1.) Santini T, Shim A, Liou JJ, Rahman N, Varela-Mattatall G, Budde MD, Inoue W, Everling S, Baron CA (2025 Feb). Investigating microstructural changes between in vivo and perfused ex vivo marmoset brains using oscillating gradient and b-tensor encoded diffusion MRI at 9.4 T. Magnetic resonance in medicine, 93(2), 788-802. . PMID: 39323069.
2.) Zhang Y, Banihashemi L, Versace A, Samolyk A, Taylor M, English G, Schmithorst VJ, Lee VK, Stiffler R, Aslam H, Panigrahy A, Hipwell AE, Phillips ML (2024 Dec 15). Early Infant Prefrontal Cortical Microstructure Predicts Present and Future Emotionality. Biological psychiatry, 96(12), 959-970. . PMID: 38604525.
3.) Tripplehorn SA, Shirra MK, Lardo SM, Marvil HG, Hainer SJ, Arndt KM (2024 Dec 6). A direct interaction between the Chd1 CHCT domain and Rtf1 controls Chd1 distribution and nucleosome positioning on active genes bioRxiv, (), 2024.12.06.627179. . PMCID: 11643122.
4.) Upadhyay S, Benali A, Jordan KD (2024 Nov 26). Capturing Correlation Effects in Positron Binding to Atoms and Molecules. Journal of chemical theory and computation, 20(22), 9879-9893. . PMID: 39288307.
5.) Kim S, Qin Y, Park HJ, Bohn RI, Yue M, Xu Z, Forno E, Chen W, Celedón JC (2024 Nov 18). MOSES: a methylation-based gene association approach for unveiling environmentally regulated genes linked to a trait or disease Clinical Epigenetics, 16(), 161. . PMCID: 11574994.
6.) Chu C, Santini T, Liou JJ, Cohen AD, Maki PM, Marsland AL, Thurston RC, Gianaros PJ, Ibrahim TS (2024 Nov 1). Brain morphometrics correlations with age among 352 participants imaged with both 3T and 7T MRI: 7T improves statistical power and reduces required sample size medRxiv, (), 2024.10.28.24316292. . PMCID: 11581096.
7.) Silvestrini ML, Solazzo R, Boral S, Cocco MJ, Closson JD, Masetti M, Gardner KH, Chong LT (2024 Oct 28). Gating residues govern ligand unbinding kinetics from the buried cavity in HIF‐2α PAS‐B Protein Science : A Publication of the Protein Society, 33(11), e5198. . PMCID: 11516114.
8.) Valenzi E, Jia M, Gerges P, Fan J, Tabib T, Behara R, Zhou Y, Sembrat J, Das J, Benos PV, Singh H, Lafyatis R (2024 Oct 28). Altered AP-1, RUNX and EGR chromatin dynamics drive fibrotic lung disease bioRxiv, (), 2024.10.23.619858. . PMCID: 11565795.
9.) Diniz E, Santini T, Helmet K, Aizenstein HJ, Ibrahim TS (2024 Oct 17). Cross-modality image translation of 3 Tesla Magnetic Resonance Imaging to 7 Tesla using Generative Adversarial Networks medRxiv, (), 2024.10.16.24315609. . PMCID: 11527090.
10.) He Y, De Souza M, Luo TY, Achar SK, Johnson JK, Rosi NL (2024 Oct 14). Leveraging Ligand Steric Demand to Control Ligand Exchange and Domain Composition in Stratified Metal-Organic Frameworks. Angewandte Chemie (International ed. in English), 63(42), e202409150. doi: 10.1002/anie.202409150. PMID: 39046732.
11.) Santini T, Shim A, Liou J, Rahman N, Varela‐Mattatall G, Budde MD, Inoue W, Everling S, Baron CA (2024 Sep 25). Investigating microstructural changes between in vivo and perfused ex vivo marmoset brains using oscillating gradient and b‐tensor encoded diffusion MRI at 9.4 T Magnetic Resonance in Medicine, 93(2), 788-802. . PMCID: 11604852.
12.) Francette AM, Arndt KM (2024 Sep 24). Multiple direct and indirect roles of the Paf1 complex in transcription elongation, splicing, and histone modifications. Cell reports, 43(9), 114730. . PMID: 39244754.
13.) Liang T, Sun ZY, Hines MG, Penrose KJ, Hao Y, Chu X, Mellors JW, Dimitrov DS, Xie XQ, Li W, Feng Z (2024 Sep 16). AI-based IsAb2.0 for antibody design Briefings in Bioinformatics, 25(5), bbae445. . PMCID: 11405125.
14.) Deng Y, He Y, Xu J, He H, Zhang M, Li G (2024 Sep 12). Cardiac Fibroblasts regulate myocardium and coronary vasculature development via the collagen signaling pathway bioRxiv, (), 2024.09.11.612512. . PMCID: 11418987.
15.) Bhatt R, Wang A, Durrant JD (2024 Sep 5). Teaching old docks new tricks with machine learning enhanced ensemble docking Scientific Reports, 14(), 20722. . PMCID: 11377811.
