Ruben Dries | Profiles RNS

Ruben Dries, PhD

Assistant Professor

Boston University School of Medicine

Dept of Medicine

Hematology & Medical Oncology

PhD, Erasmus Universiteit Rotterdam
PhD, Katholieke Univ Leuven
MS, Katholieke Univ Leuven

Websites

	Lab Website
	Personal Website
	Loop Frontiers
	R package website
	Harvard Catalyst
	Google Scholar
	ResearchGate
	LinkedIn

ORCID : 0000-0001-7650-7754

Ruben Dries, PhD combines computational data analysis with novel experimental approaches and technologies to understand basic biological concepts in health and disease. These insights could then be leveraged to target tumor specific processes or inhibit the development of treatment resistance. These interests grew dynamically throughout his research career. In his early studies Dr. Dries developed a systems biology approach to dissect the regulatory network of neural differentiating embryonic stem cells and used this knowledge at a later stage to understand how cancer cells transcriptionally respond to targeted therapies and other stress factors. More recently, he expanded this area by focusing on how cells can spatially communicate within their microenvironment and build tools to facilitate these type of analyses.

As a young and dynamic group his lab works together as a team in the following areas:

1) Establishing multi-cellular breast cancer models that better reflect spatial tumor heterogeneity

2) Building tools to explore and quantify cellular cross-talk

3) Assess the contribution of supporting cells to cancer cells within the breast tumor microenvironment

4) Document the gradual response to targeted therapy at the transcriptional and chromatin level in breast cancer cells

Assistant Professor
Boston University School of Medicine
Medicine
Computational Biomedicine

Associate Member
Boston University
Center for Regenerative Medicine

Graduate Faculty (Primary Mentor of Grad Students)
Boston University School of Medicine, Graduate Medical Sciences

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

iCite Analysis Copy PMIDs To Clipboard

Ikonomou L, Magnusson M, Dries R, Herzog EL, Hynds RE, Borok Z, Park JA, Skolasinski S, Burgess JK, Turner L, Mojarad SM, Mahoney JE, Lynch T, Lehmann M, Thannickal VJ, Hook JL, Vaughan AE, Hoffman ET, Weiss DJ, Ryan AL. Stem cells, cell therapies, and bioengineering in lung biology and disease 2021. Am J Physiol Lung Cell Mol Physiol. 2022 Sep 01; 323(3):L341-L354. PMID: 35762622

Del Rossi N, Chen JG, Yuan GC, Dries R. Analyzing Spatial Transcriptomics Data Using Giotto. Curr Protoc. 2022 Apr; 2(4):e405. PMID: 35384407; PMCID: PMC9009248; DOI: 10.1002/cpz1.405;

Vanuytsel K, Villacorta-Martin C, Lindstrom-Vautrin J, Wang Z, Garcia-Beltran WF, Vrbanac V, Parsons D, Lam EC, Matte TM, Dowrey TW, Kumar SS, Li M, Wang F, Yeung AK, Mostoslavsky G, Dries R, Campbell JD, Belkina AC, Balazs AB, Murphy GJ. Multi-modal profiling of human fetal liver hematopoietic stem cells reveals the molecular signature of engraftment. Nat Commun. 2022 03 01; 13(1):1103.View Related Profiles.

Belkina, Anna
Murphy, George
Mostoslavsky, Gustavo
Vanuytsel, Kim
Dries, Ruben

PMID: 35232959; PMCID: PMC8888592; DOI: 10.1038/s41467-022-28616-x;

Dries R, Chen J, Del Rossi N, Khan MM, Sistig A, Yuan GC. Advances in spatial transcriptomic data analysis. Genome Res. 2021 10; 31(10):1706-1718. PMID: 34599004; PMCID: PMC8494229; DOI: 10.1101/gr.275224.121;

Cao KL, Abadi AJ, Davis-Marcisak EF, Hsu L, Arora A, Coullomb A, Deshpande A, Feng Y, Jeganathan P, Loth M, Meng C, Mu W, Pancaldi V, Sankaran K, Righelli D, Singh A, Sodicoff JS, Stein-O'Brien GL, Subramanian A, Welch JD, You Y, Argelaguet R, Carey VJ, Dries R, Greene CS, Holmes S, Love MI, Ritchie ME, Yuan GC, Culhane AC, Fertig E. Author Correction: Community-wide hackathons to identify central themes in single-cell multi-omics. Genome Biol. 2021 Aug 25; 22(1):246. PMID: 34433496; PMCID: PMC8385897; DOI: 10.1186/s13059-021-02468-y;

