PubMed publications

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2017

TGF-β-Induced Quiescence Mediates Chemoresistance of Tumor-Propagating Cells in Squamous Cell Carcinoma.
Brown JA, Yonekubo Y, Hanson N, Sastre-Perona A, Basin A, Rytlewski JA, Dolgalev I, Meehan S, Tsirigos A, Beronja S, Schober M.
Cell Stem Cell. 2017 Nov 2;21(5):650-664.e8. doi: 10.1016/j.stem.2017.10.001.
PMID: 29100014
Stratification of TAD boundaries identified in reproducible Hi-C contact matrices reveals preferential insulation of super-enhancers by strong boundaries
Yixiao Gong, Charalampos Lazaris, Theodore Sakellaropoulos, Aurelie Lozano, Prabhanjan Kambadur, Panagiotis Ntziachristos, Iannis Aifantis*, Aristotelis Tsirigos* (co-corresponding authors)
biorXiv, October 2017
Low-Grade Astrocytoma Mutations in IDH1, P53, and ATRX Cooperate to Block Differentiation of Human Neural Stem Cells via Repression of SOX2.
Modrek AS, Golub D, Khan T, Bready D, Prado J, Bowman C, Deng J, Zhang G, Rocha PP, Raviram R, Lazaris C, Stafford JM, LeRoy G, Kader M, Dhaliwal J, Bayin NS, Frenster JD, Serrano J, Chiriboga L, Baitalmal R, Nanjangud G, Chi AS, Golfinos JG, Wang J, Karajannis MA, Bonneau RA, Reinberg D, Tsirigos A, Zagzag D, Snuderl M, Skok JA, Neubert TA, Placantonakis DG.
Cell Rep. 2017 Oct 31;21(5):1267-1280. doi: 10.1016/j.celrep.2017.10.009.
PMID: 29091765
Classification and Mutation Prediction from Non-Small Cell Lung Cancer Histopathology Images using Deep Learning
Coudray N, Moreira AL, Sakellaropoulos T, Fenyo D, Razavian N* and Tsirigos A* (*co-corresponding authors)
biorXiv, October 2017
Complete Genome Sequence of Kluyvera intestini sp. nov., Isolated from the Stomach of a Patient with Gastric Cancer.
Tetz G, Vecherkovskaya M, Zappile P, Dolgalev I, Tsirigos A, Heguy A, Tetz V.
Genome Announc. 2017 Oct 26;5(43). pii: e01184-17. doi: 10.1128/genomeA.01184-17.
PMID: 29074664
Notch signaling regulates metabolic heterogeneity in glioblastoma stem cells.
Bayin NS, Frenster JD, Sen R, Si S, Modrek AS, Galifianakis N, Dolgalev I, Ortenzi V, Illa-Bochaca I, Khahera A, Serrano J, Chiriboga L, Zagzag D, Golfinos JG, Doyle W, Tsirigos A, Heguy A, Chesler M, Barcellos-Hoff MH, Snuderl M, Placantonakis DG.
Oncotarget. 2017 May 23;8(39):64932-64953. doi: 10.18632/oncotarget.18117. eCollection 2017 Sep 12.
PMID: 29029402
Restoration of TET2 Function Blocks Aberrant Self-Renewal and Leukemia Progression.
Cimmino L, Dolgalev I, Wang Y, Yoshimi A, Martin GH, Wang J, Ng V, Xia B, Witkowski MT, Mitchell-Flack M, Grillo I, Bakogianni S, Ndiaye-Lobry D, Martín MT, Guillamot M, Banh RS, Xu M, Figueroa ME, Dickins RA, Abdel-Wahab O, Park CY, Tsirigos A, Neel BG, Aifantis I.
Cell. 2017 Sep 7;170(6):1079-1095.e20. doi: 10.1016/j.cell.2017.07.032. Epub 2017 Aug 17.
PMID: 28823558
Bacteriophages as potential new mammalian pathogens.
Tetz GV, Ruggles KV, Zhou H, Heguy A, Tsirigos A, Tetz V.
Sci Rep. 2017 Aug 1;7(1):7043. doi: 10.1038/s41598-017-07278-6.
PMID: 28765534
lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets.
Gong Y, Huang HT, Liang Y, Trimarchi T, Aifantis I*, Tsirigos A* (*co-corresponding authors)
BMC Genomics. 2017 Jun 5;18(1):434. doi: 10.1186/s12864-017-3817-0.
PMID: 28583068
N-BLR, a primate-specific non-coding transcript leads to colorectal cancer invasion and migration.
Rigoutsos I, Lee SK, Nam SY, Anfossi S, Pasculli B, Pichler M, Jing Y, Rodriguez-Aguayo C, Telonis AG, Rossi S, Ivan C, Catela Ivkovic T, Fabris L, Clark PM, Ling H, Shimizu M, Redis RS, Shah MY, Zhang X, Okugawa Y, Jung EJ, Tsirigos A, Huang L, Ferdin J, Gafà R, Spizzo R, Nicoloso MS, Paranjape AN, Shariati M, Tiron A, Yeh JJ, Teruel-Montoya R, Xiao L, Melo SA, Menter D, Jiang ZQ, Flores ER, Negrini M, Goel A, Bar-Eli M, Mani SA, Liu CG, Lopez-Berestein G, Berindan-Neagoe I, Esteller M, Kopetz S, Lanza G, Calin GA.
Genome Biol. 2017 May 24;18(1):98. doi: 10.1186/s13059-017-1224-0.
PMID: 28535802
Opposing functions of H2BK120 ubiquitylation and H3K79 methylation in the regulation of pluripotency by the Paf1 complex.
Strikoudis A, Lazaris C, Ntziachristos P, Tsirigos A, Aifantis I.
Cell Cycle. 2017 Mar 8:0. doi: 10.1080/15384101.2017.1295194. [Epub ahead of print]
PMID: 28272987
HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking.
Lazaris C, Kelly S, Ntziachristos P, Aifantis I*, Tsirigos A* (*co-corresponding authors)
BMC Genomics. 2017 Jan 5;18(1):22. doi: 10.1186/s12864-016-3387-6.
PMID: 28056762
Pancreatic β cell identity requires continual repression of non-β cell programs.
Gutiérrez GD, Bender AS, Cirulli V, Mastracci TL, Kelly SM, Tsirigos A, Kaestner KH, Sussel L.
J Clin Invest. 2017 Jan 3;127(1):244-259. doi: 10.1172/JCI88017. Epub 2016 Dec 12.
PMID: 27941248