16.) Guo ZC, McHaney JR, Parthasarathy A, Chandrasekaran B (2024 Aug 30). Reduced neural distinctiveness of speech representations in the middle-aged brain bioRxiv, (), 2024.08.28.609778. . PMCID: 11383304.
17.) Yates ME, Waltermire H, Mori K, Li Z, Li Y, Guzolik H, Wang X, Liu T, Atkinson JM, Hooda J, Lee AV, Oesterreich S (2024 Aug 29). ESR1 Fusions Invoke Breast Cancer Subtype-Dependent Enrichment of Ligand-Independent Oncogenic Signatures and Phenotypes Endocrinology, 165(10), bqae111. . PMCID: 11384147.
18.) Patty B, Jordan C, Lardo S, Troy K, Hainer S (2024 Aug 27). H3.3K122A results in a neomorphic phenotype in mouse embryonic stem cells Research Square, (), rs.3.rs-4824795. . PMCID: 11384023.
19.) Yates ME, Waltermire H, Mori K, Li Z, Li Y, Guzolik H, Wang X, Liu T, Atkinson JM, Hooda J, Lee AV, Oesterreich S (2024 Aug 27). ESR1 Fusions Invoke Breast Cancer Subtype-Dependent Enrichment of Ligand-Independent Oncogenic Signatures and Phenotypes. Endocrinology, 165(10), . . PMID: 39207954.
20.) Hurton MD, Miller JM, Lee MT (2024 Aug 26). H3K4me2 distinguishes a distinct class of enhancers during the maternal-to-zygotic transition bioRxiv, (), 2024.08.26.609713. . PMCID: 11383010.
21.) Liu T, Esencan D, Salgado CM, Zhao C, Lai YJ, Hutchins T, Sanyal A, Chen W, Torok KS (2024 Aug 23). Spatial Transcriptomics Identifies Cellular and Molecular Characteristics of Scleroderma Skin Lesions: Pilot Study in Juvenile Scleroderma International Journal of Molecular Sciences, 25(17), 9182. . PMCID: 11395166.
22.) Arora M, Bertocci MA, Schumer MC, Skeba AS, Bebko G, Stiffler RS, Brady TJ, Afriyie-Agyemang Y, Aslam HA, Graur S, Benjamin O, Wang Y, Phillips ML (2024 Aug 15). Sex differences in neural responses to emotional facial expressions are associated with lifetime depression and mania risk. Journal of affective disorders, 359(), 33-40. doi: 10.1016/j.jad.2024.05.042. PMID: 38735582.
23.) Abarbanel OD, Hutchison GR (2024 Aug 13). QupKake: Integrating Machine Learning and Quantum Chemistry for Micro-pK(a) Predictions. Journal of chemical theory and computation, 20(15), 6946-6956. . PMID: 38832803.
24.) Chen F, Onkar S, Zou J, Li Y, Arbore H, Maley S, Tseng G, Lucas P, Bruno T, Vignali D, Foldi J, Balic M, Lee A, Oesterreich S (2024 Aug 13). Immune Infiltration Correlates with Transcriptomic Subtypes in Primary ER+ Invasive Lobular Breast Cancer. Research square, (), . . PMID: 39184073.
25.) Andrews LP, Butler SC, Cui J, Cillo AR, Cardello C, Liu C, Brunazzi EA, Baessler A, Xie B, Kunning SR, Ngiow SF, Huang YJ, Manne S, Sharpe AH, Delgoffe GM, Wherry EJ, Kirkwood JM, Bruno TC, Workman CJ, Vignali DAA (2024 Aug 8). LAG-3 and PD-1 synergize on CD8(+) T cells to drive T cell exhaustion and hinder autocrine IFN-γ-dependent anti-tumor immunity. Cell, 187(16), 4355-4372.e22. . PMID: 39121848.
26.) Toth J, Sidleck B, Lombardi O, Hou T, Eldo A, Kerlin M, Zeng X, Saeed D, Agarwal P, Leonard D, Andrino L, Inbar T, Malina M, Insanally MN (2024 Jul 23). Dynamic gating of perceptual flexibility by non-classically responsive cortical neurons Research Square, (), rs.3.rs-4650869. . PMCID: 11302693.
27.) Yang DT, Chong LT (2024 Jul 16). WEDAP: A Python Package for Streamlined Plotting of Molecular Simulation Data Journal of Chemical Information and Modeling, 64(15), 5749-5755. . PMCID: 11323263.
28.) Zong W, Li D, Seney ML, Mcclung CA, Tseng GC (2024 Jul 13). Model-based multifacet clustering with high-dimensional omics applications. Biostatistics (Oxford, England), (), . pii: kxae020. doi: 10.1093/biostatistics/kxae020. PMID: 39002144.
29.) Zou J, Li Z, Carleton N, Oesterreich S, Lee AV, Tseng GC (2024 Jun 13). Mutual information for detecting multi-class biomarkers when integrating multiple bulk or single-cell transcriptomic studies. bioRxiv : the preprint server for biology, (), . . PMID: 38915481.
30.) Mulvey DM, Jordan KD (2024 Jun 10). Demonstrating the Connection between the Nonvalence Correlation-Bound Anions of Polyaromatic Hydrocarbons and the Image Potential States of Graphene Using a One-Electron Model Hamiltonian The Journal of Physical Chemistry Letters, 15(24), 6299-6305. . PMCID: 11194819.
