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  • Theocharidis G, Thomas BE, Sarkar D, Mumme HL, Pilcher WJR, Dwivedi B, Sandoval-Schaefer T, Sîrbulescu RF, Kafanas A, Mezghani I, Wang P, Lobao A, Vlachos IS, Dash B, Hsia HC, Horsley V, Bhasin SS, Veves A, Bhasin M. Single cell transcriptomic landscape of diabetic foot ulcers. Nat Commun 2022; 13:181. PubMed
  • Kavakiotis I, Alexiou A, Tastsoglou S, Vlachos IS, Hatzigeorgiou AG. DIANA-miTED: a microRNA tissue expression database. Nucleic Acids Res 2021. PubMed
  • Hakim A, Moll M, Brancale J, Liu J, Lasky-Su JA, Silverman EK, Vilarinho S, Jiang ZG, Pita-Juárez YH, Vlachos IS, Zhang X, Åberg F, Afdhal NH, Hobbs BD, Cho MH. Genetic variation in the mitochondrial glycerol-3-phosphate acyltransferase is associated with liver injury. Hepatology 2021. PubMed
  • Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe Å, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Biermann J, Bloom-Ackermann Z, Barkas N, Ganna A, Gomez J, Melms JC, Katsyv I, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LT, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Wang Y, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jané-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe'er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hibshoosh H, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Ellinor PT, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Izar B, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CBM, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature 2021. PubMed
  • Laliotis GI, Chavdoula E, Paraskevopoulou MD, Kaba A, La Ferlita A, Singh S, Anastas V, Nair KA, Orlacchio A, Taraslia V, Vlachos I, Capece M, Hatzigeorgiou A, Palmieri D, Tsatsanis C, Alaimo S, Sehgal L, Carbone DP, Coppola V, Tsichlis PN. AKT3-mediated IWS1 phosphorylation promotes the proliferation of EGFR-mutant lung adenocarcinomas through cell cycle-regulated U2AF2 RNA splicing. Nat Commun 2021; 12:4624. PubMed
  • Desvignes T, Loher P, Eilbeck K, Ma J, Urgese G, Fromm B, Sydes J, Aparicio-Puerta E, Barrera V, Espín R, Thibord F, Bofill-De Ros X, Londin E, Telonis AG, Ficarra E, Friedländer MR, Postlethwait JH, Rigoutsos I, Hackenberg M, Vlachos IS, Halushka MK, Pantano L. Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. Bioinformatics 2020; 36:698-703. PubMed
  • Prodromidou K, Vlachos IS, Gaitanou M, Kouroupi G, Hatzigeorgiou AG, Matsas R. MicroRNA-934 is a novel primate-specific small non-coding RNA with neurogenic function during early development. Elife 2020. PubMed
  • Handzlik JE, Tastsoglou S, Vlachos IS, Hatzigeorgiou AG. Manatee: detection and quantification of small non-coding RNAs from next-generation sequencing data. Sci Rep 2020; 10:705. PubMed
  • Fostira F, Kostantopoulou I, Apostolou P, Papamentzelopoulou MS, Papadimitriou C, Faliakou E, Christodoulou C, Boukovinas I, Razis E, Tryfonopoulos D, Barbounis V, Vagena A, Vlachos IS, Kalfakakou D, Fountzilas G, Yannoukakos D. One in three highly selected Greek patients with breast cancer carries a loss-of-function variant in a cancer susceptibility gene. J Med Genet 2020; 57:53-61. PubMed
  • Eismann J, Heng YJ, Waldschmidt JM, Vlachos IS, Gray KP, Matulonis UA, Konstantinopoulos PA, Murphy CJ, Nabavi S, Wulf GM. Transcriptome analysis reveals overlap in fusion genes in a phase I clinical cohort of TNBC and HGSOC patients treated with buparlisib and olaparib. J Cancer Res Clin Oncol 2019. PubMed