2016

Regulation of transcriptional elongation in pluripotency and cell differentiation by the PHD-finger protein Phf5a.
Strikoudis A, Lazaris C, Trimarchi T, Galvao Neto AL, Yang Y, Ntziachristos P, Rothbart S, Buckley S, Dolgalev I, Stadtfeld M, Strahl BD, Dynlacht BD, Tsirigos A*, Aifantis I* (*co-corresponding authors)
Nat Cell Biol. 2016 Nov;18(11):1127-1138. doi: 10.1038/ncb3424. Epub 2016 Oct 17.
PMID: 27749823
MED12 Regulates HSC-Specific Enhancers Independently of Mediator Kinase Activity to Control Hematopoiesis.
Aranda-Orgilles B, Saldaña-Meyer R, Wang E, Trompouki E, Fassl A, Lau S, Mullenders J, Rocha PP, Raviram R, Guillamot M, Sánchez-Díaz M, Wang K, Kayembe C, Zhang N, Amoasii L, Choudhuri A, Skok JA, Schober M, Reinberg D, Sicinski P, Schrewe H, Tsirigos A, Zon LI, Aifantis I.
Cell Stem Cell. 2016 Dec 1;19(6):784-799. doi: 10.1016/j.stem.2016.08.004. Epub 2016 Aug 25.
PMID: 27570068

