Training Grant Publications

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Students, please keep the Graduate Program Coordinator appraised of your new publications and any inaccuracies or omissions on this list. Most articles are indexed in PubMed; please provide the PubMed ID numbers (PMID) for your articles if available, to expedite the maintenance of this list. Please remember to acknowledge your grants in your papers, including the training grant if you were a recipient; see here for sample wording.

2023

Horii M, To C, Morey R, Jacobs MB, Li Y, Nelson KK, Meads M, Siegel BA, Pizzo D, Adami R, Zhang-Rutledge K, Lamale-Smith L, Laurent LC, Parast MM. "Histopathologic and Transcriptomic Profiling Identifies Novel Trophoblast Defects in Patients With Preeclampsia and Maternal Vascular Malperfusion." Mod Pathol. 2023;36(2):100035. PubMed PMC DOI
Massarat AR, Lamkin M, Reeve C, Williams AL, D'Antonio M, Gymrek M. "Haptools: a toolkit for admixture and haplotype analysis." Bioinformatics. 2023;39(3). PubMed PMC DOI
Vo D, Ghosh P, Sahoo D. "Artificial intelligence-guided discovery of gastric cancer continuum." Gastric Cancer. 2023;26(2):286-297. PubMed PMC DOI

2022

Boeder S, Kobayashi E, Ramesh G, Serences B, Kulasa K, Majithia AR. "Accuracy and Glycemic Efficacy of Continuous Glucose Monitors in Critically Ill COVID-19 Patients: A Retrospective Study." J Diabetes Sci Technol. 2022:1.93E+16. PubMed DOI
Dekel C, Morey R, Hanna J, Laurent LC, Ben-Yosef D, Amir H. "Stabilization of hESCs in two distinct substates along the continuum of pluripotency." IScience. 2022;25(12):105469. PubMed PMC DOI
Hyun JC, Monk JM, Palsson BO. "Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity." BMC Genomics. 2022;23(1):7. PubMed PMC DOI
Javadzadeh S, Rajkumar U, Nguyen N, Sarmashghi S, Luebeck J, Shang J, Bafna V. "FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA." NAR Genom Bioinform. 2022;4(2):lqac032. PubMed PMC DOI
Li J, Pinto-Duarte A, Zander M, Cuoco MS, Lai CY, Osteen J, Fang L, Luo C, Lucero JD, Gomez-Castanon R, Nery JR, Silva-Garcia I, Pang Y, Sejnowski TJ, Powell SB, Ecker JR, Mukamel EA, Behrens MM. "Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3." Elife. 2022;11. PubMed PMC DOI
Nachmanson D, Officer A, Mori H, Gordon J, Evans MF, Steward J, Yao H, O'Keefe T, Hasteh F, Stein GS, Jepsen K, Weaver DL, Hirst GL, Sprague BL, Esserman LJ, Borowsky AD, Stein JL, Harismendy O. "The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ." NPJ Breast Cancer. 2022;8(1):6. PubMed PMC DOI
Nachmanson D, Pagadala M, Steward J, Cheung C, Bruce LK, Lee NQ, O'Keefe TJ, Lin GY, Hasteh F, Morris GP, Carter H, Harismendy O. "Accurate genome-wide genotyping from archival tissue to explore the contribution of common genetic variants to pre-cancer outcomes." J Transl Med. 2022;20(1):623. PubMed PMC DOI
Nicholson-Shaw AL, Kofman ER, Yeo GW, Pasquinelli AE. "Nuclear and cytoplasmic poly(A) binding proteins (PABPs) favor distinct transcripts and isoforms." Nucleic Acids Res. 2022;50(8):4685-4702. PubMed PMC DOI
Soncin F, Morey R, Bui T, Requena DF, Cheung VC, Kallol S, Kittle R, Jackson MG, Farah O, Chousal J, Meads M, Pizzo D, Horii M, Fisch KM, Parast MM. "Derivation of functional trophoblast stem cells from primed human pluripotent stem cells." Stem Cell Reports. 2022;17(6):1303-1317. PubMed PMC DOI
Sorrentino JT, Golden GJ, Morris C, Painter CD, Nizet V, Campos AR, Smith JW, Karlsson C, Malmström J, Lewis NE, Esko JD, Gómez Toledo A. "Vascular Proteome Responses Precede Organ Dysfunction in a Murine Model of Staphylococcus aureus Bacteremia." MSystems. 2022;7(4):e0039522. PubMed PMC DOI
Zhang Y, Amaral ML, Zhu C, Grieco SF, Hou X, Lin L, Buchanan J, Tong L, Preissl S, Xu X, Ren B. "Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brain." Cell Res. 2022;32(11):1008-1021. PubMed PMC DOI

