Kimberly Glass, Ph.D. - Publications

Affiliations: 
2010 Physics University of Maryland, College Park, College Park, MD 

67 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Saha E, Fanfani V, Mandros P, Ben-Guebila M, Fischer J, Hoff-Shutta K, Glass K, DeMeo DL, Lopes-Ramos C, Quackenbush J. Bayesian Optimized sample-specific Networks Obtained By Omics data (BONOBO). Biorxiv : the Preprint Server For Biology. PMID 38014256 DOI: 10.1101/2023.11.16.567119  0.434
2023 Hsieh PH, Lopes-Ramos CM, Zucknick M, Sandve GK, Glass K, Kuijjer ML. Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data. Bioinformatics (Oxford, England). 39. PMID 37802917 DOI: 10.1093/bioinformatics/btad610  0.345
2023 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, ... ... Glass K, et al. The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks. Genome Biology. 24: 45. PMID 36894939 DOI: 10.1186/s13059-023-02877-1  0.77
2022 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. PMID 35459940 DOI: 10.1038/s41592-022-01479-2  0.754
2022 Weighill D, Ben Guebila M, Glass K, Quackenbush J, Platig J. Predicting genotype-specific gene regulatory networks. Genome Research. 32: 524-533. PMID 35193937 DOI: 10.1101/gr.275107.120  0.768
2022 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 Genomics and Bioinformatics. 4: lqac002. PMID 35156023 DOI: 10.1093/nargab/lqac002  0.387
2021 Sonawane AR, DeMeo DL, Quackenbush J, Glass K. Constructing gene regulatory networks using epigenetic data. Npj Systems Biology and Applications. 7: 45. PMID 34887443 DOI: 10.1038/s41540-021-00208-3  0.478
2021 Weighill D, Guebila MB, Lopes-Ramos C, Glass K, Quackenbush J, Platig J, Burkholz R. Gene regulatory network inference as relaxed graph matching. Proceedings of the ... Aaai Conference On Artificial Intelligence. Aaai Conference On Artificial Intelligence. 35: 10263-10272. PMID 34707916  0.76
2021 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 Research. PMID 34508353 DOI: 10.1093/nar/gkab778  0.779
2021 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. PMID 34166600 DOI: 10.1165/rcmb.2021-0016OC  0.303
2021 Weighill D, Ben Guebila M, Glass K, Platig J, Yeh JJ, Quackenbush J. Gene Targeting in Disease Networks. Frontiers in Genetics. 12: 649942. PMID 33968133 DOI: 10.3389/fgene.2021.649942  0.77
2020 Liu X, Maiorino E, Halu A, Glass K, Prasad RB, Loscalzo J, Gao J, Sharma A. Robustness and lethality in multilayer biological molecular networks. Nature Communications. 11: 6043. PMID 33247151 DOI: 10.1038/s41467-020-19841-3  0.382
2020 Kuijjer ML, Fagny M, Marin A, Quackenbush J, Glass K. PUMA: PANDA Using MicroRNA Associations. Bioinformatics (Oxford, England). PMID 32860050 DOI: 10.1093/Bioinformatics/Btaa571  0.386
2020 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. Environmental Research. 186: 109535. PMID 32668536 DOI: 10.1016/J.Envres.2020.109535  0.304
2020 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. 31: 107795. PMID 32579922 DOI: 10.1016/J.Celrep.2020.107795  0.768
2020 Samieri C, Rajendra Sonawane A, Lefèvre-Arbogast S, Helmer C, Grodstein F, Glass K. Using network science tools to identify novel diet patterns in prodromal dementia. Neurology. PMID 32321763 DOI: 10.1212/Wnl.0000000000009399  0.374
2020 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, ... ... Glass K, et al. Molecular networks in Network Medicine: Development and applications. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. e1489. PMID 32307915 DOI: 10.1002/Wsbm.1489  0.495
