Publications

Overview

Selected Publications

Sonawane AR, DeMeo DL, Quackenbush J, Glass K. Constructing gene regulatory networks using epigenetic data. NPJ Systems Biology and Applications. 2021 Dec 9;7(1):45. doi: 10.1038/s41540-021-00208-3. PubMed Resources

Kuijjer ML, Fagny M, Quackenbush J, Glass K. PUMA: PANDA Using MicroRNA Associations. Bioinformatics. 2020 Sep 15;36(18):4765-4773. doi: 10.1093/bioinformatics/btaa571. bioRxiv PubMed Resources

Lopes-Ramos CM, Chen CY, Kuijjer ML, Paulson JN, Sonawane AR, Fagny M, Platig J, Glass K, Quackenbush J, DeMeo DL. Sex Differences in gene expression and regulatory networks across 29 human tissues. Cell Reports. 2020 Jun 23. Cell Press bioRxiv Resources

Kuijjer ML*, Tung M*, Quackenbush J, Yuan GC, Glass K. Estimating Sample-Specific Regulatory Networks. iScience. 2019 Apr 26;14:226-240. doi: 10.1016/j.isci.2019.03.021. Epub 2019 Mar 28. Pubmed Cell Press arXiv Resources

Sonawane AR, Platig J, Fagny M, Chen CY, Paulson JN, Lopes-Ramos CM, Quackenbush J, Glass K†, Kuijjer ML†. Understanding Tissue-Specific Gene Regulation. Cell Reports. 2017 Oct 24;21(4):1077-1088. Pubmed Cell Press bioRxiv Resources

Lopes-Ramos CM*. Paulson JN*, Chen CY, Kuijjer ML, Fagny M, Platig J, Sonawane A, DeMeo DL, Quackenbush J, Glass K. Regulatory network changes between cell lines and their tissues of origin. BMC Genomics. 2017 Sep 12;18(1):723. doi: 10.1186/s12864-017-4111-x. Pubmed bioRxiv

Cloonan S, Glass K, Laucho-Contreras M, Bhashyam AR, Cervo M, Pabon-Porras MA, Konrad C, Polverino F, Siempos II, Perez E, Mizumura K, Ghosh MC, Parameswaran H, Williams NC, Rooney K, Chen ZH, Goldklang MP, Yuan GC, Moore SC, DeMeo DL, Rouault T, D'Armiento JM, Schon E, Manfredi G, Quackenbush J, Mahmood A, Silverman EK, Owen CA, Choi AMK. Mitochondrial iron chelation ameliorates cigarette-smoke induced bronchitis and emphysema in mice. Nature Medicine. 2016 Feb;22(2):163-74. Pubmed

Glass K, Girvan M. Finding New Order in Biological Functions from the Network Structure of Gene Annotations. PLoS Computational Biology. 2015 Nov 20;11(11):e1004565. Pubmed arXiv Resources

Glass K, Girvan M. Annotation Enrichment Analysis: An Alternative Method for Evaluating the Functional Properties of Gene Sets. Scientific Reports. 2014 Feb 26;4:4191. Pubmed arXiv Resources

Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing Messages Between Biological Networks to Refine Predicted Interactions. PLoS One. 2013 May 31;8(5):e64832. Pubmed Resources

All Publications

Journal Publications

Morgan D, DeMeo DL Glass K. Using methylation data to improve transcription factor binding prediction. (in press Epigenetics, January 2024)

De Marzio M, Glass K†, Kuiijer ML†. Single-sample network modeling on omics data. BMC Biology. 2023 Dec 29;21(1):296. doi: 10.1186/s12915-023-01783-z. PubMed

Martini L*, Baek SH*, Lo I, Silverman EK, Weiss ST, Glass K†, Halu A†. Detecting and dissecting signaling crosstalk via the multilayer network integration of signaling and regulatory interactions. Nucleic Acids Research. 2023 Nov 11:gkad1035. doi: 10.1093/nar/gkad1035. Online ahead of print. PubMed