2015

Cohesin loss alters adult hematopoietic stem cell homeostasis, leading to myeloproliferative neoplasms.
Mullenders J, Aranda-Orgilles B, Lhoumaud P, Keller M, Pae J, Wang K, Kayembe C, Rocha PP, Raviram R, Gong Y, Premsrirut PK, Tsirigos A, Bonneau R, Skok JA, Cimmino L, Hoehn D, Aifantis I.
J Exp Med. 2015 Oct 19;212(11):1833-50. doi: 10.1084/jem.20151323. Epub 2015 Oct 5.
PMID: 26438359
FBXW7 modulates cellular stress response and metastatic potential through ​HSF1 post-translational modification.
Kourtis N, Moubarak RS, Aranda-Orgilles B, Lui K, Aydin IT, Trimarchi T, Darvishian F, Salvaggio C, Zhong J, Bhatt K, Chen EI, Celebi JT, Lazaris C, Tsirigos A, Osman I, Hernando E, Aifantis I.
Nat Cell Biol. 2015 Mar;17(3):322-332. doi: 10.1038/ncb3121.
PMID: 25720964

2014

Combinatorial modulation of signaling pathways reveals cell-type-specific requirements for highly efficient and synchronous iPSC reprogramming.
Vidal SE, Amlani B, Chen T, Tsirigos A, Stadtfeld M.
Stem Cell Reports. 2014 Oct 14;3(4):574-84. doi: 10.1016/j.stemcr.2014.08.003.
PMID: 25358786
Control of embryonic stem cell identity by BRD4-dependent transcriptional elongation of super-enhancer-associated pluripotency genes.
Di Micco R, Fontanals-Cirera B, Low V, Ntziachristos P, Yuen SK, Lovell CD, Dolgalev I, Yonekubo Y, Zhang G, Rusinova E, Gerona-Navarro G, Cañamero M, Ohlmeyer M, Aifantis I, Zhou MM, Tsirigos A*, Hernando E* (*co-corresponding authors)
Cell Rep. 2014 Oct 9;9(1):234-47. doi: 10.1016/j.celrep.2014.08.055. Epub 2014 Sep 26.
PMID: 25263550
Contrasting roles of histone 3 lysine 27 demethylases in acute lymphoblastic leukaemia.
Ntziachristos P, Tsirigos A*, Welstead GG, Trimarchi T, Bakogianni S, Xu L, Loizou E, Holmfeldt L, Strikoudis A, King B, Mullenders J, Becksfort J, Nedjic J, Paietta E, Tallman MS, Rowe JM, Tonon G, Satoh T, Kruidenier L, Prinjha R, Akira S, Van Vlierberghe P, Ferrando AA, Jaenisch R, Mullighan CG, Aifantis I (*co-first and co-corresponding author)
Nature. 2014 Oct 23;514(7523):513-7. doi: 10.1038/nature13605. Epub 2014 Aug 17.
PMID: 25132549
Genome-wide mapping and characterization of Notch-regulated long noncoding RNAs in acute leukemia.
Trimarchi T, Bilal E, Ntziachristos P, Fabbri G, Dalla-Favera R, Tsirigos A*, Aifantis I* (*co-corresponding authors)
Cell. 2014 Jul 31;158(3):593-606. doi: 10.1016/j.cell.2014.05.049.
PMID: 25083870
SOX2 is a cancer-specific regulator of tumour initiating potential in cutaneous squamous cell carcinoma.
Siegle JM, Basin A, Sastre-Perona A, Yonekubo Y, Brown J, Sennett R, Rendl M, Tsirigos A, Carucci JA, Schober M.
Nat Commun. 2014 Jul 31;5:4511. doi: 10.1038/ncomms5511.
PMID: 25077433
JNK1 stress signaling is hyper-activated in high breast density and the tumor stroma: connecting fibrosis, inflammation, and stemness for cancer prevention.
Lisanti MP, Tsirigos A, Pavlides S, Reeves KJ, Peiris-Pagès M, Chadwick AL, Sanchez-Alvarez R, Lamb R, Howell A, Martinez-Outschoorn UE, Sotgia F.
Cell Cycle. 2014;13(4):580-99. doi: 10.4161/cc.27379. Epub 2013 Dec 5.
PMID: 24434780