31.) Santini T, Chen C, Zhu W, Liou JJ, Walker E, Venkatesh S, Farhat N, Sajewski A, Alkhateeb S, Saranathan M, Xia Z, Ibrahim TS (2024 Jun). Hippocampal subfields and thalamic nuclei associations with clinical outcomes in multiple sclerosis: An ultrahigh field MRI study. Multiple sclerosis and related disorders, 86(), 105520. . PMID: 38582026.
32.) Eckles D, Mossel E, Rahimian MA, Sen S (2024 Jun). Long ties accelerate noisy threshold-based contagions. Nature human behaviour, 8(6), 1057-1064. doi: 10.1038/s41562-024-01865-0. PMID: 38649461.
33.) Xu J, Deng Y, Li G (2024 May 20). Keratin 19 (Krt19) is a novel marker gene for epicardial cells Frontiers in Genetics, 15(), 1385867. . PMCID: 11145414.
34.) Martins T, de Almeida B, Wu M, Wilckens KA, Minhas D, Ibinson JW, Aizenstein HJ, Santini T, Ibrahim TS (2024 May 9). Characterization of pulsations in the brain and cerebrospinal fluid using ultra-high field magnetic resonance imaging Frontiers in Neuroscience, 18(), 1305939. . PMCID: 11112101.
35.) Bogetti AT, Zwier MC, Chong LT (2024 May 8). Revisiting Textbook Azide-Clock Reactions: A "Propeller-Crawling" Mechanism Explains Differences in Rates. Journal of the American Chemical Society, 146(18), 12828-12835. . PMID: 38687173.
36.) Verdejo-Torres O, Klein DC, Novoa-Aponte L, Carrazco-Carrillo J, Bonilla-Pinto D, Rivera A, Fitisemanu F, Jiménez-González ML, Flinn L, Pezacki AT, Lanzirotti A, Ortiz-Frade LA, Chang CJ, Navea JG, Blaby-Haas C, Hainer SJ, Padilla-Benavides T (2024 May 5). Cysteine Rich Intestinal Protein 2 is a copper-responsive regulator of skeletal muscle differentiation bioRxiv, (), 2024.05.03.592485. . PMCID: 11092763.
37.) Bogetti AT, Zwier MC, Chong LT (2024 Apr 30). Revisiting textbook azide-clock reactions: A “propeller-crawling” mechanism explains differences in rates Journal of the American Chemical Society, 146(18), 12828-12835. . PMCID: 11078601.
38.) DePoy LM, Petersen KA, Zong W, Ketchesin KD, Matthaei RC, Yin R, Perez MS, Vadnie CA, Becker-Krail D, Scott MR, Tseng GC, McClung CA (2024 Apr 27). Cell-type and sex-specific rhythmic gene expression in the nucleus accumbens Molecular psychiatry, 29(10), 3117-3127. . PMCID: 11449664.
39.) Francette AM, Arndt KM (2024 Apr 25). Multiple direct and indirect roles of Paf1C in elongation, splicing, and histone post-translational modifications bioRxiv, (), 2024.04.25.591159. . PMCID: 11071476.
40.) Liu Z, Chiu YC, Chen Y, Huang Y (2024 Apr 25). A Metastatic Cancer Expression Generator (MetGen): A Generative Contrastive Learning Framework for Metastatic Cancer Generation Cancers, 16(9), 1653. . PMCID: 11083328.
41.) Alaufey R, Zhao L, Lindsay A, Siboonruang T, Wu Q, Keith JA, Wood E, Tang M (2024 Apr 18). Interplay between Catalyst Corrosion and Homogeneous Reactive Oxygen Species in Electrochemical Ozone Production ACS Catalysis, 14(9), 6868-6880. . PMCID: 11197020.
42.) Leonard-Murali S, Bhaskarla C, Yadav GS, Maurya SK, Galiveti CR, Tobin JA, Kann RJ, Ashwat E, Murphy PS, Chakka AB, Soman V, Cantalupo PG, Zhuo X, Vyas G, Kozak DL, Kelly LM, Smith E, Chandran UR, Hsu YM, Kammula US (2024 Apr 16). Uveal melanoma immunogenomics predict immunotherapy resistance and susceptibility Nature Communications, 15(), 2863. . PMCID: 11021475.
43.) Proe KR, Towarnicky A, Fertig A, Lu Z, Mpourmpakis G, Matson EM (2024 Apr 9). Impact of Surface Ligand Identity and Density on the Thermodynamics of H Atom Uptake at Polyoxovanadate-Alkoxide Surfaces Inorganic Chemistry, 63(16), 7206-7217. . PMCID: 11040723.
44.) Lee S, Cho Y, Li Y, Li R, Brown D, McAuliffe P, Lee AV, Oesterreich S, Zervantonakis IK, Osmanbeyoglu HU (2024 Mar 26). Cancer-cell derived S100A11 promotes macrophage recruitment in ER+ breast cancer bioRxiv, (), 2024.03.21.586041. . PMCID: 10996512.