2021

Brannan KW, Chaim IA, Marina RJ, Yee BA, Kofman ER, Lorenz DA, Jagannatha P, Dong KD, Madrigal AA, Underwood JG, Yeo GW. "Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes." Nat Methods. 2021;18(5):507-519. PubMed PMC DOI
Golden GJ, Toledo AG, Marki A, Sorrentino JT, Morris C, Riley RJ, Spliid C, Chen Q, Cornax I, Lewis NE, Varki N, Le D, Malmström J, Karlsson C, Ley K, Nizet V, Esko JD. "Endothelial Heparan Sulfate Mediates Hepatic Neutrophil Trafficking and Injury during Staphylococcus aureus Sepsis." MBio. 2021;12(5):e0118121. PubMed PMC DOI
Gómez Toledo A, Sorrentino JT, Sandoval DR, Malmström J, Lewis NE, Esko JD. "A Systems View of the Heparan Sulfate Interactome." J Histochem Cytochem. 2021;69(2):105-119. PubMed PMC DOI
Horii M, Morey R, Bui T, Touma O, Nelson KK, Cho HY, Rishik H, Laurent LC, Parast MM. "Modeling preeclampsia using human induced pluripotent stem cells." Sci Rep. 2021;11(1):5877. PubMed PMC DOI
Kellman BP, Baghdassarian HM, Pramparo T, Shamie I, Gazestani V, Begzati A, Li S, Nalabolu S, Murray S, Lopez L, Pierce K, Courchesne E, Lewis NE. "Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing." BMC Genomics. 2021;22(1):69. PubMed PMC DOI
Klie A, Tsui BY, Mollah S, Skola D, Dow M, Hsu CN, Carter H. "Increasing metadata coverage of SRA BioSample entries using deep learning-based named entity recognition." Database (Oxford). 2021;2021. PubMed PMC DOI
Massarat AR, Sen A, Jaureguy J, Tyndale ST, Fu Y, Erikson G, McVicker G. "Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq." Nucleic Acids Res. 2021. PubMed DOI
Maurya MR, Gupta S, Li JY, Ajami NE, Chen ZB, Shyy JY, Chien S, Subramaniam S. "Longitudinal shear stress response in human endothelial cells to atheroprone and atheroprotective conditions." Proc Natl Acad Sci U S A. 2021;118(4). PubMed PMC DOI
Mitra I, Huang B, Mousavi N, Ma N, Lamkin M, Yanicky R, Shleizer-Burko S, Lohmueller KE, Gymrek M. "Patterns of de novo tandem repeat mutations and their role in autism." Nature. 2021;589(7841):246-250. PubMed PMC DOI
Morey R, Farah O, Kallol S, Requena DF, Meads M, Moretto-Zita M, Soncin F, Laurent LC, Parast MM. "Transcriptomic Drivers of Differentiation, Maturation, and Polyploidy in Human Extravillous Trophoblast." Front Cell Dev Biol. 2021;9:702046. PubMed PMC DOI
Vo DT, Fuller MR, Tindle C, Anandachar MS, Das S, Sahoo D, Ghosh P. "SPT6 loss permits the transdifferentiation of keratinocytes into an intestinal fate that resembles Barrett's metaplasia." IScience. 2021;24(10):103121. PubMed PMC DOI