2020 Paci P, Fiscon G, Conte F, Licursi V, Morrow J, Hersh C, Cho M, Castaldi P, Glass K, Silverman EK, Farina L. Integrated transcriptomic correlation network analysis identifies COPD molecular determinants. Scientific Reports. 10: 3361. PMID 32099002 DOI: 10.1038/S41598-020-60228-7  0.514
2020 Lopes-Ramos CM, Kuijjer M, Glass K, DeMeo D, Quackenbush J. Abstract 6569: Regulatory networks of liver carcinoma reveal sex specific patterns of gene regulation Cancer Research. 80: 6569-6569. DOI: 10.1158/1538-7445.Am2020-6569  0.405
2019 Kuijjer ML, Hsieh PH, Quackenbush J, Glass K. lionessR: single sample network inference in R. Bmc Cancer. 19: 1003. PMID 31653243 DOI: 10.1186/S12885-019-6235-7  0.454
2019 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, et al. Microbiome-Transcriptome Interactions Related to Severity of Respiratory Syncytial Virus Infection. Scientific Reports. 9: 13824. PMID 31554845 DOI: 10.1038/S41598-019-50217-W  0.368
2019 Stubbs BJ, Gopaulakrishnan S, Glass K, Pochet N, Everaert C, Raby B, Carey V. TFutils: Data structures for transcription factor bioinformatics. F1000research. 8: 152. PMID 31297189 DOI: 10.12688/F1000Research.17976.2  0.36
2019 Sonawane AR, Weiss ST, Glass K, Sharma A. Network Medicine in the Age of Biomedical Big Data. Frontiers in Genetics. 10: 294. PMID 31031797 DOI: 10.3389/Fgene.2019.00294  0.494
2019 Lopes-Ramos CM, Kuijjer ML, Ogino S, Fuchs CS, DeMeo DL, Glass K, Quackenbush J. Correction: Gene Regulatory Network Analysis Identifies Sex-Linked Differences in Colon Cancer Drug Metabolism. Cancer Research. 79: 2084. PMID 30987980 DOI: 10.1158/0008-5472.Can-19-0678  0.372
2019 Kuijjer ML, Tung MG, Yuan G, Quackenbush J, Glass K. Estimating Sample-Specific Regulatory Networks. Iscience. 14: 226-240. PMID 30981959 DOI: 10.1016/J.Isci.2019.03.021  0.509
2019 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. Respiratory Research. 20: 65. PMID 30940135 DOI: 10.1186/S12931-019-1032-Z  0.444
2019 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. 9: 3499. PMID 30837613 DOI: 10.1038/S41598-019-40167-8  0.421
2018 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. PMID 30409783 DOI: 10.2337/Db18-0892  0.327
2018 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 Research. 78: 5538-5547. PMID 30275053 DOI: 10.1158/0008-5472.Can-18-0454  0.425
2018 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. Scientific Reports. 8: 12750. PMID 30143676 DOI: 10.1038/S41598-018-30781-3  0.346
2018 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. Human Genomics. 12: 1. PMID 29335020 DOI: 10.1186/S40246-018-0132-Z  0.713
2018 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 COPD Genome-wide Association Loci. American Journal of Respiratory and Critical Care Medicine. PMID 29313708 DOI: 10.1164/Rccm.201707-1434Oc  0.302
2017 Schlauch D, Glass K, Hersh CP, Silverman EK, Quackenbush J. Estimating drivers of cell state transitions using gene regulatory network models. Bmc Systems Biology. 11: 139. PMID 29237467 DOI: 10.1186/S12918-017-0517-Y  0.476
2017 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 Reports. 21: 1077-1088. PMID 29069589 DOI: 10.1016/J.Celrep.2017.10.001  0.765
2017 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. 18: 437. PMID 28974199 DOI: 10.1186/S12859-017-1847-X  0.691
