Harvard Catalyst Profiles

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Kimberly R. Glass

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Research
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. K25HL133599 (GLASS, KIMBERLY RENEE) Aug 1, 2016 - May 31, 2021
    NIH
    Using Integrative Networks to Explore Heterogeneous Phenotypes in COPD
    Role: Principal Investigator

Bibliographic
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.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. 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. Nat Methods. 2022 May; 19(5):511-513. PMID: 35459940.
    Citations:    Fields:    
  2. Röhl A, Baek SH, Kachroo P, Morrow JD, 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. Respir Res. 2022 Mar 24; 23(1):69. PMID: 35331221.
    Citations:    Fields:    Translation:HumansCells
  3. Weighill D, Ben Guebila M, Glass K, Quackenbush J, Platig J. Predicting genotype-specific gene regulatory networks. Genome Res. 2022 03; 32(3):524-533. PMID: 35193937.
    Citations: 1     Fields:    Translation:HumansCells
  4. Shrestha S, Lamattina A, Pacheco-Rodriguez G, Ng J, Liu X, Sonawane A, Imani J, Qiu W, Kosmas K, Louis P, Hentschel A, Steagall WK, Onishi R, Christou H, Henske EP, Glass K, Perrella MA, Moss J, Tantisira K, El-Chemaly S. ETV2 regulates PARP-1 binding protein to induce ER stress-mediated death in tuberin-deficient cells. Life Sci Alliance. 2022 05; 5(5). PMID: 35181635.
    Citations:    Fields:    Translation:Humans
  5. Guebila MB, Morgan DC, Glass K, Kuijjer ML, DeMeo DL, Quackenbush J. gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit. NAR Genom Bioinform. 2022 Mar; 4(1):lqac002. PMID: 35156023.
    Citations:    
  6. 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 network models across human conditions. Nucleic Acids Res. 2022 01 07; 50(D1):D610-D621. PMID: 34508353.
    Citations: 4     Fields:    Translation:Humans
  7. Sonawane AR, DeMeo DL, Quackenbush J, Glass K. Constructing gene regulatory networks using epigenetic data. NPJ Syst Biol Appl. 2021 12 09; 7(1):45. PMID: 34887443.
    Citations: 2     Fields:    
  8. Gong L, Bates S, Li J, Qiao D, Glass K, Wei W, Hsu VW, Zhou X, Silverman EK. Connecting COPD GWAS Genes: FAM13A Controls TGFß2 Secretion by Modulating AP-3 Transport. Am J Respir Cell Mol Biol. 2021 11; 65(5):532-543. PMID: 34166600.
    Citations: 2     Fields:    Translation:HumansCells
  9. De Marzio M, Kiliç A, Maiorino E, Mitchel JA, Mwase C, O'Sullivan MJ, McGill M, Chase R, Fredberg JJ, Park JA, Glass K, Weiss ST. Genomic signatures of the unjamming transition in compressed human bronchial epithelial cells. Sci Adv. 2021 07; 7(30). PMID: 34301595.
    Citations: 3     Fields:    Translation:HumansCells
  10. Weighill D, Guebila MB, Lopes-Ramos C, Glass K, Quackenbush J, Platig J, Burkholz R. Gene regulatory network inference as relaxed graph matching. Proc Conf AAAI Artif Intell. 2021 Feb; 35(11):10263-10272. PMID: 34707916.
    Citations: 1     
  11. Weighill D, Ben Guebila M, Glass K, Platig J, Yeh JJ, Quackenbush J. Gene Targeting in Disease Networks. Front Genet. 2021; 12:649942. PMID: 33968133.
    Citations: 1     
  12. Peng C, DuPre N, VoPham T, Heng YJ, Baker GM, Rubadue CA, Glass K, Sonawane A, 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. PMID: 32723380.
    Citations: 1     Fields:    Translation:HumansCellsPHPublic Health
  13. 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 Rep. 2020 06 23; 31(12):107795. PMID: 32579922.
    Citations: 47     Fields:    Translation:HumansCells
  14. 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. Neurology. 2020 05 12; 94(19):e2014-e2025. PMID: 32321763.
    Citations: 4     Fields:    Translation:Humans
  15. 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 Interdiscip Rev Syst Biol Med. 2020 11; 12(6):e1489. PMID: 32307915.