45.) Ding K, Chen L, Levine K, Sikora M, Tasdemir N, Dabbs D, Jankowitz R, Hazan R, Shah OS, Atkinson JM, Lee AV, Oesterreich S (2024 Mar 20). Estrogen regulation and functional role of FGFR4 in estrogen receptor positive breast cancer. bioRxiv : the preprint server for biology, (), . . PMID: 38562741.
46.) Spencer MA, Holzapfel NP, You KE, Mpourmpakis G, Augustyn V (2024 Mar 14). Participation of electrochemically inserted protons in the hydrogen evolution reaction on tungsten oxides Chemical Science, 15(14), 5385-5402. . PMCID: 10988594.
47.) Luo Z, Wan Z, Ren P, Zhang B, Huang Y, West RE III, Huang H, Chen Y, Nolin TD, Xie W, Wang J, Li S, Sun J (2024 Mar 14). In Situ Formation of Fibronectin‐Enriched Protein Corona on Epigenetic Nanocarrier for Enhanced Synthetic Lethal Therapy Advanced Science, 11(19), 2307940. . PMCID: 11109615.
48.) Zhang H, Lee S, Muthakana RR, Lu B, Boone DN, Lee D, Wang XS (2024 Mar 4). Intragenic rearrangement burden associates with immune cell infiltration and response to immune checkpoint blockade in cancer Cancer immunology research, 12(3), 287-295. . PMCID: 11107381.
49.) Zhang H, Lee S, Muthakana RR, Lu B, Boone DN, Lee D, Wang XS (2024 Mar 4). Intragenic Rearrangement Burden Associates with Immune Cell Infiltration and Response to Immune Checkpoint Blockade in Cancer. Cancer immunology research, 12(3), 287-295. . PMID: 38345376.
50.) Callahan D, Smita S, Joachim S, Hoehn K, Kleinstein S, Weisel F, Chikina M, Shlomchik M (2024 Mar). Memory B cell subsets have divergent developmental origins that are coupled to distinct imprinted epigenetic states. Nature immunology, 25(3), 562-575. doi: 10.1038/s41590-023-01721-9. PMID: 38200277.
51.) Bertocci MA, Rozovsky R, Wolfe M, Abdul-Waalee H, Chobany M, Malgireddy G, Hart JA, Skeba A, Brady T, Lepore B, Versace A, Chase HW, Birmaher B, Phillips ML, Diler RS (2024 Mar). Neural markers of mania that distinguish inpatient adolescents with bipolar disorder from those with other psychopathology. Psychiatry research, 333(), 115747. . PMID: 38301286.
52.) Wang LJ, Ning M, Nayak T, Kasper MJ, Monga SP, Huang Y, Chen Y, Chiu YC (2024 Feb 9). shinyDeepDR: A user-friendly R Shiny app for predicting anti-cancer drug response using deep learning. Patterns (New York, N.Y.), 5(2), 100894. . PMID: 38370127.
53.) Miranda O, Fan P, Qi X, Wang H, Brannock MD, Kosten T, Ryan ND, Kirisci L, Wang L (2024 Feb 1). Prediction of adverse events risk in patients with comorbid post-traumatic stress disorder and alcohol use disorder using electronic medical records by deep learning models. Drug and alcohol dependence, 255(), 111066. . PMID: 38217979.
54.) Huang Z, Li T, Li B, Dong Q, Smith J, Li S, Xu L, Wang G, Chi M, Hu L (2024 Jan 24). Tailoring Local Chemical Ordering via Elemental Tuning in High-Entropy Alloys. Journal of the American Chemical Society, 146(3), 2167-2173. doi: 10.1021/jacs.3c12048. PMID: 38214166.
55.) Duan B, Qiu C, Lockless SW, Sze SH, Kaplan CD (2024 Jan 21). Higher-order epistasis within Pol II trigger loop haplotypes bioRxiv, (), 2024.01.20.576280. . PMCID: 10827151.
56.) Miranda O, Fan P, Qi X, Wang H, Brannock MD, Kosten TR, Ryan ND, Kirisci L, Wang L (2024 Jan 14). DeepBiomarker2: Prediction of Alcohol and Substance Use Disorder Risk in Post-Traumatic Stress Disorder Patients Using Electronic Medical Records and Multiple Social Determinants of Health. Journal of personalized medicine, 14(1), . . PMID: 38248795.
57.) Liu S, Yu YP, Ren BG, Ben-Yehezkel T, Obert C, Smith M, Wang W, Ostrowska A, Soto-Gutierrez A, Luo JH (2024 Jan 11). Long-read single-cell sequencing reveals expressions of hypermutation clusters of isoforms in human liver cancer cells. eLife, 12(), . . PMID: 38206124.
58.) Zou J, Shah O, Chiu YC, Ma T, Atkinson JM, Oesterreich S, Lee AV, Tseng GC (2024 Jan 10). Systems approach for congruence and selection of cancer models towards precision medicine PLOS Computational Biology, 20(1), e1011754. . PMCID: 10805322.