2020

Baxter SL, Klie AR, Radha Saseendrakumar B, Ye GY, Hogarth M. "Text Processing for Detection of Fungal Ocular Involvement in Critical Care Patients: Cross-Sectional Study." J Med Internet Res. 2020;22(8):e18855. PubMed PMC DOI
Baxter SL, Klie AR, Saseendrakumar BR, Ye GY, Hogarth M, Nemati S. "Predicting Mortality in Critical Care Patients with Fungemia Using Structured and Unstructured Data." Annu Int Conf IEEE Eng Med Biol Soc. 2020;2020:5459-5463. PubMed PMC DOI
Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, Afzal V, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Garvin TH, Pham QT, Harrington AN, Mannion BJ, Lee EA, Fukuda-Yuzawa Y, He Y, Preissl S, Chee S, Han JY, Williams BA, Trout D, Amrhein H, Yang H, Cherry JM, Wang W, Gaulton K, Ecker JR, Shen Y, Dickel DE, Visel A, Pennacchio LA, Ren B. "An atlas of dynamic chromatin landscapes in mouse fetal development." Nature. 2020;583(7818):744-751. PubMed PMC DOI
Hyun JC, Kavvas ES, Monk JM, Palsson BO. "Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens." PLoS Comput Biol. 2020;16(3):e1007608. PubMed PMC DOI
Jakubosky D, D'Antonio M, Bonder MJ, Smail C, Donovan MKR, Young Greenwald WW, Matsui H, i2QTL Consortium, D'Antonio-Chronowska A, Stegle O, Smith EN, Montgomery SB, DeBoever C, Frazer KA. "Properties of structural variants and short tandem repeats associated with gene expression and complex traits." Nat Commun. 2020;11(1):2927. PubMed PMC DOI
Nachmanson D, Steward J, Yao H, Officer A, Jeong E, O'Keefe TJ, Hasteh F, Jepsen K, Hirst GL, Esserman LJ, Borowsky AD, Harismendy O. "Mutational profiling of micro-dissected pre-malignant lesions from archived specimens." BMC Med Genomics. 2020;13(1):173. PubMed PMC DOI
Xie X, Shah S, Holtz A, Rose J, Basisty N, Schilling B. "Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization." J Vis Exp. 2020(156). PubMed PMC DOI

2019

Banerjee S, Wei T, Wang J, Lee JJ, Gutierrez HL, Chapman O, Wiley SE, Mayfield JE, Tandon V, Juarez EF, Chavez L, Liang R, Sah RL, Costello C, Mesirov JP, de la Vega L, Cooper KL, Dixon JE, Xiao J, Lei X. "Inhibition of dual-specificity tyrosine phosphorylation-regulated kinase 2 perturbs 26S proteasome-addicted neoplastic progression." Proc Natl Acad Sci U S A. 2019;116(49):24881-24891. PubMed PMC DOI
Brigidi GS, Hayes MGB, Delos Santos NP, Hartzell AL, Texari L, Lin PA, Bartlett A, Ecker JR, Benner C, Heinz S, Bloodgood BL. "Genomic Decoding of Neuronal Depolarization by Stimulus-Specific NPAS4 Heterodimers." Cell. 2019;179(2):373-391.e27. PubMed PMC DOI
D'Antonio M, Reyna J, Jakubosky D, Donovan MK, Bonder MJ, Matsui H, Stegle O, Nariai N, D'Antonio-Chronowska A, Frazer KA. "Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease." Elife. 2019;8. PubMed PMC DOI
Deshpande V, Luebeck J, Nguyen ND, Bakhtiari M, Turner KM, Schwab R, Carter H, Mischel PS, Bafna V. "Exploring the landscape of focal amplifications in cancer using AmpliconArchitect." Nat Commun. 2019;10(1):392. PubMed PMC DOI
Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R. "Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads." Genome Biol. 2019;20(1):226. PubMed PMC DOI
Sauls JT, Cox SE, Do Q, Castillo V, Ghulam-Jelani Z, Jun S. "Control of Bacillus subtilis Replication Initiation during Physiological Transitions and Perturbations." MBio. 2019;10(6). PubMed PMC DOI
Zaramela LS, Martino C, Alisson-Silva F, Rees SD, Diaz SL, Chuzel L, Ganatra MB, Taron CH, Secrest P, Zuñiga C, Huang J, Siegel D, Chang G, Varki A, Zengler K. "Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates." Nat Microbiol. 2019. PubMed DOI
Zhang Y, Li T, Preissl S, Amaral ML, Grinstein JD, Farah EN, Destici E, Qiu Y, Hu R, Lee AY, Chee S, Ma K, Ye Z, Zhu Q, Huang H, Fang R, Yu L, Izpisua Belmonte JC, Wu J, Evans SM, Chi NC, Ren B. "Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells." Nat Genet. 2019;51(9):1380-1388. PubMed PMC DOI