    Citations: 46     Fields:    Translation:HumansAnimals
  16. DuPré NC, Heng YJ, Raby BA, Glass K, Hart JE, Chu JH, Askew C, Eliassen AH, Hankinson SE, Kraft P, Laden F, Tamimi RM. Involvement of fine particulate matter exposure with gene expression pathways in breast tumor and adjacent-normal breast tissue. Environ Res. 2020 07; 186:109535. PMID: 32668536.
    Citations:    Fields:    Translation:HumansCellsPHPublic Health
  17. Peng C, Heng YJ, Lu D, DuPre NC, Kensler KH, Glass K, Zeleznik OA, Kraft P, Feldman D, Hankinson SE, Rexrode K, Eliassen AH, Tamimi RM. Prediagnostic 25-Hydroxyvitamin D Concentrations in Relation to Tumor Molecular Alterations and Risk of Breast Cancer Recurrence. Cancer Epidemiol Biomarkers Prev. 2020 06; 29(6):1253-1263. PMID: 32238406.
    Citations: 1     Fields:    Translation:Humans
  18. Penney KL, Townsend MK, Turman C, Glass K, Staller K, Kraft P, Grodstein F, Minassian VA. Genome-Wide Association Study for Urinary and Fecal Incontinence in Women. J Urol. 2020 May; 203(5):978-983. PMID: 31729902.
    Citations: 3     Fields:    Translation:Humans
  19. Sonawane AR, Tian L, Chu CY, Qiu X, Wang L, Holden-Wiltse J, Grier A, Gill SR, Caserta MT, Falsey AR, Topham DJ, Walsh EE, Mariani TJ, Weiss ST, Silverman EK, Glass K, Liu YY. Microbiome-Transcriptome Interactions Related to Severity of Respiratory Syncytial Virus Infection. Sci Rep. 2019 09 25; 9(1):13824. PMID: 31554845.
    Citations: 16     Fields:    Translation:HumansCells
  20. Sonawane AR, Weiss ST, Glass K, Sharma A. Network Medicine in the Age of Biomedical Big Data. Front Genet. 2019; 10:294. PMID: 31031797.
    Citations: 47     
  21. Morrow JD, Chase RP, Parker MM, 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. Respir Res. 2019 Apr 02; 20(1):65. PMID: 30940135.
    Citations: 16     Fields:    Translation:HumansCells
  22. Peng C, Van Meel ER, Cardenas A, Rifas-Shiman SL, Sonawane AR, Glass KR, 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 05; 14(5):445-466. PMID: 30876376.
    Citations: 14     Fields:    Translation:HumansCells
  23. Stubbs BJ, Gopaulakrishnan S, Glass K, Pochet N, Everaert C, Raby B, Carey V. TFutils: Data structures for transcription factor bioinformatics. F1000Res. 2019; 8:152. PMID: 31297189.
    Citations: 1     Fields:    
  24. Huang T, Glass K, Zeleznik OA, Kang JH, Ivey KL, Sonawane AR, Birmann BM, Hersh CP, Hu FB, Tworoger SS. A Network Analysis of Biomarkers for Type 2 Diabetes. Diabetes. 2019 02; 68(2):281-290. PMID: 30409783.
    Citations: 11     Fields:    Translation:Humans
  25. 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. Cancer Res. 2018 10 01; 78(19):5538-5547. PMID: 30275053.
    Citations: 33     Fields:    Translation:Humans
  26. Glass K, Thibault D, Guo F, Mitchel JA, Pham B, Qiu W, Li Y, Jiang Z, Castaldi PJ, Silverman EK, Raby B, Park JA, Yuan GC, Zhou X. Integrative epigenomic analysis in differentiated human primary bronchial epithelial cells exposed to cigarette smoke. Sci Rep. 2018 08 24; 8(1):12750. PMID: 30143676.
    Citations: 4     Fields:    Translation:HumansCells
  27. Morrow JD, Glass K, Cho MH, Hersh CP, 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 Quantitative Trait Loci Colocalize with Chronic Obstructive Pulmonary Disease Genome-Wide Association Loci. Am J Respir Crit Care Med. 2018 05 15; 197(10):1275-1284. PMID: 29313708.