59.) Zhang L, Cascio S, Mellors JW, Buckanovich RJ, Osmanbeyoglu HU (2024 Jan 5). Single-cell analysis reveals the stromal dynamics and tumor-specific characteristics in the microenvironment of ovarian cancer Communications Biology, 7(), 20. . PMCID: 10770164.
60.) Luo Z, Huang Y, Batra N, Chen Y, Huang H, Wang Y, Zhang Z, Li S, Chen CY, Wang Z, Sun J, Wang QJ, Yang D, Lu B, Conway JF, Li LY, Yu AM, Li S (2024 Jan 4). Inhibition of iRhom1 by CD44-targeting nanocarrier for improved cancer immunochemotherapy Nature Communications, 15(), 255. . PMCID: 10766965.
61.) Zhu Y, Vvedenskaya IO, Sze SH, Nickels BE, Kaplan CD (2024 Jan 4). Quantitative analysis of transcription start site selection in Saccharomyces cerevisiae reveals control by DNA sequence, RNA Polymerase II activity, and NTP levels Nature structural & molecular biology, 31(1), 190-202. . PMCID: 10928753.
62.) Santhouse JR, Leung JMG, Chong LT, Horne WS (2024 Jan 3). Effects of altered backbone composition on the folding kinetics and mechanism of an ultrafast-folding protein. Chemical science, 15(2), 675-682. . PMID: 38179541.
63.) Zhu Y, Vvedenskaya IO, Sze SH, Nickels BE, Kaplan CD (2024 Jan). Quantitative analysis of transcription start site selection reveals control by DNA sequence, RNA polymerase II activity and NTP levels. Nature structural & molecular biology, 31(1), 190-202. . PMID: 38177677.
64.) Zhu B, Liu S, David NL, Dion W, Doshi NK, Siegel LB, Amorim T, Andrews RE, Naveen Kumar GV, Li H, Irfan S, Pesaresi T, Sharma AX, Sun M, Fazeli PK, Steinhauser ML (2023 Dec 23). Evidence for conservation of primordial ~12-hour ultradian gene programs in humans under free-living conditions. bioRxiv : the preprint server for biology, (), . . PMID: 37205600.
65.) King JE, Koes DR (2023 Dec 15). Interpreting forces as deep learning gradients improves quality of predicted protein structures Biophysical Journal, 123(17), 2730-2739. . PMCID: 11393680.
66.) Shah OS, Chen F, Wedn A, Kashiparekh A, Knapick B, Chen J, Savariau L, Clifford B, Hooda J, Christgen M, Xavier J, Oesterreich S, Lee AV (2023 Dec 12). Multi-omic characterization of ILC and ILC-like cell lines as part of ILC cell line encyclopedia (ICLE) defines new models to study potential biomarkers and explore therapeutic opportunities. bioRxiv : the preprint server for biology, (), . . PMID: 37808708.
67.) Culbertson EM, Levin TC (2023 Dec 8). Eukaryotic CD-NTase, STING, and viperin proteins evolved via domain shuffling, horizontal transfer, and ancient inheritance from prokaryotes PLOS Biology, 21(12), e3002436. . PMCID: 10732462.
68.) Redlich R, Kowalczyk A, Tene M, Sestili HH, Foley K, Saputra E, Clark N, Chikina M, Meyer WK, Pfenning A (2023 Dec 7). RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution bioRxiv, (), 2023.12.06.570425. . PMCID: 10723433.
69.) Martins T, Santini T, de Almeida B, Wu M, Wilckens KA, Minhas D, Ibinson JW, Aizenstein HJ, Ibrahim TS (2023 Dec 6). Characterization of oscillations in the brain and cerebrospinal fluid using ultra-high field magnetic resonance imaging medRxiv, (), 2023.12.05.23299452. . PMCID: 10723515.
70.) Bogetti AT, Leung JM, Chong LT (2023 Dec 4). LPATH: A Semiautomated Python Tool for Clustering Molecular Pathways Journal of Chemical Information and Modeling, 63(24), 7610-7616. . PMCID: 10751797.
71.) Lyu L, Cheng Y, Wahed AS (2023 Dec). Imputation-based Q-learning for optimizing dynamic treatment regimes with right-censored survival outcome. Biometrics, 79(4), 3676-3689. doi: 10.1111/biom.13872. PMID: 37129942.
72.) Lee S, Sun M, Hu Y, Wang Y, Islam MN, Goerlitz D, Lucas PC, Lee AV, Swain SM, Tang G, Wang XS (2023 Nov 30). iGenSig-Rx: an integral genomic signature based white-box tool for modeling cancer therapeutic responses using multi-omics data. Research square, (), . . PMID: 38077030.
73.) Wang H, Stevens T, Lu J, Roberts A, Land CV, Muzumdar R, Gong Z, Vockley J, Prochownik EV (2023 Nov 27). The Myc-Like Mlx Network Impacts Aging and Metabolism. bioRxiv : the preprint server for biology, (), . . PMID: 38076995.
74.) Fan Z, Sun J, Thorpe H, Lee S, Kim S, Park HJ (2023 Nov 22). Deep neural network learning biological condition information refines gene-expression-based cell subtypes. Briefings in bioinformatics, 25(1), . . PMID: 38233089.