Hsieh PH, Lopes-Ramos C, Zucknick M, Sandve GK, Glass K, Kuijjer ML. Adjustment of spurious correlations in co-expression measurements. Bioinformatics. 2023 Oct 3;39(10):btad610. doi: 10.1093/bioinformatics/btad610. PubMed

Leonardo TR, Chen L, Schrementi ME, Shi J, Marucha PT, Glass K, DiPietro LA. Transcriptional changes in human palate and skin healing. Wound Repair and Regeneration. 2023 Mar;31(2):156-170. doi: 10.1111/wrr.13068. Epub 2023 Jan 16. PubMed

Ben Guebila M, Wang T, Lopes-Ramos CM, Fanfani V, Weighill D, Burkholz R, Schlauch D, Paulson JN, Altenbuchinger M, Shutta KH, Sonawane AR, Lim J, Calderer G, Van Ijzendoorn DGP, Morgan D, Marin A, Chen CY, Song Q, Saha E, DeMeo DL, Padi M, Platig J, Kuijjer ML, Glass K, Quackenbush J. The Network Zoo: a multilingual package for the inference and analysis of biological networks. Genome Biology. 2023 Mar 9;24(1):45. doi: 10.1186/s13059-023-02877-1. PubMed

Quinn M, Chung A, Glass K. Automated Selection of Changepoints using Empirical P-values and Trimming. JAMIA Open. 2022 Oct 29;5(4):ooac090. doi: 10.1093/jamiaopen/ooac090. eCollection 2022 Dec. PubMed

Yassine HN, Samieri C, Livingston G, Glass K, Wagner M, Tangney C, Plassman BL, Ikram MA, Voigt RM, Gu Y, O’Bryant S, Minihane AM, Craft S, Fink HA, Judd S, Andrieu S, Bowman GL, Richard E, Albensi B, Meyers E, Khsovarian S, Solis M, Carrillo MC, Snyder H, Grodstein F, Scarmeas N, Schneider LS. Nutrition state of science and dementia prevention: recommendations of the Nutrition for Dementia Prevention Working Group. The Lancet Healthy Longevity. 2022 Jul;3(7):e501-e512. doi: 10.1016/s2666-7568(22)00120-9. Epub 2022 Jul 4. PubMed

Fagny M, Glass K, Kuijjer ML. Editorial: Applications and Methods in Genomic Networks. Frontiers in Genetics. 2022 June 08. doi: 10.3389/fgene.2022.936015. eCollection 2022. PubMed

Baek SH, Maiorino E, Kim H, Glass K, Raby BA, Yuan K. Single cell transcriptomic analysis reveals organ-specific pericyte markers and identities. Frontiers in Cardiovascular Medicine. 2022 June 01. doi: 10.3389/fcvm.2022.876591. PubMed

Ben Guebila M, Weighill D, Lopes-Ramos CM, Burkholz R, Pop RT, Palepu K, Shapoval M, Fagny M, Schlauch D, Glass K, Altenbuchinger M, Kuijjer ML, Platig J, Quackenbush J. An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks. Nature Methods. 2022 May;19(5):511-513. doi: 10.1038/s41592-022-01479-2. PubMed

Rohl A, Baek SH, Kachroo P, Morrow J, Tantisira K, Silverman EK, Weiss ST, Sharma A, Glass K, DeMeo DL. Protein interaction networks provide insight into fetal origins of chronic obstructive pulmonary disease. Respiratory Research. 2022 Mar 24;23(1):69. doi: 10.1186/s12931-022-01963-5. PubMed

Weighill D, Ben Guebila M, Glass K, Quackenbush J, Platig J. Predicting genotype-specific gene regulatory networks. Genome Research. 2022 Mar;32(3):524-533. doi: 10.1101/gr.275107.120. Epub 2022 Feb 22. PubMed

Shrestha S, Lamattina A, Pacheco-Rodriguez G, Ng J, Liu X, Sonawane AR, Imani J, Qiu W, Kosmas K, Louis P, Hentschel A, Christou H, Henske EP, Glass K, Perrella M, Moss J, Tantisira K, El-Chemaly S. ETV2 regulates PARP-1 binding protein to induce ER stress-mediated death in tuberin-deficient cells. Life Science Alliance. 2022 Feb 18;5(5):e202201369. doi: 10.26508/lsa.202201369. Print 2022 May. PubMed