2012

Mitochondria "fuel" breast cancer metabolism: fifteen markers of mitochondrial biogenesis label epithelial cancer cells, but are excluded from adjacent stromal cells.
Sotgia F, Whitaker-Menezes D, Martinez-Outschoorn UE, Salem AF, Tsirigos A, Lamb R, Sneddon S, Hulit J, Howell A, Lisanti MP.
Cell Cycle. 2012 Dec 1;11(23):4390-401. doi: 10.4161/cc.22777. Epub 2012 Nov 21.
PMID: 23172368
The milk protein α-casein functions as a tumor suppressor via activation of STAT1 signaling, effectively preventing breast cancer tumor growth and metastasis.
Bonuccelli G, Castello-Cros R, Capozza F, Martinez-Outschoorn UE, Lin Z, Tsirigos A, Xuanmao J, Whitaker-Menezes D, Howell A, Lisanti MP, Sotgia F.
Cell Cycle. 2012 Nov 1;11(21):3972-82. doi: 10.4161/cc.22227. Epub 2012 Oct 9.
PMID: 23047602
Autophagy and senescence in cancer-associated fibroblasts metabolically supports tumor growth and metastasis via glycolysis and ketone production.
Capparelli C, Guido C, Whitaker-Menezes D, Bonuccelli G, Balliet R, Pestell TG, Goldberg AF, Pestell RG, Howell A, Sneddon S, Birbe R, Tsirigos A, Martinez-Outschoorn U, Sotgia F, Lisanti MP.
Cell Cycle. 2012 Jun 15;11(12):2285-302. doi: 10.4161/cc.20718. Epub 2012 Jun 15.
PMID: 22684298
Genetic Inactivation of the PRC2 Complex in T-Cell Acute Lymphoblastic Leukemia
Ntziachristos P, Tsirigos A* et al. (*co-first and co-corresponding author)
Nature Medicine, February 2012
PMID: 22237151
Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia.
Ntziachristos P, Tsirigos A, Van Vlierberghe P, Nedjic J, Trimarchi T, Flaherty MS, Ferres-Marco D, da Ros V, Tang Z, Siegle J, Asp P, Hadler M, Rigo I, De Keersmaecker K, Patel J, Huynh T, Utro F, Poglio S, Samon JB, Paietta E, Racevskis J, Rowe JM, Rabadan R, Levine RL, Brown S, Pflumio F, Dominguez M, Ferrando A, Aifantis I.
Nat Med. 2012 Feb 6;18(2):298-301. doi: 10.1038/nm.2651.
PMID: 22237151
Is cancer a metabolic rebellion against host aging? In the quest for immortality, tumor cells try to save themselves by boosting mitochondrial metabolism.
Ertel A, Tsirigos A, Whitaker-Menezes D, Birbe RC, Pavlides S, Martinez-Outschoorn UE, Pestell RG, Howell A, Sotgia F, Lisanti MP.
Cell Cycle. 2012 Jan 15;11(2):253-63. doi: 10.4161/cc.11.2.19006. Epub 2012 Jan 15.
PMID: 22234241