75.) Kim S, Qin Y, Park HJ, Yue M, Xu Z, Forno E, Chen W, Celedón JC (2023 Nov 15). Methyl-TWAS: A powerful method for in silico transcriptome-wide association studies (TWAS) using long-range DNA methylation. bioRxiv : the preprint server for biology, (), . . PMID: 38014125.
76.) Salem M, Loevlie DJ, Mpourmpakis G (2023 Nov 13). Single Atom Alloys Segregation in the Presence of Ligands The Journal of Physical Chemistry. C, Nanomaterials and Interfaces, 127(46), 22790-22798. . PMCID: 10683009.
77.) Kour S, Fortuna T, Anderson EN, Mawrie D, Bilstein J, Sivasubramanian R, Ward C, Roy R, Rajasundaram D, Sterneckert J, Pandey UB (2023 Nov 10). Drosha-dependent microRNAs modulate FUS-mediated neurodegeneration in vivo. Nucleic acids research, 51(20), 11258-11276. . PMID: 37791873.
78.) Gui Y, Palanza Z, Gupta P, Li H, Pan Y, Wang Y, Hargis G, Kreutzer DL, Wang Y, Bastacky SI, Liu Y, Liu S, Zhou D (2023 Nov 8). Calponin 2 regulates ketogenesis to mitigate acute kidney injury. JCI insight, 8(21), . . PMID: 37751293.
79.) Singh-Varma A, Shah AM, Liu S, Zamora R, Monga SP, Vodovotz Y (2023 Nov 1). Defining spatiotemporal gene modules in liver regeneration using Analytical Dynamic Visual Spatial Omics Representation (ADViSOR). Hepatology communications, 7(11), . . PMID: 37889540.
80.) Bhatt R, Koes DR, Durrant JD (2023 Oct 21). CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks bioRxiv, (), 2023.10.18.562959. . PMCID: 10614872.
81.) Pederson MR, Withanage KPK, Hooshmand Z, Johnson AI, Baruah T, Yamamoto Y, Zope RR, Kao DY, Shukla PB, Johnson JK, Peralta JE, Jackson KA (2023 Oct 21). Use of FLOSIC for understanding anion-solvent interactions. The Journal of chemical physics, 159(15), . pii: 154112. doi: 10.1063/5.0172300. PMID: 37861122.
82.) Munyoki SK, Goff JP, Kolobaric A, Long A, Mullett SJ, Burns JK, Jenkins AK, DePoy L, Wendell SG, McClung CA, Morrison KE, Jašarević E (2023 Oct 20). Intestinal microbial circadian rhythms drive sex differences in host immunity and metabolism. iScience, 26(10), 107999. . PMID: 37841582.
83.) Bogetti AT, Leung JMG, Chong LT (2023 Oct 19). LPATH: A semi-automated Python tool for clustering molecular pathways. bioRxiv : the preprint server for biology, (), . . PMID: 37645995.
84.) Nilsson S, El Berch JN, Albinsson D, Fritzsche J, Mpourmpakis G, Langhammer C (2023 Oct 5). The Role of Grain Boundary Sites for the Oxidation of Copper Catalysts during the CO Oxidation Reaction ACS Nano, 17(20), 20284-20298. . PMCID: 10604102.
85.) Phelps WA, Hurton MD, Ayers TN, Carlson AE, Rosenbaum JC, Lee MT (2023 Oct 3). Hybridization led to a rewired pluripotency network in the allotetraploid Xenopus laevis eLife, 12(), e83952. . PMCID: 10569791.
86.) Buck SA, Rubin SA, Kunkhyen T, Treiber CD, Xue X, Fenno LE, Mabry SJ, Sundar VR, Yang Z, Shah D, Ketchesin KD, Becker-Krail DD, Vasylieva I, Smith MC, Weisel FJ, Wang W, Erickson-Oberg MQ, O'Leary EI, Aravind E, Ramakrishnan C, Kim YS, Wu Y, Quick M, Coleman JA, MacDonald WA, Elbakri R, De Miranda BR, Palladino MJ, McCabe BD, Fish KN, Seney ML, Rayport S, Mingote S, Deisseroth K, Hnasko TS, Awatramani R, Watson AM, Waddell S, Cheetham CEJ, Logan RW, Freyberg Z (2023 Oct 3). Sexually dimorphic mechanisms of VGLUT-mediated protection from dopaminergic neurodegeneration. bioRxiv : the preprint server for biology, (), . . PMID: 37873436.
87.) Augustin RC, Newman S, Li A, Joy M, Lyons M, Pham MP, Lucas P, Smith K, Sander C, Isett B, Davar D, Najjar YG, Zarour HM, Kirkwood JM, Luke JJ, Bao R (2023 Oct). Identification of tumor-intrinsic drivers of immune exclusion in acral melanoma. Journal for immunotherapy of cancer, 11(10), . . PMID: 37857525.
88.) Nobile NA, Erickson JR, Ríos C, Zhang Y, Hu J, Vitale SA, Xiong F, Youngblood N (2023 Sep 29). Time-Resolved Temperature Mapping Leveraging the Strong Thermo-Optic Effect in Phase-Change Materials ACS Photonics, 10(10), 3576-3585. . PMCID: 10588450.