Ben Guebila M, Morgan DC, Glass K, Kuijjer ML, DeMeo DL, Quackenbush J. gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit. Nucleic Acids Research Genomics and Bioinformatics. 2022 Feb 8;4(1):lqac002. doi: 10.1093/nargab/lqac002. eCollection 2022 Mar. PubMed

Benedetti R, Benincasa G, Glass K, Chianese U, Vietri MT, Congi R, Altucci L, Napoli C. Effects of novel SGLT2 inhibitors on cancer incidence in hyperglycemic patients: a meta-analysis of randomized clinical trials. Pharmacological Research. 2022 Jan;175:106039. doi: 10.1016/j.phrs.2021.106039. Epub 2021 Dec 18. PubMed

Ben Guebila M*, Lopes-Ramos CM*, Weighill D, Sonawane AR, Burkholz R, Shamsaei B, Platig J, Glass K, Kuijjer ML, Quackenbush J. GRAND: A database of gene regulatory models across human conditions. Nucleic Acids Research. 2022 Jan 7;50(D1):D610-D621. doi: 10.1093/nar/gkab778. PubMed

De Marzio M*, Kilic A*, Maiorino E, Mitchel JA, Mwase C, O’Sullivan M, McGill M, Chase R, Fredberg JJ, Park JA, Glass K†, Weiss ST†. Genomic signatures of the unjamming transition in compressed human bronchial epithelial cells. Science Advances. 2021 Jul 23;7(30):eabf1088. doi: 10.1126/sciadv.abf1088. Print 2021 Jul. PubMed

Gong L, Bates S, Li J, Qiao D, Glass K, Wei W, Hsu VW, Zhou X, Silverman EK. Connecting COPD GWAS genes: FAM13A controls TGFβ2 secretion by modulating AP-3 transport. American Journal of Respiratory Cell and Molecular Biology. 2021 Nov;65(5):532-543. doi: 10.1165/rcmb.2021-0016OC. PubMed

Weighill D, Ben Guebila M, Lopes-Ramos C, Glass K, Quackenbush J, Platig J†, Bukholz R†. Gene Regulatory Network Inference as Relaxed Graph Matching. Proceedings of the AAAI (Association for the Advancement of Artificial Intelligence) Conference on Artificial Intelligence. 2021 Feb;35(11):10263-10272. Epub 2021 May 18. bioRxiv PubMed

Weighill D, Ben Guebila M, Glass K, Platig J, Yeh JJ, Quackenbush J. Gene targeting in disease networks. Frontiers in Genetics. 2021 Apr 23;12:649942. doi: 10.3389/fgene.2021.649942. eCollection 2021. arXiv PubMed

Sarno F, Benincasa G, List M, Barabasi AL, Baumbach J, Ciardiello F, Filetti S, Glass K, Loscalzo J, Marchese C, Maron BA, Paci P, Parini P, Petrillo E, Silverman EK, Verrienti A, Altucci L, Napoli C. Clinical epigenetics settings for cancer and cardiovascular diseases: real-life applications of network medicine at the bedside. Clinical Epigenetics. 2021 Mar 30;13(1):66. doi: 10.1186/s13148-021-01047-z. PubMed

Benincasa G, DeMeo DL, Glass K, Silverman EK, Napoli C. Epigenetics and pulmonary diseases in the horizon of precision medicine: a review. European Respiratory Journal. 2020 Nov 19;2003406. doi: 10.1183/13993003.03406-2020. PubMed

Liu X*, Maiorino E*, Halu A, Glass K, Loscalzo J, Gao J, Sharma A. Robustness and lethality in multilayer biological molecular networks. Nature Communications. 2020 Nov 27;11(1):6043. doi: 10.1038/s41467-020-19841-3. PubMed