2017 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. 18: 723. PMID 28899340 DOI: 10.1186/S12864-017-4111-X  0.725
2017 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 Sciences of the United States of America. PMID 28851834 DOI: 10.1073/Pnas.1707375114  0.762
2017 Qiu W, Guo F, Glass K, Guo Cheng Yuan, Quackenbush J, Zhou X, Tantisira KG. Differential Connectivity of Gene Regulatory Networks Distinguishes Corticosteroid Response in Asthma. The Journal of Allergy and Clinical Immunology. PMID 28736268 DOI: 10.1016/J.Jaci.2017.05.052  0.317
2017 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. 18: 304. PMID 28623901 DOI: 10.1186/S12859-017-1718-5  0.396
2017 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. 8: 15011. PMID 28387224 DOI: 10.1038/Ncomms15011  0.337
2017 Schlauch D, Paulson JN, Young A, Glass K, Quackenbush J. Estimating Gene Regulatory Networks with pandaR. Bioinformatics (Oxford, England). PMID 28334344 DOI: 10.1093/Bioinformatics/Btx139  0.538
2017 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, et al. Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue. Scientific Reports. 7: 44232. PMID 28287180 DOI: 10.1038/Srep44232  0.486
2017 Yun JH, Morrow J, Owen CA, Qiu W, Glass K, Lao T, Jiang Z, Perrella M, Silverman EK, Zhou X, Hersh CP. Transcriptomic Analysis of Lung Tissue from Cigarette Smoke Induced Emphysema Murine Models and Human COPD Show Shared and Distinct Pathways. American Journal of Respiratory Cell and Molecular Biology. PMID 28248572 DOI: 10.1165/Rcmb.2016-0328Oc  0.379
2016 Morrow JD, Cho MH, Hersh CP, Pinto-Plata V, Celli B, Marchetti N, Criner G, Bueno R, Washko G, Glass K, Choi AM, Quackenbush J, Silverman EK, DeMeo DL. DNA methylation profiling in human lung tissue identifies genes associated with COPD. Epigenetics. 0. PMID 27564456 DOI: 10.1080/15592294.2016.1226451  0.382
2016 Vargas AJ, Quackenbush J, Glass K. Diet-induced weight loss leads to a switch in gene regulatory network control in the rectal mucosa. Genomics. PMID 27524493 DOI: 10.1016/J.Ygeno.2016.08.001  0.41
2016 van IJzendoorn DG, Glass K, Quackenbush J, Kuijjer ML. PyPanda: a Python package for gene regulatory network reconstruction. Bioinformatics (Oxford, England). PMID 27402905 DOI: 10.1093/Bioinformatics/Btw422  0.506
2016 Chang Y, Glass K, Liu YY, Silverman EK, Crapo JD, Tal-Singer R, Bowler R, Dy J, Cho M, Castaldi P. COPD subtypes identified by network-based clustering of blood gene expression. Genomics. PMID 26773458 DOI: 10.1016/J.Ygeno.2016.01.004  0.457
2015 Glass K, Girvan M. Finding New Order in Biological Functions from the Network Structure of Gene Annotations. Plos Computational Biology. 11: e1004565. PMID 26588252 DOI: 10.1371/Journal.Pcbi.1004565  0.683
2015 Glass K, Quackenbush J, Spentzos D, Haibe-Kains B, Yuan GC. A network model for angiogenesis in ovarian cancer. Bmc Bioinformatics. 16: 115. PMID 25888305 DOI: 10.1186/S12859-015-0551-Y  0.474
2015 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 Medicine. 7: 12. PMID 25763110 DOI: 10.1186/S13073-015-0137-3  0.422
2015 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. Molecular Cell. 57: 304-16. PMID 25578878 DOI: 10.1016/J.Molcel.2014.12.009  0.347
2015 Kuijjer ML, Glass K, Quackenbush J. Abstract B1-20: Gene regulation by transcription factors and microRNAs in ovarian cancer Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-B1-20  0.463