89.) Badrane H, Cheng S, Dupont CL, Hao B, Driscoll E, Morder K, Liu G, Newbrough A, Fleres G, Kaul D, Espinoza JL, Clancy CJ, Nguyen MH (2023 Sep 22). Genotypic diversity and unrecognized antifungal resistance among populations of Candida glabrata from positive blood cultures Nature Communications, 14(), 5918. . PMCID: 10516878.
90.) Ye J, Collinger JL, Wehbe L, Gaunt R (2023 Sep 22). Neural Data Transformer 2: Multi-context Pretraining for Neural Spiking Activity bioRxiv, (), 2023.09.18.558113. . PMCID: 10541112.
91.) Yates ME, Li Z, Li Y, Guzolik H, Wang X, Liu T, Hooda J, Atkinson JM, Lee AV, Oesterreich S (2023 Sep 19). ESR1 fusion proteins invoke breast cancer subtype-dependent enrichment of ligand independent pro-oncogenic signatures and phenotypes. bioRxiv : the preprint server for biology, (), . . PMID: 37790296.
92.) Miranda O, Fan P, Qi X, Wang H, Brannock MD, Kosten T, Ryan ND, Kirisci L, Wang L (2023 Sep 18). Prediction of Adverse Events Risk in Patients with Comorbid Post- Traumatic Stress Disorder and Alcohol Use Disorder Using Electronic Medical Records by Deep Learning Models. Research square, (), . . PMID: 37790550.
93.) Elangovan A, Bossart EA, Basudan A, Tasdemir N, Shah OS, Ding K, Meier C, Heim T, Neumann C, Attaran S, Brown L, Hooda J, Miller L, Liu T, Puhalla SL, Gurda G, Lucas PC, McAuliffe PF, Atkinson JM, Lee AV, Oesterreich S (2023 Sep 17). WCRC-25: A novel luminal Invasive Lobular Carcinoma cell line model bioRxiv, (), 2023.09.15.558023. . PMCID: 10516031.
94.) Mulvey DM, Jordan KD (2023 Sep 7). Application of a Fluctuating Charge Polarization Model to Large Polyaromatic Hydrocarbons and Graphene Nanoflakes. The journal of physical chemistry letters, 14(35), 7869-7875. . PMID: 37639228.
95.) Culbertson EM, Levin TC (2023 Sep 1). Eukaryotic antiviral immune proteins arose via convergence, horizontal transfer, and ancient inheritance bioRxiv, (), 2023.06.27.546753. . PMCID: 10327000.
96.) Huo Z, Watkins KF, Jeong BC, Statt A, Laaser JE (2023 Aug 24). Preferential Mechanochemical Activation of Short Chains in Bidisperse Triblock Elastomers ACS Macro Letters, 12(9), 1213-1217. . PMCID: 10515626.
97.) Luke JJ, Dadey RE, Augustin RC, Newman S, Singh KB, Doerfler R, Behr S, Lee P, Isett B, Deitrick C, Li A, Joy M, Reeder C, Smith K, Urban J, Sellitto L, Jelinek M, Christner SM, Beumer JH, Villaruz LC, Kulkarni A, Davar D, Poklepovic AS, Najjar Y, Zandberg DP, Soloff AC, Bruno TC, Vujanović L, Skinner HD, Ferris RL, Bao R (2023 Aug 19). Tumor cell p38 inhibition to overcome immunotherapy resistance. Research square, (), . . PMID: 37645831.
98.) Hellemann E, Durrant JD (2023 Aug 16). Worth the Weight: Sub-Pocket EXplorer (SubPEx), a Weighted Ensemble Method to Enhance Binding-Pocket Conformational Sampling Journal of Chemical Theory and Computation, 19(17), 5677-5689. . PMCID: 10500992.
99.) Li Z, Li T, Yates ME, Wu Y, Ferber A, Chen L, Brown DD, Carroll JS, Sikora MJ, Tseng GC, Oesterreich S, Lee AV (2023 Aug 15). The EstroGene Database Reveals Diverse Temporal, Context-Dependent, and Bidirectional Estrogen Receptor Regulomes in Breast Cancer. Cancer research, 83(16), 2656-2674. . PMID: 37272757.
100.) Gabdulkhakova A, Krutsenko Y, Zhu J, Liu S, Poddar M, Singh S, Ma X, Nejak-Bowen K, Monga SP, Molina LM (2023 Aug 9). Loss of TAZ after YAP deletion severely impairs foregut development and worsens cholestatic hepatocellular injury Hepatology Communications, 7(9), e0220. . PMCID: 10412434.
101.) Fan P, Zeng L, Ding Y, Kofler J, Silverstein J, Krivinko J, Sweet RA, Wang L (2023 Aug). Combination of antidepressants and antipsychotics as a novel treatment option for psychosis in Alzheimer's disease. CPT: pharmacometrics & systems pharmacology, 12(8), 1119-1131. . PMID: 37128639.