Wang J, Peng C, Askew C, Heng YJ, Glass K, Eliassen AH, Tamimi R, Polyak K, Hankinson S. Early-life Body Adiposity and the Breast Tumor Transcriptome. Journal of the National Cancer Institute. 2020 Nov 2;djaa169. doi: 10.1093/jnci/djaa169. Online ahead of print. PubMed

Kuijjer ML, Fagny M, Quackenbush J, Glass K. PUMA: PANDA Using MicroRNA Associations. Bioinformatics. 2020 Sep 15;36(18):4765-4773. doi: 10.1093/bioinformatics/btaa571. bioRxiv PubMed

Peng C, DuPre N, VoPham T, Heng YJ, Baker GM, Rubadue CA, Glass K, Sonawane AR, Zeleznik O, Kraft P, Hankinson SE, Eliassen AH, Hart JE, Laden F, Tamimi RM. Low dose environmental radon exposure and breast tumor gene expression. BMC Cancer. 2020 Jul 28;20(1):695. doi: 10.1186/s12885-020-07184-7.

DuPré NC, Heng YJ, Raby BA, Glass K, Hart JE, Chu J, Askew C, Eliassen AH, Hankinson SE, Kraft P, Laden F, Tamimi RM. Laden F†, Tamimi RM†. Involvement of fine particulate matter exposure with gene expression pathways in breast tumor and adjacent-normal breast tissue. Environmental Research. 2020 Jul;186:109535. doi: 10.1016/j.envres.2020.109535. Epub 2020 Apr 15. PubMed

Samieri C*, Sonawane AR*, Lefèvre-Arbogast S, Helmer C, Grodstein F, Glass K. Using network science tools to identify novel diet patterns in prodromal dementia: The Three-City Study. Neurology. 2020 Apr 22;10.1212/WNL.0000000000009399. doi: 10.1212/WNL.0000000000009399. Online ahead of print. PubMed Press Coverage

Silverman EK, Schmidt HHHW, Anastasiadou E, Altucci L, Angelini M, Badimon L, Balligand JL, Benincasa G, Capasso G, Conte F, Di Costanzo A, Farina L, Fiscon G, Gatto L, Gentili M, Loscalzo J, Marchese C, Napoli C, Paci P, Petti M, Quackenbush J, Tieri P, Viggiano D, Vilahur G, Glass K, Baumbach J. Molecular Networks in Network Medicine: Development and Applications. Wiley Interdisciplinary Reviews in Systems Biology and Medicine. 2020 Apr 19;e1489. doi: 10.1002/wsbm.1489. Online ahead of print. PubMed

Peng C, Heng YJ, Lu D, DuPré NC, Kensler KH, Glass K, Zeleznik OA, Kraft P, Feldman D, Hankinson SE, Rexrode K, Eliassen AH, Tamimi RM. Pre-diagnostic 25-hydroxyvitamin D concentrations in relation to tumor molecular alterations and risk of breast cancer recurrence. Cancer Epidemiology, Biomarkers, and Prevention. 2020 Apr 1;cebp.1217.2019. doi: 10.1158/1055-9965.EPI-19-1217. Online ahead of print. PubMed

Paci P, Fiscon G, Conte F, Licursi V, Morrow J, Hersh CP, Cho MH, Castaldi P, Glass K, Silverman EK, Farina L. Integrated transcriptomic correlation network analysis identifies COPD molecular determinants. Scientific Reports. 2020 Feb 25;10(1):3361. doi: 10.1038/s41598-020-60228-7. PubMed

Penney KL, Townsend MK, Turman C, Glass K, Staller K, Kraft P, Grodstein F, Minnassian VA. Genome-Wide Association Study for Urinary and Fecal Incontinence in Women. Journal of Urology. 2019 Nov 15:101097JU0000000000000655. doi: 10.1097/JU.0000000000000655. PubMed

Kuijjer ML, Hsieh PH, Quackenbush J, Glass K. lionessR: An R package for generating single-sample networks. BMC Cancer. 2019 Oct 25;19(1):1003. doi: 10.1186/s12885-019-6235-7. PubMed