2018

Beyter D, Lin MS, Yu Y, Pieper R, Bafna V. "ProteoStorm: An Ultrafast Metaproteomics Database Search Framework." Cell Syst. 2018;7(4):463-467.e6. PubMed PMC DOI
Bui N, Huang JK, Bojorquez-Gomez A, Licon K, Sanchez KS, Tang SN, Beckett AN, Wang T, Zhang W, Shen JP, Kreisberg JF, Ideker T. "Disruption of NSD1 in Head and Neck Cancer Promotes Favorable Chemotherapeutic Responses Linked to Hypomethylation." Mol Cancer Ther. 2018;17(7):1585-1594. PubMed PMC DOI
Huang JK, Carlin DE, Yu MK, Zhang W, Kreisberg JF, Tamayo P, Ideker T. "Systematic Evaluation of Molecular Networks for Discovery of Disease Genes." Cell Syst. 2018;6(4):484-495.e5. PubMed PMC DOI
Huang JK, Jia T, Carlin DE, Ideker T. "pyNBS: a Python implementation for network-based stratification of tumor mutations." Bioinformatics. 2018;34(16):2859-2861. PubMed PMC DOI
Kuo CC, Chiang AW, Shamie I, Samoudi M, Gutierrez JM, Lewis NE. "The emerging role of systems biology for engineering protein production in CHO cells." Curr Opin Biotechnol. 2018;51:64-69. PubMed PMC DOI
Miao Y, Ajami NE, Huang TS, Lin FM, Lou CH, Wang YT, Li S, Kang J, Munkacsi H, Maurya MR, Gupta S, Chien S, Subramaniam S, Chen Z. "Enhancer-associated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial function." Nat Commun. 2018;9(1):292. PubMed PMC DOI
Nguyen ND, Deshpande V, Luebeck J, Mischel PS, Bafna V. "ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer." Nucleic Acids Res. 2018;46(7):3309-3325. PubMed PMC DOI
Preissl S, Fang R, Huang H, Zhao Y, Raviram R, Gorkin DU, Zhang Y, Sos BC, Afzal V, Dickel DE, Kuan S, Visel A, Pennacchio LA, Zhang K, Ren B. "Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation." Nat Neurosci. 2018;21(3):432-439. PubMed PMC DOI

2017

Ajami NE, Gupta S, Maurya MR, Nguyen P, Li JY, Shyy JY, Chen Z, Chien S, Subramaniam S. "Systems biology analysis of longitudinal functional response of endothelial cells to shear stress." Proc Natl Acad Sci U S A. 2017;114(41):10990-10995. PubMed PMC DOI
Kramer MH, Farré JC, Mitra K, Yu MK, Ono K, Demchak B, Licon K, Flagg M, Balakrishnan R, Cherry JM, Subramani S, Ideker T. "Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy." Mol Cell. 2017;65(4):761-774.e5. PubMed PMC DOI
Panopoulos AD, D'Antonio M, Benaglio P, Williams R, Hashem SI, Schuldt BM, DeBoever C, Arias AD, Garcia M, Nelson BC, Harismendy O, Jakubosky DA, Donovan MKR, Greenwald WW, Farnam K, Cook M, Borja V, Miller CA, Grinstein JD, Drees F, Okubo J, Diffenderfer KE, Hishida Y, Modesto V, Dargitz CT, Feiring R, Zhao C, Aguirre A, McGarry TJ, Matsui H, Li H, Reyna J, Rao F, O'Connor DT, Yeo GW, Evans SM, Chi NC, Jepsen K, Nariai N, Müller FJ, Goldstein LSB, Izpisua Belmonte JC, Adler E, Loring JF, Berggren WT, D'Antonio-Chronowska A, Smith EN, Frazer KA. "iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types." Stem Cell Reports. 2017;8(4):1086-1100. PubMed PMC DOI
Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P. "Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions." Nat Methods. 2017;14(6):573-576. PubMed PMC DOI
Si F, Li D, Cox SE, Sauls JT, Azizi O, Sou C, Schwartz AB, Erickstad MJ, Jun Y, Li X, Jun S. "Invariance of Initiation Mass and Predictability of Cell Size in Escherichia coli." Curr Biol. 2017;27(9):1278-1287. PubMed PMC DOI