Lê Cao KA, Abadi AJ, Davis-Marcisak EF, Hsu L, Arora A, Coullomb A, Deshpande A, Feng Y, Jeganathan P, Loth M, Meng C, Mu W, Pancaldi V, Sankaran K, Righelli D, Singh A, Sodicoff JS, Stein-O'Brien GL, Subramanian A, Welch JD, You Y, Argelaguet R, Carey VJ, Dries R, Greene CS, Holmes S, Love MI, Ritchie ME, Yuan GC, Culhane AC, Fertig E. Community-wide hackathons to identify central themes in single-cell multi-omics. Genome Biol. 2021 08 05; 22(1):220. PMID: 34353350; PMCID: PMC8340473; DOI: 10.1186/s13059-021-02433-9;

Huang H, Gont A, Kee L, Dries R, Pfeifer K, Sharma B, Debruyne DN, Harlow M, Sengupta S, Guan J, Yeung CM, Wang W, Hallberg B, Palmer RH, Irwin MS, George RE. Extracellular domain shedding of the ALK receptor mediates neuroblastoma cell migration. Cell Rep. 2021 07 13; 36(2):109363. PMID: 34260934; PMCID: PMC8328392; DOI: 10.1016/j.celrep.2021.109363;

Jiang B, Gao Y, Che J, Lu W, Kaltheuner IH, Dries R, Kalocsay M, Berberich MJ, Jiang J, You I, Kwiatkowski N, Riching KM, Daniels DL, Sorger PK, Geyer M, Zhang T, Gray NS. Discovery and resistance mechanism of a selective CDK12 degrader. Nat Chem Biol. 2021 06; 17(6):675-683. PMID: 33753926; PMCID: PMC8590456; DOI: 10.1038/s41589-021-00765-y;

Dries R, Zhu Q, Dong R, Eng CL, Li H, Liu K, Fu Y, Zhao T, Sarkar A, Bao F, George RE, Pierson N, Cai L, Yuan GC. Giotto: a toolbox for integrative analysis and visualization of spatial expression data. Genome Biol. 2021 03 08; 22(1):78. PMID: 33685491; PMCID: PMC7938609; DOI: 10.1186/s13059-021-02286-2;

Deryckere A, Stappers E, Dries R, Peyre E, van den Berghe V, Conidi A, Zampeta FI, Francis A, Bresseleers M, Stryjewska A, Vanlaer R, Maas E, Smal IV, van IJcken WFJ, Grosveld FG, Nguyen L, Huylebroeck D, Seuntjens E. Multifaceted actions of Zeb2 in postnatal neurogenesis from the ventricular-subventricular zone to the olfactory bulb. Development. 2020 05 26; 147(10). PMID: 32253238

Showing 10 of 28 results. Show More

Zhang H, Christensen CL, Dries R, Oser MG, Deng J, Diskin B, Li F, Pan Y, Zhang X, Yin Y, Papadopoulos E, Pyon V, Thakurdin C, Kwiatkowski N, Jani K, Rabin AR, Castro DM, Chen T, Silver H, Huang Q, Bulatovic M, Dowling CM, Sundberg B, Leggett A, Ranieri M, Han H, Li S, Yang A, Labbe KE, Almonte C, Sviderskiy VO, Quinn M, Donaghue J, Wang ES, Zhang T, He Z, Velcheti V, Hammerman PS, Freeman GJ, Bonneau R, Kaelin WG, Sutherland KD, Kersbergen A, Aguirre AJ, Yuan GC, Rothenberg E, Miller G, Gray NS, Wong KK. CDK7 Inhibition Potentiates Genome Instability Triggering Anti-tumor Immunity in Small Cell Lung Cancer. Cancer Cell. 2020 01 13; 37(1):37-54.e9. PMID: 31883968; PMCID: PMC7277075; DOI: 10.1016/j.ccell.2019.11.003;

Dries R, Stryjewska A, Coddens K, Okawa S, Notelaers T, Birkhoff J, Dekker M, Verfaillie CM, Del Sol A, Mulugeta E, Conidi A, Grosveld FG, Huylebroeck D. Integrative and perturbation-based analysis of the transcriptional dynamics of TGFß/BMP system components in transition from embryonic stem cells to neural progenitors. Stem Cells. 2020 02; 38(2):202-217. PMID: 31675135; PMCID: PMC7027912; DOI: 10.1002/stem.3111;