Sonawane AR*, Tian L*, Chu CY, Qiu X, Wang L, Holden-Wiltse J, Grier A, Gill S, Caserta M, Walsh E, Mariani TJ, Silverman EK, Glass K†, Liu YY†. Integrative Analysis of Nasal Microbiome, Host Transcriptome, and Clinical Outcomes in infants with Respiratory Syncytial virus infection. Scientific Reports. 2019 Sep 25;9(1):13824. doi: 10.1038/s41598-019-50217-w. PubMed

Stubbs BJ, Gopaulakrishnan S, Glass K, Pochet N, Everaert C, Raby B, Carey V. TFutils: Data Structures for Transcription Factor Bioinformatics. F1000, May 2019. F1000

Sonawane AR, Weiss ST, Glass K, Sharma A. Network Medicine in the Age of Biomedical Big Data. Frontiers in Genetics. 2019 Apr 11;10:294. doi: 10.3389/fgene.2019.00294. eCollection 2019. arXiv PubMed

Morrow JD, Chase RP, Parker M, Glass K, Seo M, Divo M, Owen CA, Castaldi P, DeMeo DL, Silverman EK, Hersh CP. RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD. Respiratory Research. 2019 Apr 2;20(1):65. doi: 10.1186/s12931-019-1032-z. Pubmed

Peng C, van Meel E, Cardenas A, Rifas-Shiman SL, Sonawane AR, Glass K, Gold DR, Platts-Mills TA, Lin X, Oken E, Hivert MF, Baccarelli AA, de Jong NW, Felix JF, Jaddoe VW, Duijts L, Litonjua AA, DeMeo DL. Epigenome-wide association study reveals methylation pathways associated with childhood allergic sensitization. Epigenetics. 2019 May;14(5):445-466. doi: 10.1080/15592294.2019.1590085. Epub 2019 Mar 28. Pubmed

Yu D, Zhang Z, Glass K, Su J, DeMeo DL, Tantisira K, Weiss ST, Qiu W. New Statistical Methods for Constructing Robust Differential Correlation Networks to characterize the interactions among microRNAs. Scientific Reports. 2019 Mar 5;9(1):3499. doi: 10.1038/s41598-019-40167-8. Pubmed bioRxiv

Huang T, Glass K, Zeleznik OA, Kang JH, Ivey KL, Sonawane AR, Birmann B, Hersh C, Hu FB, Tworoger SS. A network analysis of biomarkers for type 2 diabetes. Diabetes. 2019 Feb;68(2):281-290. doi: 10.2337/db18-0892. Epub 2018 Nov 8. Pubmed

Lopes-Ramos CM, Kuijjer ML, Ogino S, Fuchs CS, DeMeo DL, Glass K, Quackenbush J. Gene regulatory network analysis identifies sex-linked differences in colon cancer drug metabolism processes. Cancer Research. 2018 Oct 1;78(19):5538-5547. Pubmed bioRxiv

Glass K, Thibault D, Guo F, Mitchel JA, Pham B, Qui W, Yan Li, Jiang Z, Castaldi P, Silverman EK, Raby B, Park JA, Yuan GC, Zhou X. Integrative epigenomic analysis in differentiated human primary bronchial epithelial cells exposed to cigarette smoke. Scientific Reports. 2018 Aug 24;8(1):12750. Pubmed

Morrow JD, Cho MH, Platig J, Zhou X, DeMeo DL, Qui W, Celli B, Marchetti N, Criner GJ, Bueno R, Washko GR, Glass K, Quackenbush J, Silverman EK, Hersh CP. Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease. Human Genomics. 2018 Jan 15;12(1):1. doi: 10.1186/s40246-018-0132-z. Pubmed

Morrow JD, Glass K, Cho MH, Hersh CP, Chase RP, Pinto-Plata V, Celli B, Marchetti N, Criner G, Bueno R, Washko G, Choi AMK, Quackenbush J, Silverman EK, DeMeo DL. Human lung DNA methylation QTL colocalize with COPD loci. American Journal of Respiratory and Critical Care Medicine. 2018 Jan 9. doi: 10.1164/rccm.201707-1434OC. [Epub ahead of print]. Pubmed