    Citations: 17     Fields:    Translation:HumansCells
  28. Morrow JD, Cho MH, Platig J, Zhou X, DeMeo DL, Qiu 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. Hum Genomics. 2018 01 15; 12(1):1. PMID: 29335020.
    Citations: 12     Fields:    Translation:Humans
  29. Schlauch D, Glass K, Hersh CP, Silverman EK, Quackenbush J. Estimating drivers of cell state transitions using gene regulatory network models. BMC Syst Biol. 2017 Dec 13; 11(1):139. PMID: 29237467.
    Citations: 5     Fields:    Translation:Humans
  30. Sonawane AR, Platig J, Fagny M, Chen CY, Paulson JN, Lopes-Ramos CM, DeMeo DL, Quackenbush J, Glass K, Kuijjer ML. Understanding Tissue-Specific Gene Regulation. Cell Rep. 2017 Oct 24; 21(4):1077-1088. PMID: 29069589.
    Citations: 116     Fields:    Translation:HumansCells
  31. Paulson JN, Chen CY, Lopes-Ramos CM, Kuijjer ML, Platig J, Sonawane AR, Fagny M, Glass K, Quackenbush J. Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. BMC Bioinformatics. 2017 Oct 03; 18(1):437. PMID: 28974199.
    Citations: 18     Fields:    Translation:Humans
  32. Lopes-Ramos CM, Paulson JN, Chen CY, Kuijjer ML, Fagny M, Platig J, Sonawane AR, 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. PMID: 28899340.
    Citations: 18     Fields:    Translation:HumansCells
  33. 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. Proc Natl Acad Sci U S A. 2017 09 12; 114(37):E7841-E7850. PMID: 28851834.
    Citations: 45     Fields:    Translation:HumansCells
  34. Qiu W, Guo F, Glass K, Yuan GC, Quackenbush J, Zhou X, Tantisira KG. Differential connectivity of gene regulatory networks distinguishes corticosteroid response in asthma. J Allergy Clin Immunol. 2018 04; 141(4):1250-1258. PMID: 28736268.
    Citations: 12     Fields:    Translation:HumansCells
  35. Schlauch D, Paulson JN, Young A, Glass K, Quackenbush J. Estimating gene regulatory networks with pandaR. Bioinformatics. 2017 Jul 15; 33(14):2232-2234. PMID: 28334344.
    Citations: 5     Fields:    Translation:HumansCells
  36. Yun JH, Morrow J, Owen CA, Qiu W, Glass K, Lao T, Jiang Z, Perrella MA, 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. Am J Respir Cell Mol Biol. 2017 07; 57(1):47-58. PMID: 28248572.
    Citations: 15     Fields:    Translation:HumansAnimalsCells
  37. 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. PMID: 28623901.
    Citations: 7     Fields:    Translation:Humans
  38. 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. Nat Commun. 2017 04 07; 8:15011. PMID: 28387224.
    Citations: 17     Fields:    Translation:HumansCells
  39. Morrow JD, Zhou X, Lao T, Jiang Z, DeMeo DL, Cho MH, Qiu W, Cloonan S, Pinto-Plata V, Celli B, Marchetti N, Criner GJ, Bueno R, Washko GR, Glass K, Quackenbush J, Choi AM, Silverman EK, Hersh CP. Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue. Sci Rep. 2017 03 13; 7:44232. PMID: 28287180.
    Citations: 49     Fields:    Translation:HumansAnimalsCTClinical Trials
  40. Hardin M, Cho MH, Sharma S, 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 JD, Beaty TH, Laird N, Silverman EK, DeMeo DL. Sex-Based Genetic Association Study Identifies CELSR1 as a Possible Chronic Obstructive Pulmonary Disease Risk Locus among Women. Am J Respir Cell Mol Biol. 2017 03; 56(3):332-341. PMID: 27854507.
    Citations: 17     Fields:    Translation:Humans
  41. 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 Oct 02; 11(10):730-739. PMID: 27564456.
    Citations: 31     Fields:    
  42. Vargas AJ, Quackenbush J, Glass K. Diet-induced weight loss leads to a switch in gene regulatory network control in the rectal mucosa. Genomics. 2016 10; 108(3-4):126-133. PMID: 27524493.