Debruyne DN, Dries R, Sengupta S, Seruggia D, Gao Y, Sharma B, Huang H, Moreau L, McLane M, Day DS, Marco E, Chen T, Gray NS, Wong KK, Orkin SH, Yuan GC, Young RA, George RE. BORIS promotes chromatin regulatory interactions in treatment-resistant cancer cells. Nature. 2019 08; 572(7771):676-680. PMID: 31391581; PMCID: PMC7010522; DOI: 10.1038/s41586-019-1472-0;

Tracy S, Yuan GC, Dries R. RESCUE: imputing dropout events in single-cell RNA-sequencing data. BMC Bioinformatics. 2019 Jul 12; 20(1):388. PMID: 31299886; PMCID: PMC6624880; DOI: 10.1186/s12859-019-2977-0;

Krajewska M, Dries R, Grassetti AV, Dust S, Gao Y, Huang H, Sharma B, Day DS, Kwiatkowski N, Pomaville M, Dodd O, Chipumuro E, Zhang T, Greenleaf AL, Yuan GC, Gray NS, Young RA, Geyer M, Gerber SA, George RE. CDK12 loss in cancer cells affects DNA damage response genes through premature cleavage and polyadenylation. Nat Commun. 2019 04 15; 10(1):1757. PMID: 30988284; PMCID: PMC6465371; DOI: 10.1038/s41467-019-09703-y;

Eng CL, Lawson M, Zhu Q, Dries R, Koulena N, Takei Y, Yun J, Cronin C, Karp C, Yuan GC, Cai L. Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. Nature. 2019 04; 568(7751):235-239. PMID: 30911168; PMCID: PMC6544023; DOI: 10.1038/s41586-019-1049-y;

Zhu Q, Shah S, Dries R, Cai L, Yuan GC. Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data. Nat Biotechnol. 2018 Oct 29. PMID: 30371680; PMCID: PMC6488461; DOI: 10.1038/nbt.4260;

Liu Y, Li Y, Liu S, Adeegbe DO, Christensen CL, Quinn MM, Dries R, Han S, Buczkowski K, Wang X, Chen T, Gao P, Zhang H, Li F, Hammerman PS, Bradner JE, Quayle SN, Wong KK. NK Cells Mediate Synergistic Antitumor Effects of Combined Inhibition of HDAC6 and BET in a SCLC Preclinical Model. Cancer Res. 2018 07 01; 78(13):3709-3717. PMID: 29760044; PMCID: PMC6450092; DOI: 10.1158/0008-5472.CAN-18-0161;

Drapkin BJ, George J, Christensen CL, Mino-Kenudson M, Dries R, Sundaresan T, Phat S, Myers DT, Zhong J, Igo P, Hazar-Rethinam MH, Licausi JA, Gomez-Caraballo M, Kem M, Jani KN, Azimi R, Abedpour N, Menon R, Lakis S, Heist RS, Büttner R, Haas S, Sequist LV, Shaw AT, Wong KK, Hata AN, Toner M, Maheswaran S, Haber DA, Peifer M, Dyson N, Thomas RK, Farago AF. Genomic and Functional Fidelity of Small Cell Lung Cancer Patient-Derived Xenografts. Cancer Discov. 2018 05; 8(5):600-615.View Related Profiles.

Myers, David
Dries, Ruben

PMID: 29483136; PMCID: PMC6369413; DOI: 10.1158/2159-8290.CD-17-0935;

Deng J, Wang ES, Jenkins RW, Li S, Dries R, Yates K, Chhabra S, Huang W, Liu H, Aref AR, Ivanova E, Paweletz CP, Bowden M, Zhou CW, Herter-Sprie GS, Sorrentino JA, Bisi JE, Lizotte PH, Merlino AA, Quinn MM, Bufe LE, Yang A, Zhang Y, Zhang H, Gao P, Chen T, Cavanaugh ME, Rode AJ, Haines E, Roberts PJ, Strum JC, Richards WG, Lorch JH, Parangi S, Gunda V, Boland GM, Bueno R, Palakurthi S, Freeman GJ, Ritz J, Haining WN, Sharpless NE, Arthanari H, Shapiro GI, Barbie DA, Gray NS, Wong KK. CDK4/6 Inhibition Augments Antitumor Immunity by Enhancing T-cell Activation. Cancer Discov. 2018 02; 8(2):216-233. PMID: 29101163; PMCID: PMC5809273; DOI: 10.1158/2159-8290.CD-17-0915;