Driesbaugh KH, Branchetti E, Grau JB, Keeney SJ, Glass K, Oyama MA, Rioux N, Ayoub S, Sacks MS, Quackenbush J, Levy RJ, Ferrari G. Serotonin Receptor 2B Signaling with Interstitial Cell Activation and Leaflet Remodeling in Degenerative Mitral Regurgitation. Journal of Molecular and Cellular Cardiology. 2017 Dec 29. pii: S0022-2828(17)30370-X. doi: 10.1016/j.yjmcc.2017.12.014. Pubmed

Schlauch D, Glass K, Hersh CP, Silverman EK, Quackenbush J. Estimating Drivers of Cell State Transitions using Gene Regulatory Network Models. BMC Systems Biology. 2017 Dec 13;11:139. Doi: 10.1186/s12918-017-0517-y. Pubmed Resources

Paulson JN, Chen CY, Lopes-Ramos CM, Kuijjer ML, Platig J, Sonawane A, Fagny M, Glass K, Quackenbush J. Tissue-aware RNA-seq processing and normalization for heterogeneous and sparse data. BMC Bioinformatics. 2017 Oct 3;18(1):437. Pubmed bioRxiv

Fagny M, Paulson JN, Kuijjer ML, Sonawane AR, Chen CY, Lopes-Ramos CM, Glass K, Quackenbush J, Platig J. Exploring regulation in tissues with eQTL networks. Proceedings of the National Academy of Science. 2017 Aug 29. pii: 201707375. doi: 10.1073/pnas.1707375114. [Epub ahead of print] Pubmed bioRxiv

Qui W*, Guo F*, Glass K, Yuan GC, Quackenbush J, Zhou X, Tantisira KG. Differential connectivity of gene regulatory networks distinguishes corticosteroid response in asthma. The Journal of Allergy and Clinical Immunology. 2017 Jul 20. pii: S0091-6749(17)31109-0. doi: 10.1016/j.jaci.2017.05.052. [Epub ahead of print]. Pubmed

Yun JH, Morrow J, Qui W, Glass K, Lao T, Jiang Z, Owen CA, Perrella M, Silverman EK, Zhou X, Hersh CP. Transcriptomic Analysis of Lung Tissue from Cigarette Smoke-Induced Emphysema Murine Models and Human Chronic Obstructive Pulmonary Disease Show Shared and Distinct Pathways. American Journal of Respiratory Cell and Molecular Biology. 2017 Jul;57(1):47-58. doi: 10.1165/rcmb.2016-0328OC.Pubmed

Nishihara R, Glass K, Mima K, Hamada T, Nowak JA, Qian ZR, Kraft P, Giovannucci EL, Fuchs CS, Chan AT, Quackenbush J, Ogino S†, Onnela JP†. Biomarker correlation network in colorectal carcinoma by tumor anatomic location. BMC Bioinformatics. 2017 Jun 17;18(1):304. doi: 10.1186/s12859-017-1718-5. Pubmed

Marco E, Meuleman W, Huang J, Glass K, Pinello L, Wang J, Kellis M†, Yuan GC†. Multi-scale chromatin state annotation using a hierarchical hidden Markov model. Nature Communications. 2017 Apr 7;8:15011. Pubmed

Morrow JD, Zhou X, Lao T, Jiang Z, DeMeo D, Cho M, Qui W, Cloonan S, Pinto-Plata V, Celli B, Marchetti N, Criner G, Bueno R, Washko G, Glass K, Quackenbush J, Choi AMK, Silverman EK, Hersh CP. Functional interactors of genome-wide association study genes are differentially expressed in severe COPD lung tissue. Scientific Reports. 2017 Mar 13;7:44232. doi: 10.1038/srep44232. Pubmed

Schlauch D*, Paulson JN*, Young A, Glass K, Quackenbush J. Estimating Gene Regulatory Networks with pandaR. Bioinformatics. 2017 Mar 11. [Epub ahead of print]. Pubmed Resources

