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
Diversity, Equity, Inclusion and Accessibility
I believe that diversity and inclusion (D&I) is a core part of science and I am fully committed to serving as an advocate for D&I in my lab and academic scientific ecosystem. From a social justice perspective, D&I is critical for eliminating barriers to higher education like inequality and prejudice, and evening the playing field for the next generation of scientists from diverse backgrounds. Diverse research teams have been shown to lead to more impactful research. In my lab, I openly welcome scientists from a variety of backgrounds and at all stages of their careers to foster an inclusive and interdisciplinary research environment. It is clear to me that D&I provide major benefits to science and is absolutely necessary for upholding rigorous science. Without D&I in science, it is impossible to grasp human biology that varies from people with diverse ethnic and socioeconomic backgrounds.
In August 2020, I launched my lab with the goal of creating an inclusive culture for people from diverse backgrounds. I remind myself of the importance of D&I in my interactions with students, coworkers, and leadership, and I actively encourage others to take part in activities that will advance D&I initiatives. My desire to contribute to D&I is also reflected in the types of research problems I pursue. My lab recently established a research collaboration with Massachusetts General Hospital, the Boston University Medical Center (BUMC) Cancer Center, and other researchers in my lab to investigate therapies for predominantly Black women with late-stage breast cancer.
In short, I consider promoting D&I to be one of the most important aspects of my role as a research professor and mentor. In the future, I will continue to promote D&I efforts in my scientific community. My goal is to serve as an advocate for D&I in my scientific ecosystem at BUMC. I will continue to work closely with other labs and leadership who are also dedicated to this goal and improving D&I in my scientific academic ecosystem.
Assistant Professor
Boston University Chobanian & Avedisian School of Medicine
Medicine
Computational Biomedicine
Associate Member
Boston University
Center for Regenerative Medicine
Graduate Faculty (Primary Mentor of Grad Students)
Boston University Chobanian & Avedisian School of Medicine, Graduate Medical Sciences
This tab shows grant data from BMC Sponsored Research. It includes:
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- Data is sorted by project end date, and updated monthly.
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- PI name, if this person is not the PI (the name will link if PI has a BU Profile)
- Funding source(s). An arrow indicates the flow of funding if multiple sponsors.
- Some grants will show an agency award/project number, and may be a link.
- Data is sorted by project end date, and updated monthly.
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from BU or BMC sources.
- Grant title
- Project period and this person’s role on the grant
- PI name, if this person is not the PI (the name will link if PI has a BU Profile)
- Funding source(s). An arrow indicates the flow of funding if multiple sponsors.
- Some grants will show an agency award/project number, and may be a link.
- Data is sorted by project end date, and updated monthly.
This tab shows grant data from the Boston VA. We are only showing grant title, and only for people in the role of PI.
Multiscale analysis of metabolic inflammation as a driver of breast cancer09/01/2022 - 08/31/2025 (Subcontract PI)
PI:
Ruben Dries, PhDTrustees of Boston University, BUMC NIH NCI
Targeting the biological underpinnings of pulmonary metastasis in osteosarcoma05/02/2022 - 05/01/2025 (Subcontract PI)
PI:
Ruben Dries, PhDDana Farber Cancer Institute ALSF-Alex Lemonade
Enhancing Giotto for spatial multi-resolution technologies (EOSS-5)11/14/2022 - 10/31/2024 (PI)
Chan Zuckerberg Initiative
dkNET Coordinating Unit: An information network for FAIR resources and data07/01/2022 - 06/30/2024 (Subcontract PI)
PI:
Ruben Dries, PhDTrustees of Boston University, BUMC NIH NIDDK
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Publications listed below are automatically derived from MEDLINE/PubMed and other
sources, which might result in incorrect or missing publications. Faculty can
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to make corrections and additions.