Akbay EA, Koyama S, Liu Y, Dries R, Bufe LE, Silkes M, Alam MM, Magee DM, Jones R, Jinushi M, Kulkarni M, Carretero J, Wang X, Warner-Hatten T, Cavanaugh JD, Osa A, Kumanogoh A, Freeman GJ, Awad MM, Christiani DC, Bueno R, Hammerman PS, Dranoff G, Wong KK. Interleukin-17A Promotes Lung Tumor Progression through Neutrophil Attraction to Tumor Sites and Mediating Resistance to PD-1 Blockade. J Thorac Oncol. 2017 08; 12(8):1268-1279. PMID: 28483607; PMCID: PMC5532066; DOI: 10.1016/j.jtho.2017.04.017;

Adeegbe DO, Liu Y, Lizotte PH, Kamihara Y, Aref AR, Almonte C, Dries R, Li Y, Liu S, Wang X, Warner-Hatten T, Castrillon J, Yuan GC, Poudel-Neupane N, Zhang H, Guerriero JL, Han S, Awad MM, Barbie DA, Ritz J, Jones SS, Hammerman PS, Bradner J, Quayle SN, Wong KK. Synergistic Immunostimulatory Effects and Therapeutic Benefit of Combined Histone Deacetylase and Bromodomain Inhibition in Non-Small Cell Lung Cancer. Cancer Discov. 2017 08; 7(8):852-867. PMID: 28408401; PMCID: PMC5540748; DOI: 10.1158/2159-8290.CD-16-1020;

Stryjewska A, Dries R, Pieters T, Verstappen G, Conidi A, Coddens K, Francis A, Umans L, van IJcken WF, Berx G, van Grunsven LA, Grosveld FG, Goossens S, Haigh JJ, Huylebroeck D. Zeb2 Regulates Cell Fate at the Exit from Epiblast State in Mouse Embryonic Stem Cells. Stem Cells. 2017 03; 35(3):611-625. PMID: 27739137; PMCID: PMC5396376; DOI: 10.1002/stem.2521;

Lizotte PH, Ivanova EV, Awad MM, Jones RE, Keogh L, Liu H, Dries R, Almonte C, Herter-Sprie GS, Santos A, Feeney NB, Paweletz CP, Kulkarni MM, Bass AJ, Rustgi AK, Yuan GC, Kufe DW, Jänne PA, Hammerman PS, Sholl LM, Hodi FS, Richards WG, Bueno R, English JM, Bittinger MA, Wong KK. Multiparametric profiling of non-small-cell lung cancers reveals distinct immunophenotypes. JCI Insight. 2016 09 08; 1(14):e89014. PMID: 27699239; PMCID: PMC5033841; DOI: 10.1172/jci.insight.89014;

Gomes Fernandes M, Dries R, Roost MS, Semrau S, de Melo Bernardo A, Davis RP, Ramakrishnan R, Szuhai K, Maas E, Umans L, Abon Escalona V, Salvatori D, Deforce D, Van Criekinge W, Huylebroeck D, Mummery C, Zwijsen A, de Sousa Lopes SM. BMP-SMAD Signaling Regulates Lineage Priming, but Is Dispensable for Self-Renewal in Mouse Embryonic Stem Cells. Stem Cell Reports. 2016 Jan 12; 6(1):85-94. PMID: 26711875; PMCID: PMC4720007; DOI: 10.1016/j.stemcr.2015.11.012;

van den Berghe V, Stappers E, Vandesande B, Dimidschstein J, Kroes R, Francis A, Conidi A, Lesage F, Dries R, Cazzola S, Berx G, Kessaris N, Vanderhaeghen P, van Ijcken W, Grosveld FG, Goossens S, Haigh JJ, Fishell G, Goffinet A, Aerts S, Huylebroeck D, Seuntjens E. Directed migration of cortical interneurons depends on the cell-autonomous action of Sip1. Neuron. 2013 Jan 09; 77(1):70-82. PMID: 23312517

Conidi A, Cazzola S, Beets K, Coddens K, Collart C, Cornelis F, Cox L, Joke D, Dobreva MP, Dries R, Esguerra C, Francis A, Ibrahimi A, Kroes R, Lesage F, Maas E, Moya I, Pereira PN, Stappers E, Stryjewska A, van den Berghe V, Vermeire L, Verstappen G, Seuntjens E, Umans L, Zwijsen A, Huylebroeck D. Few Smad proteins and many Smad-interacting proteins yield multiple functions and action modes in TGFß/BMP signaling in vivo. Cytokine Growth Factor Rev. 2011 Oct-Dec; 22(5-6):287-300. PMID: 22119658

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 28 publications over 10 distinct years, with a maximum of 6 publications in 2019 and 2021