Hardin, ME, Cho MH, Sharma SS, Glass K, Castaldi PJ, McDonald ML, Aschard H, Senter-Sylvia J, Tantisira K, Weiss ST, Hersh CP, Morrow JD, Lomas D, Agusti A, Bakke P, Gulsvik A,, O’Connor GT, Dupuis J, Hokanson J, Crapo J, Beaty TH, Laird N, Silverman EK, DeMeo DL and the COPDGene and ECLIPSE Investigators. Sex-based genetic association study identifies CELSR1 as a possible COPD risk locus among women. American Journal of Respiratory Cell and Molecular Biology. 2017 Mar;56(3):332-341. Pubmed

Morrow JD, Cho MH, Hersh CP, Pinto-Plata V, Celli B, Marchetti N, Criner G, Bueno R, Washko G, Glass K, Choi AMK, Quackenbush J, Silverman EK, DeMeo DL. DNA methylation profiling in human lung tissue identifies genes associated with COPD. Epigenetics. 2016 Aug 26:1-10. [Epub ahead of print] Pubmed

Vargas A, Quackenbush J, Glass K. Diet-induced weight loss leads to a switch in gene regulatory network control in the rectal mucosa. Genomics. 2016 Oct;108(3-4):126-133. doi: 10.1016/j.ygeno.2016.08.001. Epub 2016 Aug 11. Pubmed

van ijzendoorn D, Glass K, Quackenbush J, Kuijjer M. PyPanda: A Python package for gene regulatory network reconstruction. Bioinformatics. 2016 Nov 1;32(21):3363-3365. Epub 2016 Jul 10. Pubmed Arxiv Resources

Glass K, Glass CR, Lynch RJ. Student engagement and affordances for interaction with diverse peers: A network analysis. Journal of Diversity in Higher Education. Vol 9(2), Jun 2016, 170-187. APA

Chang Y, Glass K, Lui YY, Silverman EK, Crapo JD, Tal-Singer R, Bowler R, Dy J, Cho MH, Castaldi P. COPD subtypes identified by network-based clustering of blood gene expression. Genomics. 2016 Mar;107(2-3):51-8. Pubmed

Glass K, Girvan M. Finding New Order in Biological Functions from the Network Structure of Gene Annotations. PLoS Computational Biology. 2015 Nov 20;11(11):e1004565. Pubmed arXiv Resources

Glass K, Quackenbush J, Kepner J. High Performance Computing of Gene Regulatory Networks Using a Message-Passing Model. IEEE High Performance Extreme Computer (HPEC) conference. Sept 15-17, 2015. Waltham, MA. IEEE arXiv

Glass K, Spentzos D, Quackenbush J, Haibe-Kains B, Yuan GC. A Network Model for Angiogenesis in Ovarian Cancer. BMC Bioinformatics. 2015 Apr 11;16(1):115. Pubmed Resources

Lao T, Glass K, Qui W, Polverino F, Gupta K, Gupta K, Morrow JD, Mancini JD, Vuong L, Perrella MA, Hersh CP, Owen CA, Quackenbush J, Yuan GC, Silverman EK, Zhou X. Haploinsufficiency of Hedgehog interacting protein sensitizes mice to cigarette smoke-induced emphysema through network rewiring. Genome Medicine. 2015 Feb 14; 7:12. Pubmed

Xu J*, Shao Z*, Li D, Xie H, Kim W, Huang J, Taylor JE, Pinello L, Glass K, Jafe JD, Yuan GC, Orkin SH. Developmental control of Polycomb subunit composition by GATA factors mediates a switch to non-canonical functions. Molecular Cell. 2015 Jan 22;57(2):304-16. Pubmed

Glass K, Quackenbush J, Silverman E, Celli B, Rennard S, Yuan GC, DeMeo DL. Sexually-Dimorphic Targeting of Functionally-Related Genes in COPD. BMC Systems Biology. 2014 Nov 28;8(1):118. Pubmed