2015 Glass K, Quackenbush J, Kepner J. High performance computing of gene regulatory networks using a message-passing model 2015 Ieee High Performance Extreme Computing Conference, Hpec 2015. DOI: 10.1109/HPEC.2015.7322475  0.343
2014 Glass K, Quackenbush J, Silverman EK, Celli B, Rennard SI, Yuan GC, DeMeo DL. Sexually-dimorphic targeting of functionally-related genes in COPD. Bmc Systems Biology. 8: 118. PMID 25431000 DOI: 10.1186/S12918-014-0118-Y  0.466
2014 Glass K, Girvan M. Annotation enrichment analysis: an alternative method for evaluating the functional properties of gene sets. Scientific Reports. 4: 4191. PMID 24569707 DOI: 10.1038/Srep04191  0.673
2014 Xu J, Shao Z, Li D, Xie H, Kim W, Huang J, Pinello L, Glass K, Yuan G, Orkin SH. Developmental Control of Polycomb Subunit Composition Mediates a Switch to Non-Canonical Functions during Hematopoiesis Blood. 124: 241-241. DOI: 10.1182/Blood.V124.21.241.241  0.389
2013 Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. Plos One. 8: e64832. PMID 23741402 DOI: 10.1371/Journal.Pone.0064832  0.508
2013 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, et al. ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients. Genes & Development. 27: 683-98. PMID 23512661 DOI: 10.1101/Gad.211011.112  0.322
2013 Perez-Pinera P, Ousterout DG, Brunger JM, Farin AM, Glass KA, Guilak F, Crawford GE, Hartemink AJ, Gersbach CA. Synergistic and tunable human gene activation by combinations of synthetic transcription factors. Nature Methods. 10: 239-42. PMID 23377379 DOI: 10.1038/Nmeth.2361  0.331
2013 Baena E, Shao Z, Linn D, Glass K, Hamblen M, Fujiwara Y, Kim J, Nguyen M, Zhang X, Godinho F, Bronson RT, Mucci L, Loda M, Yuan G, Li Z, et al. Abstract 5393: ETV1 directs androgen metabolism and confers aggressive prostate cancer in engineered mice and patients. Cancer Research. 73: 5393-5393. DOI: 10.1158/1538-7445.Am2013-5393  0.319
2012 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. Developmental Cell. 23: 796-811. PMID 23041383 DOI: 10.1016/J.Devcel.2012.09.003  0.41
2012 Glass K, Ott E, Losert W, Girvan M. Implications of functional similarity for gene regulatory interactions. Journal of the Royal Society, Interface / the Royal Society. 9: 1625-36. PMID 22298814 DOI: 10.1098/Rsif.2011.0585  0.692
2012 Xu J, Shao Z, Glass K, Bauer DE, Pinello L, Van Handel B, Hou S, Stamatoyannopoulos JA, Mikkola HKA, Yuan G, Orkin SH. Genomic Determinants of Human Fetal and Adult Erythroid Gene Expression Blood. 120: 1227-1227. DOI: 10.1182/Blood.V120.21.1227.1227  0.449
2012 Baena E, Shao Z, Linn D, Hamblen M, Glass K, Saumyadipta P, Fujiwara Y, Godinho F, Kim J, Al-Shhrour F, Nguyen M, Yuan G, Bronson RT, Loda M, Orkin SH, et al. Abstract 2965: ERG and ETV1 regulate a common transcriptional network in prostate cells but in an opposite fashion Cancer Research. 72: 2965-2965. DOI: 10.1158/1538-7445.Am2012-2965  0.315
2011 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. 46: 175-92. PMID 21321096 DOI: 10.1530/Jme-10-0172  0.301
2008 Rozenberg JM, Shlyakhtenko A, Glass K, Rishi V, Myakishev MV, 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. PMID 18252004 DOI: 10.1186/1471-2164-9-67  0.357
2006 Samieri C, Sonawane A, Helmer C, Grodstein F, Glass K. P1-591: USING NETWORK SCIENCE TOOLS TO IDENTIFY NOVEL DIET PATTERNS IN PRODROMAL DEMENTIA: THE THREE-CITY STUDY Alzheimer's & Dementia. 14: P563-P563. DOI: 10.1016/J.Jalz.2018.06.603  0.351
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