    Citations: 9     Fields:    Translation:Humans
  43. Glass K, Girvan M. Finding New Order in Biological Functions from the Network Structure of Gene Annotations. PLoS Comput Biol. 2015 Nov; 11(11):e1004565. PMID: 26588252.
    Citations: 5     Fields:    Translation:Humans
  44. Glass K, Quackenbush J, Spentzos D, Haibe-Kains B, Yuan GC. A network model for angiogenesis in ovarian cancer. BMC Bioinformatics. 2015 Apr 11; 16:115. PMID: 25888305.
    Citations: 26     Fields:    Translation:Humans
  45. Lao T, Glass K, Qiu W, Polverino F, Gupta K, Morrow J, Mancini JD, Vuong L, Perrella MA, Hersh CP, Owen CA, Quackenbush J, Yuan GC, Silverman EK, Zhou X. Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring. Genome Med. 2015; 7(1):12. PMID: 25763110.
    Citations: 28     Fields:    
  46. Xu J, Shao Z, Li D, Xie H, Kim W, Huang J, Taylor JE, Pinello L, Glass K, Jaffe JD, Yuan GC, Orkin SH. Developmental control of polycomb subunit composition by GATA factors mediates a switch to non-canonical functions. Mol Cell. 2015 Jan 22; 57(2):304-316. PMID: 25578878.
    Citations: 58     Fields:    Translation:HumansCells
  47. Glass K, Quackenbush J, Silverman EK, Celli B, Rennard SI, Yuan GC, DeMeo DL. Sexually-dimorphic targeting of functionally-related genes in COPD. BMC Syst Biol. 2014 Nov 28; 8:118. PMID: 25431000.
    Citations: 27     Fields:    Translation:Humans
  48. Mizumura K, Cloonan SM, Nakahira K, Bhashyam AR, Cervo M, Kitada T, Glass K, Owen CA, Mahmood A, Washko GR, Hashimoto S, Ryter SW, Choi AM. Mitophagy-dependent necroptosis contributes to the pathogenesis of COPD. J Clin Invest. 2014 Sep; 124(9):3987-4003. PMID: 25083992.
    Citations: 211     Fields:    Translation:AnimalsCells
  49. Glass K, Girvan M. Annotation enrichment analysis: an alternative method for evaluating the functional properties of gene sets. Sci Rep. 2014 Feb 26; 4:4191. PMID: 24569707.
    Citations: 25     Fields:    
  50. Black JC, Manning AL, Van Rechem C, Kim J, Ladd B, Cho J, Pineda CM, Murphy N, Daniels DL, Montagna C, Lewis PW, Glass K, Allis CD, Dyson NJ, Getz G, Whetstine JR. KDM4A lysine demethylase induces site-specific copy gain and rereplication of regions amplified in tumors. Cell. 2013 Aug 01; 154(3):541-55. PMID: 23871696.
    Citations: 114     Fields:    Translation:HumansCells
  51. Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. PLoS One. 2013; 8(5):e64832. PMID: 23741402.
    Citations: 67     Fields:    Translation:AnimalsCells
  52. Baena E, Shao Z, Linn DE, Glass K, Hamblen MJ, Fujiwara Y, Kim J, Nguyen M, Zhang X, Godinho FJ, Bronson RT, Mucci LA, Loda M, Yuan GC, Orkin SH, Li Z. ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients. Genes Dev. 2013 Mar 15; 27(6):683-98. PMID: 23512661.
    Citations: 84     Fields:    Translation:HumansAnimalsCells
  53. Xu J, Shao Z, Glass K, Bauer DE, Pinello L, Van Handel B, Hou S, Stamatoyannopoulos JA, Mikkola HK, Yuan GC, Orkin SH. Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Dev Cell. 2012 Oct 16; 23(4):796-811. PMID: 23041383.
    Citations: 112     Fields:    Translation:HumansCells
  54. Glass K, Ott E, Losert W, Girvan M. Implications of functional similarity for gene regulatory interactions. J R Soc Interface. 2012 Jul 07; 9(72):1625-36. PMID: 22298814.
    Citations: 4     Fields:    Translation:AnimalsCells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.