Mizumura K, Cloonan S, Nakahira K, Bhashyam AR, Cervo M, Owen CA, Glass K, Mahmood A, Washko G, Hashimoto S, Ryter S, Choi AMK. Mitophagy-dependent necroptosis contributes to the pathogenesis of COPD. Journal of Clinical Investigation. 2014 Sep 2;124(9):3987-4003. Pubmed

Glass K, Girvan M. Annotation Enrichment Analysis: An Alternative Method for Evaluating the Functional Properties of Gene Sets. Scientific Reports. 2014 Feb 26;4:4191. Pubmed arXiv Resources

Rozenberg JM, Bhattacharya P, Chatterjee R, Glass K, Vinson C. Combinatorial recruitment of CREB, C/EBPb and Jun determines activation of promoters upon keratinocyte differentiation. PLoS One. 2013 Nov 7;8(11):e78179. Pubmed

Black J*, Manning A*, Van Rechem C*, Kim J*, Ladd B¥, Cho J¥, Pineda C, Murphy N, Daniels D, Montagna C, Lewis P, Glass K, Allis C, Dyan N, Getz G, Whetstine J. Lysine Demethylase KDM4A Promotes Site Specific Copy Gain and Re-replication of Regions Amplified in Human Tumors. Cell. 2013 Aug 1; 154(3):541-55. Pubmed

Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing Messages Between Biological Networks to Refine Predicted Interactions. PLoS One. 2013 May 31;8(5):e64832. Pubmed Resources

Baena E, Shao Z¥, Linn D¥, Glass K, Hamblen M, Fujiwara Y, Kim J, Saumyadipta P, Nguyen M, Zhang X, Godhino F, Bronson R, Mucci L, Loda M, Yuan GC, Orkin S, Li Z. ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients. Genes and Development. 2013 Mar 15;27(6):683-98. Pubmed

Xu J*, Shao Z*, Glass K¥, Bauer D¥, Pinello L, Van Handel B, Hou S, Stamatoyannopoulos J, Mikkola H, Yuan GC, Orkin S. Developmental Stage-Specific Enhancers Control Gene Expression Programs during Human Erythropoiesis. Developmental Cell. 2012 Oct 3:S1534-5807(12)00414-5. Pubmed

Glass K, Ott E, Losert W, Girvan M. Implications of Functional Similarity for Gene Regulatory Interactions. Journal of the Royal Society Interface. 2012 Jul 7;9(72):1625-36. Pubmed Resources

Warren CL, Zhao J, Glass K, Rishi V, Dervan P, Ansari A, Vinson C. Fabrication of duplex DNA microarrays incorporating methyl-5-cytosine. Lab on a Chip. 2012; 12(2):376-380. Pubmed

Chatterjee R, Bhattacharya P, Gavrilova O, Glass K, Moitra J, Myakishev M, Pack S, Jou W, Feigenbaum L, Eckhaus M, Vinson C. Suppression of the C/EBP family of transcription factors in adipose tissue causes lipodystrophy. Journal of Molecular Endocrinology. 2011; 46(3):175-92. Pubmed

Rishi V*, Bhattacharya P*, Chatterjee R*, Rozenberg JM*, Zhao J*, Glass K, FitzGerald PC, Vinson C. CpG methylation of half-CRE sequences creates C/EBPα binding sites that activate some tissue-specific genes. Proceedings of the National Academy of Science. 2010; 107(47):20311-6. Pubmed

Rozenberg JM, Shlyakhtenko A, Glass K, Rishi V, Myakishev M, FitzGerald PC, Vinson C. All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues. BMC Genomics. 9: 67, 2008. Pubmed

* co-first-author

¥ co-second-author

+ co-senior-author

Other Publications

Glass K, Quackenbush J. Network Medicine: Complex Systems in Human Disease and Therapeutics (book chapter in Network Medicine, edited by Laszlo Barabasi, Joe Loscalzo and Ed Silverman, Harvard University Press, January 2017) Amazon

Glass K. Patterns and Complexity in Biological Systems: A Study of Sequence Structure and Ontology-based Networks. (thesis, published by the University of Maryland, College Park, May 2010) UMD