  • Patsopoulos NA, Baranzini SE, Santaniello A, Shoostari P, Cotsapas C, Wong G, Beecham AH, James T, Replogle J, Vlachos IS, McCabe C, Pers TH, Brandes A, White C, Keenan B, Cimpean M, Winn P, Panteliadis IP, Robbins A, Andlauer TFM, Zarzycki O, Dubois B, Goris A, Søndergaard HB, Sellebjerg F, Sorensen PS, Ullum H, Thørner LW, Saarela J, Cournu-Rebeix I, Damotte V, Fontaine B, Guillot-Noel L, Lathrop M, Vukusic S, Berthele A, Pongratz V, Buck D, Gasperi C, Graetz C, Grummel V, Hemmer B, Hoshi M, Knier B, Korn T, Lill CM, Luessi F, Mühlau M, Zipp F, Dardiotis E, Agliardi C, Amoroso A, Barizzone N, Benedetti MD, Bernardinelli L, Cavalla P, Clarelli F, Comi G, Cusi D, Esposito F, Ferrè L, Galimberti D, Guaschino C, Leone MA, Martinelli V, Moiola L, Salvetti M, Sorosina M, Vecchio D, Zauli A, Santoro S, Mancini N, Zuccalà M, Mescheriakova J, van Duijn C, Bos SD, Celius EG, Spurkland A, Comabella M, Montalban X, Alfredsson L, Bomfim IL, Gomez-Cabrero D, Hillert J, Jagodic M, Lindén M, Piehl F, Jelčić I, Martin R, Sospedra M, Baker A, Ban M, Hawkins C, Hysi P, Kalra S, Karpe F, Khadake J, Lachance G, Molyneux P, Neville M, Thorpe J, Bradshaw E, Caillier SJ, Calabresi P, Cree BAC, Cross A, Davis M, de Bakker PWI, Delgado S, Dembele M, Edwards K, Fitzgerald K, Frohlich IY, Gourraud PA, Haines JL, Hakonarson H, Kimbrough D, Isobe N, Konidari I, Lathi E, Lee MH, Li T, An D, Zimmer A, Madireddy L, Manrique CP, Mitrovic M, Olah M, Patrick E, Pericak-Vance MA, Piccio L, Schaefer C, Weiner H, Lage K, Compston A, Hafler D, Harbo HF, Hauser SL, Stewart G, D'Alfonso S, Hadjigeorgiou G, Taylor B, Barcellos LF, Booth D, Hintzen R, Kockum I, Martinelli-Boneschi F, McCauley JL, Oksenberg JR, Oturai A, Sawcer S, Ivinson AJ, Olsson T, De Jager PL. Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility. Science 2021. PubMed
  • Paraskevopoulou MD, Karagkouni D, Vlachos IS, Tastsoglou S, Hatzigeorgiou AG. microCLIP super learning framework uncovers functional transcriptome-wide miRNA interactions. Nat Commun 2019; 9:3601. PubMed
  • Kouroupi G, Taoufik E, Vlachos IS, Tsioras K, Antoniou N, Papastefanaki F, Chroni-Tzartou D, Wrasidlo W, Bohl D, Stellas D, Politis PK, Vekrellis K, Papadimitriou D, Stefanis L, Bregestovski P, Hatzigeorgiou AG, Masliah E, Matsas R. Defective synaptic connectivity and axonal neuropathology in a human iPSC-based model of familial Parkinson's disease. Proc Natl Acad Sci U S A 2018; 114:E3679-E3688. PubMed
  • Georgakilas G, Vlachos IS, Zagganas K, Vergoulis T, Paraskevopoulou MD, Kanellos I, Tsanakas P, Dellis D, Fevgas A, Dalamagas T, Hatzigeorgiou AG. DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators. Nucleic Acids Res 2018; 44:D190-5. PubMed
  • Paraskevopoulou MD, Vlachos IS, Karagkouni D, Georgakilas G, Kanellos I, Vergoulis T, Zagganas K, Tsanakas P, Floros E, Dalamagas T, Hatzigeorgiou AG. DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts. Nucleic Acids Res 2019; 44:D231-8. PubMed
  • Vlachos IS, Vergoulis T, Paraskevopoulou MD, Lykokanellos F, Georgakilas G, Georgiou P, Chatzopoulos S, Karagkouni D, Christodoulou F, Dalamagas T, Hatzigeorgiou AG. DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data. Nucleic Acids Res 2018; 44:W128-34. PubMed
  • Vlachos IS, Zagganas K, Paraskevopoulou MD, Georgakilas G, Karagkouni D, Vergoulis T, Dalamagas T, Hatzigeorgiou AG. DIANA-miRPath v3.0: deciphering microRNA function with experimental support. Nucleic Acids Res 2020; 43:W460-6. PubMed
  • Vlachos IS, Paraskevopoulou MD, Karagkouni D, Georgakilas G, Vergoulis T, Kanellos I, Anastasopoulos IL, Maniou S, Karathanou K, Kalfakakou D, Fevgas A, Dalamagas T, Hatzigeorgiou AG. DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions. Nucleic Acids Res 2019; 43:D153-9. PubMed
  • Georgakilas G, Vlachos IS, Paraskevopoulou MD, Yang P, Zhang Y, Economides AN, Hatzigeorgiou AG. microTSS: accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs. Nat Commun 2015; 5:5700. PubMed
  • Paraskevopoulou MD, Georgakilas G, Kostoulas N, Vlachos IS, Vergoulis T, Reczko M, Filippidis C, Dalamagas T, Hatzigeorgiou AG. DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows. Nucleic Acids Res 2018; 41:W169-73. PubMed
  • Kotoula V, Lakis S, Vlachos IS, Giannoulatou E, Zagouri F, Alexopoulou Z, Gogas H, Pectasides D, Aravantinos G, Efstratiou I, Pentheroudakis G, Papadopoulou K, Chatzopoulos K, Papakostas P, Sotiropoulou M, Nicolaou I, Razis E, Psyrri A, Kosmidis P, Papadimitriou C, Fountzilas G. Tumor Infiltrating Lymphocytes Affect the Outcome of Patients with Operable Triple-Negative Breast Cancer in Combination with Mutated Amino Acid Classes. PLoS ONE 2021; 11:e0163138. PubMed