2011

Hyperactivation of oxidative mitochondrial metabolism in epithelial cancer cells in situ: visualizing the therapeutic effects of metformin in tumor tissue.
Whitaker-Menezes D, Martinez-Outschoorn UE, Flomenberg N, Birbe RC, Witkiewicz AK, Howell A, Pavlides S, Tsirigos A, Ertel A, Pestell RG, Broda P, Minetti C, Lisanti MP, Sotgia F.
Cell Cycle. 2011 Dec 1;10(23):4047-64. doi: 10.4161/cc.10.23.18151. Epub 2011 Dec 1.
PMID: 22134189
GenomicTools: a computational platform for developing high-throughput analytics in genomics.
Tsirigos A*, Haiminen N, Bilal E, Utro F (*corresponding author)
Bioinformatics. 2012 Jan 15;28(2):282-3. doi: 10.1093/bioinformatics/btr646. Epub 2011 Nov 22.
PMID: 22113082
Molecular profiling of a lethal tumor microenvironment, as defined by stromal caveolin-1 status in breast cancers.
Witkiewicz AK, Kline J, Queenan M, Brody JR, Tsirigos A, Bilal E, Pavlides S, Ertel A, Sotgia F, Lisanti MP.
Cell Cycle. 2011 Jun 1;10(11):1794-809. Epub 2011 Jun 1.
PMID: 21521946
Ketones and lactate increase cancer cell "stemness," driving recurrence, metastasis and poor clinical outcome in breast cancer: achieving personalized medicine via Metabolo-Genomics.
Martinez-Outschoorn UE, Prisco M, Ertel A, Tsirigos A, Lin Z, Pavlides S, Wang C, Flomenberg N, Knudsen ES, Howell A, Pestell RG, Sotgia F, Lisanti MP.
Cell Cycle. 2011 Apr 15;10(8):1271-86. doi: 10.4161/cc.10.8.15330.
PMID: 21512313
The autophagic tumor stroma model of cancer or "battery-operated tumor growth": A simple solution to the autophagy paradox.
Martinez-Outschoorn UE, Whitaker-Menezes D, Pavlides S, Chiavarina B, Bonuccelli G, Casey T, Tsirigos A, Migneco G, Witkiewicz A, Balliet R, Mercier I, Wang C, Flomenberg N, Howell A, Lin Z, Caro J, Pestell RG, Sotgia F, Lisanti MP.
Cell Cycle. 2010 Nov 1;9(21):4297-306. Epub 2010 Nov 30. Review.
PMID: 21051947

2010

OMiR: Identification of associations between OMIM diseases and microRNAs.
Rossi S, Tsirigos A*, Amoroso A, Mascellani N, Rigoutsos I, Calin GA, Volinia S (*co-first author)
Genomics. 2011 Feb;97(2):71-6. doi: 10.1016/j.ygeno.2010.10.004. Epub 2010 Oct 23.
PMID: 20974243
The autophagic tumor stroma model of cancer: Role of oxidative stress and ketone production in fueling tumor cell metabolism.
Pavlides S, Tsirigos A, Migneco G, Whitaker-Menezes D, Chiavarina B, Flomenberg N, Frank PG, Casimiro MC, Wang C, Pestell RG, Martinez-Outschoorn UE, Howell A, Sotgia F, Lisanti MP.
Cell Cycle. 2010 Sep 1;9(17):3485-505. doi: 10.4161/cc.9.17.12721.
PMID: 20861672
Understanding the "lethal" drivers of tumor-stroma co-evolution: emerging role(s) for hypoxia, oxidative stress and autophagy/mitophagy in the tumor micro-environment.
Lisanti MP, Martinez-Outschoorn UE, Chiavarina B, Pavlides S, Whitaker-Menezes D, Tsirigos A, Witkiewicz A, Lin Z, Balliet R, Howell A, Sotgia F.
Cancer Biol Ther. 2010 Sep 15;10(6):537-42. doi: 10.4161/cbt.10.6.13370. Epub 2010 Sep 19. Review.
PMID: 20861671
Ketones and lactate "fuel" tumor growth and metastasis: Evidence that epithelial cancer cells use oxidative mitochondrial metabolism.
Bonuccelli G, Tsirigos A, Whitaker-Menezes D, Pavlides S, Pestell RG, Chiavarina B, Frank PG, Flomenberg N, Howell A, Martinez-Outschoorn UE, Sotgia F, Lisanti MP.
Cell Cycle. 2010 Sep 1;9(17):3506-14. Epub 2010 Sep 21.
PMID: 20818174
Glycolytic cancer associated fibroblasts promote breast cancer tumor growth, without a measurable increase in angiogenesis: evidence for stromal-epithelial metabolic coupling.
Migneco G, Whitaker-Menezes D, Chiavarina B, Castello-Cros R, Pavlides S, Pestell RG, Fatatis A, Flomenberg N, Tsirigos A, Howell A, Martinez-Outschoorn UE, Sotgia F, Lisanti MP.
Cell Cycle. 2010 Jun 15;9(12):2412-22. Epub 2010 Jun 15.
PMID: 20562527
Loss of stromal caveolin-1 leads to oxidative stress, mimics hypoxia and drives inflammation in the tumor microenvironment, conferring the "reverse Warburg effect": a transcriptional informatics analysis with validation.
Pavlides S, Tsirigos A, Vera I, Flomenberg N, Frank PG, Casimiro MC, Wang C, Fortina P, Addya S, Pestell RG, Martinez-Outschoorn UE, Sotgia F, Lisanti MP.
Cell Cycle. 2010 Jun 1;9(11):2201-19.
PMID: 20519932
Transcriptional evidence for the "Reverse Warburg Effect" in human breast cancer tumor stroma and metastasis: similarities with oxidative stress, inflammation, Alzheimer's disease, and "Neuron-Glia Metabolic Coupling".
Pavlides S, Tsirigos A, Vera I, Flomenberg N, Frank PG, Casimiro MC, Wang C, Pestell RG, Martinez-Outschoorn UE, Howell A, Sotgia F, Lisanti MP.
Aging (Albany NY). 2010 Apr;2(4):185-99.
PMID: 20442453
Dynamic changes in the human methylome during differentiation.
Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, Low HM, Kin Sung KW, Rigoutsos I, Loring J, Wei CL.
Genome Res. 2010 Mar;20(3):320-31. doi: 10.1101/gr.101907.109. Epub 2010 Feb 4.
PMID: 20133333