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Reinecke JB, Jimenez Garcia L, Gross AC, Cam M, Cannon MV, Gust MJ, Sheridan JP, Gryder BE, Dries R, Roberts RD. Aberrant activation of wound healing programs within the metastatic niche facilitates lung colonization by osteosarcoma cells. Clin Cancer Res. 2024 Nov 14. PMID: 39540841
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Sarfraz I, Wang Y, Shastry A, Teh WK, Sokolov A, Herb BR, Creasy HH, Virshup I, Dries R, Degatano K, Mahurkar A, Schnell DJ, Madrigal P, Hilton J, Gehlenborg N, Tickle T, Campbell JD. MAMS: matrix and analysis metadata standards to facilitate harmonization and reproducibility of single-cell data. Genome Biol. 2024 Aug 01; 25(1):205.View Related Profiles. PMID: 39090672; DOI: 10.1186/s13059-024-03349-w;
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Reinecke JB, Gross AC, Cam M, Garcia LJ, Cannon MV, Dries R, Gryder BE, Roberts RD. Aberrant activation of wound healing programs within the metastatic niche facilitates lung colonization by osteosarcoma cells. bioRxiv. 2024 Jan 12. PMID: 38260361; DOI: 10.1101/2024.01.10.575008;
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Chen JG, Chávez-Fuentes JC, O'Brien M, Xu J, Ruiz E, Wang W, Amin I, Sarfraz I, Guckhool P, Sistig A, Yuan GC, Dries R. Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem. bioRxiv. 2023 Nov 27. PMID: 38077085; DOI: 10.1101/2023.11.26.568752;
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Wang Y, Sarfraz I, Teh WK, Sokolov A, Herb BR, Creasy HH, Virshup I, Dries R, Degatano K, Mahurkar A, Schnell DJ, Madrigal P, Hilton J, Gehlenborg N, Tickle T, Campbell JD. Matrix and analysis metadata standards (MAMS) to facilitate harmonization and reproducibility of single-cell data. bioRxiv. 2023 Mar 07. PMID: 36945543; DOI: 10.1101/2023.03.06.531314;
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Wang Y, Sarfraz I, Teh WK, Sokolov A, Herb BR, Creasy HH, Virshup I, Dries R, Degatano K, Mahurkar A, Schnell DJ, Madrigal P, Hilton J, Gehlenborg N, Tickle T, Campbell JD. Matrix and analysis metadata standards (MAMS) to facilitate harmonization and reproducibility of single-cell data. bioRxiv. 2023 Mar 07. PMID: 36945543; PMCID: PMC10028847; DOI: 10.1101/2023.03.06.531314;
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Ennis CS, Llevenes P, Qiu Y, Dries R, Denis GV. The crosstalk within the breast tumor microenvironment in type II diabetes: Implications for cancer disparities. Front Endocrinol (Lausanne). 2022; 13:1044670.View Related Profiles. PMID: 36531496; DOI: 10.3389/fendo.2022.1044670;
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Sengupta S, Das S, Crespo AC, Cornel AM, Patel AG, Mahadevan NR, Campisi M, Ali AK, Sharma B, Rowe JH, Huang H, Debruyne DN, Cerda ED, Krajewska M, Dries R, Chen M, Zhang S, Soriano L, Cohen MA, Versteeg R, Jaenisch R, Spranger S, Romee R, Miller BC, Barbie DA, Nierkens S, Dyer MA, Lieberman J, George RE. Mesenchymal and adrenergic cell lineage states in neuroblastoma possess distinct immunogenic phenotypes. Nat Cancer. 2022 Oct; 3(10):1228-1246. PMID: 36138189; DOI: 10.1038/s43018-022-00427-5;
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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; DOI: 10.1152/ajplung.00113.2022;
Showing 10 of 37 results.
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Del Rossi N, Chen JG, Yuan GC, Dries R. Analyzing Spatial Transcriptomics Data Using Giotto. Curr Protoc. 2022 Apr; 2(4):e405. PMID: 35384407; DOI: 10.1002/cpz1.405;
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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. PMID: 35232959; DOI: 10.1038/s41467-022-28616-x;
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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; DOI: 10.1186/s13059-021-02468-y;
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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; DOI: 10.1186/s13059-021-02433-9;
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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; DOI: 10.1016/j.celrep.2021.109363;
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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; DOI: 10.1038/s41589-021-00765-y;
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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; DOI: 10.1186/s13059-021-02286-2;
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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
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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 Jan 01. PMID: 34004812
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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; DOI: 10.1016/j.ccell.2019.11.003;
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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; DOI: 10.1002/stem.3111;
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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; DOI: 10.1038/s41586-019-1472-0;
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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; DOI: 10.1186/s12859-019-2977-0;
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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; DOI: 10.1038/s41467-019-09703-y;
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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; DOI: 10.1038/s41586-019-1049-y;
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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; DOI: 10.1038/nbt.4260;
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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; DOI: 10.1158/0008-5472.CAN-18-0161;
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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. PMID: 29483136; DOI: 10.1158/2159-8290.CD-17-0935;
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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; DOI: 10.1158/2159-8290.CD-17-0915;
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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; DOI: 10.1016/j.jtho.2017.04.017;
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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; DOI: 10.1158/2159-8290.CD-16-1020;
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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; DOI: 10.1002/stem.2521;
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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; DOI: 10.1172/jci.insight.89014;
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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; DOI: 10.1016/j.stemcr.2015.11.012;
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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
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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.
| Year | Publications |
|---|
| 2011 | 1 |
| 2013 | 1 |
| 2015 | 1 |
| 2016 | 2 |
| 2017 | 3 |
| 2018 | 3 |
| 2019 | 6 |
| 2020 | 2 |
| 2021 | 6 |
| 2022 | 5 |
| 2023 | 2 |
| 2024 | 4 |
2018 Abstract selected for oral talk at the Keystone meeting
2015 Abstract selected for oral talk at the Syboss meeting
2014 Abstract selected for oral talk at the BSCDB meeting
2010 IWT Fellowship: Strategic Basic Research Fund
2009 Ioannina University:
International summer internship
2008 Tsinghua University:
Travel and study fellowship