Publications | Bioinformatics and Systems Biology

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

Campos FA, Bruno S, Fu Y, Del Vecchio D, Williams RJ. "Comparison Theorems for Stochastic Chemical Reaction Networks." Bull Math Biol. 2023;85(5):39. PubMed PMC DOI
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
Jia BB, Jussila A, Kern C, Zhu Q, Ren B. "A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH." Nat Biotechnol. 2023. PubMed DOI
Kathman SG, Koo SJ, Lindsey GL, Her HL, Blue SM, Li H, Jaensch S, Remsberg JR, Ahn K, Yeo GW, Ghosh B, Cravatt BF. "Remodeling oncogenic transcriptomes by small molecules targeting NONO." Nat Chem Biol. 2023. PubMed DOI
Lorenz DA, Her HL, Shen KA, Rothamel K, Hutt KR, Nojadera AC, Bruns SC, Manakov SA, Yee BA, Chapman KB, Yeo GW. "Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP." Nat Methods. 2023;20(1):65-69. 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
Song BP, Ragsac MF, Tellez K, Jindal GA, Grudzien JL, Le SH, Farley EK. "Diverse logics and grammar encode notochord enhancers." Cell Rep. 2023;42(2):112052. PubMed 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

Armingol E, Baghdassarian HM, Martino C, Perez-Lopez A, Aamodt C, Knight R, Lewis NE. "Context-aware deconvolution of cell-cell communication with Tensor-cell2cell." Nat Commun. 2022;13(1):3665. PubMed PMC DOI
Armingol E, Ghaddar A, Joshi CJ, Baghdassarian H, Shamie I, Chan J, Her HL, Berhanu S, Dar A, Rodriguez-Armstrong F, Yang O, O'Rourke EJ, Lewis NE. "Inferring a spatial code of cell-cell interactions across a whole animal body." PLoS Comput Biol. 2022;18(11):e1010715. PubMed PMC DOI
Armstrong G, Martino C, Morris J, Khaleghi B, Kang J, DeReus J, Zhu Q, Roush D, McDonald D, Gonazlez A, Shaffer JP, Carpenter C, Estaki M, Wandro S, Eilert S, Akel A, Eno J, Curewitz K, Swafford AD, Moshiri N, Rosing T, Knight R. "Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases." MSystems. 2022:e0137821. PubMed DOI
Armstrong G, Rahmn G, Martino C, McDonald D, Gonzalez A, Mishne G, Knight R. "Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data." Front Bioinform. 2022;2:821861. DOI
Bergstrom EN, Luebeck J, Petljak M, Khandekar A, Barnes M, Zhang T, Steele CD, Pillay N, Landi MT, Bafna V, Mischel PS, Harris RS, Alexandrov LB. "Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA." Nature. 2022;602(7897):510-517. PubMed PMC DOI
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
Ghosh P, Campos VJ, Vo DT, Guccione C, Goheen-Holland V, Tindle C, Mazzini GS, He Y, Alexandrov LB, Lippman SM, Gurski RR, Das S, Yadlapati R, Curtius K, Sahoo D. "AI-assisted discovery of an ethnicity-influenced driver of cell transformation in esophageal and gastroesophageal junction adenocarcinomas." JCI Insight. 2022;7(18). PubMed PMC DOI
Her HL, Boyle E, Yeo GW. "Metadensity: a background-aware python pipeline for summarizing CLIP signals on various transcriptomic sites." Bioinform Adv. 2022;2(1):vbac083. 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
Liu Y, Ding B, Zheng L, Xu P, Liu Z, Chen Z, Wu P, Zhao Y, Pan Q, Guo Y, Wang W, Wei W. "Regulatory elements can be essential for maintaining broad chromatin organization and cell viability." Nucleic Acids Res. 2022. PubMed 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
Pekar JE, Magee A, Parker E, Moshiri N, Izhikevich K, Havens JL, Gangavarapu K, Malpica Serrano LM, Crits-Christoph A, Matteson NL, Zeller M, Levy JI, Wang JC, Hughes S, Lee J, Park H, Park MS, Ching KZY, Lin RTP, Mat Isa MN, Noor YM, Vasylyeva TI, Garry RF, Holmes EC, Rambaut A, Suchard MA, Andersen KG, Worobey M, Wertheim JO. "The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2." Science. 2022:eabp8337. PubMed DOI