2009

Alu and B1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes.
Tsirigos A*, Rigoutsos I* (*co-corresponding authors)
PLoS Comput Biol. 2009 Dec;5(12):e1000610. doi: 10.1371/journal.pcbi.1000610. Epub 2009 Dec 18.
PMID: 20019790
A conserved activation element in BMP signaling during Drosophila development.
Weiss A, Charbonnier E, Ellertsdóttir E, Tsirigos A, Wolf C, Schuh R, Pyrowolakis G, Affolter M.
Nat Struct Mol Biol. 2010 Jan;17(1):69-76. doi: 10.1038/nsmb.1715. Epub 2009 Dec 13.
PMID: 20010841
Anterior-posterior positional information in the absence of a strong Bicoid gradient.
Ochoa-Espinosa A, Yu D, Tsirigos A, Struffi P, Small S.
Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3823-8. doi: 10.1073/pnas.0807878105. Epub 2009 Feb 23.
PMID: 19237583

2008

Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs.
Tsirigos A, Rigoutsos I.
Nucleic Acids Res. 2008 Jun;36(10):3484-93. doi: 10.1093/nar/gkn155. Epub 2008 May 1.
PMID: 18450818

2006

Accurate phylogenetic classification of variable-length DNA fragments.
McHardy AC, Martín HG, Tsirigos A, Hugenholtz P, Rigoutsos I.
Nat Methods. 2007 Jan;4(1):63-72. Epub 2006 Dec 10.
PMID: 17179938
Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes.
Rigoutsos I, Huynh T, Miranda K, Tsirigos A, McHardy A, Platt D.
Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6605-10. Epub 2006 Apr 24.
PMID: 16636294

2005

A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes.
Tsirigos A, Rigoutsos I.
Nucleic Acids Res. 2005 Jul 8;33(12):3699-707. Print 2005.
PMID: 16006619
A new computational method for the detection of horizontal gene transfer events.
Tsirigos A, Rigoutsos I.
Nucleic Acids Res. 2005 Feb 16;33(3):922-33. Print 2005.
PMID: 15716310