2016

Cremer J, Segota I, Yang CY, Arnoldini M, Sauls JT, Zhang Z, Gutierrez E, Groisman A, Hwa T. "Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel." Proc Natl Acad Sci U S A. 2016;113(41):11414-11419. PubMed PMC DOI
Sauls JT, Li D, Jun S. "Adder and a coarse-grained approach to cell size homeostasis in bacteria." Curr Opin Cell Biol. 2016;38:38-44. PubMed PMC DOI
Srivas R, Shen JP, Yang CC, Sun SM, Li J, Gross AM, Jensen J, Licon K, Bojorquez-Gomez A, Klepper K, Huang J, Pekin D, Xu JL, Yeerna H, Sivaganesh V, Kollenstart L, van Attikum H, Aza-Blanc P, Sobol RW, Ideker T. "A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy." Mol Cell. 2016;63(3):514-25. PubMed PMC DOI
Yu MK, Kramer M, Dutkowski J, Srivas R, Licon K, Kreisberg J, Ng CT, Krogan N, Sharan R, Ideker T. "Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems." Cell Syst. 2016;2(2):77-88. PubMed PMC DOI

2015

Bliven SE, Bourne PE, Prlić A. "Detection of circular permutations within protein structures using CE-CP." Bioinformatics. 2015;31(8):1316-8. PubMed PMC DOI
Choueiri MB, Shen JP, Gross AM, Huang JK, Ideker T, Fanta P. "ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer." PLoS One. 2015;10(6):e0126898. PubMed PMC DOI
Taheri-Araghi S, Brown SD, Sauls JT, McIntosh DB, Jun S. "Single-Cell Physiology." Annu Rev Biophys. 2015;44:123-42. PubMed PMC DOI

2014

Dutkowski J, Ono K, Kramer M, Yu M, Pratt D, Demchak B, Ideker T. "NeXO Web: the NeXO ontology database and visualization platform." Nucleic Acids Res. 2014;42(Database issue):D1269-74. PubMed PMC DOI
Liu JK, O'Brien EJ, Lerman JA, Zengler K, Palsson BO, Feist AM. "Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale." BMC Syst Biol. 2014;8:110. PubMed PMC DOI
Myers-Turnbull D, Bliven SE, Rose PW, Aziz ZK, Youkharibache P, Bourne PE, Prlić A. "Systematic detection of internal symmetry in proteins using CE-Symm." J Mol Biol. 2014;426(11):2255-68. PubMed PMC DOI
Neumann S, Campbell GE, Szpankowski L, Goldstein LS, Encalada SE. "Characterizing the composition of molecular motors on moving axonal cargo using 'cargo mapping' analysis." J Vis Exp. 2014(92):e52029. PubMed PMC DOI

2013

Kaikkonen MU, Spann NJ, Heinz S, Romanoski CE, Allison KA, Stender JD, Chun HB, Tough DF, Prinjha RK, Benner C, Glass CK. "Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription." Mol Cell. 2013;51(3):310-25. PubMed PMC DOI
Kim S, Jeong K, Bhutani K, Lee J, Patel A, Scott E, Nam H, Lee H, Gleeson JG, Bafna V. "Virmid: accurate detection of somatic mutations with sample impurity inference." Genome Biol. 2013;14(8):R90. PubMed PMC DOI
Lo JH, von Maltzahn G, Douglass J, Park JH, Sailor MJ, Ruoslahti E, Bhatia SN. "Nanoparticle amplification via photothermal unveiling of cryptic collagen binding sites." J Mater Chem B. 2013;1(39):5235-5240. PubMed PMC DOI
Massanella M, Singhania A, Beliakova-Bethell N, Pier R, Lada SM, White CH, Pérez-Santiago J, Blanco J, Richman DD, Little SJ, Woelk CH. "Differential gene expression in HIV-infected individuals following ART." Antiviral Res. 2013;100(2):420-8. PubMed PMC DOI

2012

Szpankowski L, Encalada SE, Goldstein LS. "Subpixel colocalization reveals amyloid precursor protein-dependent kinesin-1 and dynein association with axonal vesicles." Proc Natl Acad Sci U S A. 2012;109(22):8582-7. PubMed PMC DOI

2011

Encalada SE, Szpankowski L, Xia CH, Goldstein LS. "Stable kinesin and dynein assemblies drive the axonal transport of mammalian prion protein vesicles." Cell. 2011;144(4):551-65. PubMed PMC DOI
Narayanan T, Gersten M, Subramaniam S, Grama A. "Modularity detection in protein-protein interaction networks." BMC Res Notes. 2011;4:569. PubMed PMC DOI

2006

Payne SH, Loomis WF. "Retention and loss of amino acid biosynthetic pathways based on analysis of whole-genome sequences." Eukaryot Cell. 2006;5(2):272-6. PubMed PMC DOI

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