102.) Das A, Meng W, Liu Z, Hasib MM, Galloway H, Ramos da Silva S, Chen L, Sica GL, Paniz-Mondolfi A, Bryce C, Grimes Z, Sordillo EM, Cordon-Cardo C, Rivera KP, Flores M, Chiu YC, Huang Y, Gao SJ (2023 Aug). Molecular and immune signatures, and pathological trajectories of fatal COVID-19 lungs defined by in situ spatial single-cell transcriptome analysis. Journal of medical virology, 95(8), e29009. . PMID: 37563850.
103.) Guo X, Liu S, Sheng Y, Zenati M, Billiar T, Herbert A, Wang Q (2023 Jul 25). ADAR1 Zα domain P195A mutation activates the MDA5-dependent RNA-sensing signaling pathway in brain without decreasing overall RNA editing. Cell reports, 42(7), 112733. . PMID: 37421629.
104.) Valenzi E, Bahudhanapati H, Tan J, Tabib T, Sullivan DI, Nouraie M, Sembrat J, Fan L, Chen K, Liu S, Rojas M, Lafargue A, Felsher DW, Tran PT, Kass DJ, Lafyatis R (2023 Jul). Single-nucleus chromatin accessibility identifies a critical role for TWIST1 in idiopathic pulmonary fibrosis myofibroblast activity. The European respiratory journal, 62(1), . . PMID: 37142338.
105.) Balcı AT, Ebeid MM, Benos PV, Kostka D, Chikina M (2023 Jun 30). An intrinsically interpretable neural network architecture for sequence-to-function learning Bioinformatics, 39(), i413-i422. . PMCID: 10311317.
106.) Fan P, Miranda O, Qi X, Kofler J, Sweet RA, Wang L (2023 Jun 21). Unveiling the Enigma: Exploring Risk Factors and Mechanisms for Psychotic Symptoms in Alzheimer's Disease through Electronic Medical Records with Deep Learning Models. Pharmaceuticals (Basel, Switzerland), 16(7), . . PMID: 37513822.
107.) Wallace ML, Mentch L, Wheeler BJ, Tapia AL, Richards M, Zhou S, Yi L, Redline S, Buysse DJ (2023 Jun 19). Use and misuse of random forest variable importance metrics in medicine: demonstrations through incident stroke prediction BMC Medical Research Methodology, 23(), 144. . PMCID: 10280951.
108.) Achar SK, Bernasconi L, Johnson JK (2023 Jun 13). Machine Learning Electron Density Prediction Using Weighted Smooth Overlap of Atomic Positions Nanomaterials, 13(12), 1853. . PMCID: 10303543.
109.) Kwon H, Mpourmpakis G (2023 Jun 13). Ab Initio Thermochemistry of Highly Flexible Molecules for Thermal Decomposition Analysis Journal of Chemical Theory and Computation, 19(12), 3652-3663. . PMCID: 10308812.
110.) Mhatre CV, Wardzala JJ, Shukla PB, Agrawal M, Johnson JK (2023 Jun 2). Calculation of Self, Corrected, and Transport Diffusivities of Isopropyl Alcohol in UiO-66 Nanomaterials, 13(11), 1793. . PMCID: 10254453.
111.) Faget DV, Luo X, Inkman MJ, Ren Q, Su X, Ding K, Waters MR, Raut GK, Pandey G, Dodhiawala PB, Ramalho-Oliveira R, Ye J, Cole T, Murali B, Zheleznyak A, Shokeen M, Weiss KR, Monahan JB, DeSelm CJ, Lee AV, Oesterreich S, Weilbaecher KN, Zhang J, DeNardo DG, Stewart SA (2023 Jun 2). p38MAPKα Stromal Reprogramming Sensitizes Metastatic Breast Cancer to Immunotherapy. Cancer discovery, 13(6), 1454-1477. . PMID: 36883955.
112.) An P, Sáenz Robles MT, Cantalupo PG, Naik AS, Sealfon R, Imperiale MJ, Pipas JM (2023 May 31). Cultured Renal Proximal Tubular Epithelial Cells Resemble a Stressed/Damaged Kidney While Supporting BK Virus Infection. Journal of virology, 97(5), e0034323. . PMID: 37166336.
113.) Achar SK, Bernasconi L, DeMaio RI, Howard KR, Johnson JK (2023 May 31). In Silico Demonstration of Fast Anhydrous Proton Conduction on Graphanol. ACS applied materials & interfaces, 15(21), 25873-25883. . PMID: 37192530.
114.) Miranda O, Fan P, Qi X, Wang H, Brannock MD, Kosten T, Ryan ND, Kirisci L, Wang L (2023 May 25). DeepBiomarker2: Prediction of alcohol and substance use disorder risk in post-traumatic stress disorder patients using electronic medical records and multiple social determinants of health. Research square, (), . . PMID: 37292589.
115.) Hellemann E, Durrant JD (2023 May 5). Worth the weight: Sub-Pocket EXplorer (SubPEx), a weighted-ensemble method to enhance binding-pocket conformational sampling bioRxiv, (), 2023.05.03.539330. . PMCID: 10214482.
116.) Zhu B, Liu S (2023 May 2). Preservation of ∼12-hour ultradian rhythms of gene expression of mRNA and protein metabolism in the absence of canonical circadian clock. bioRxiv : the preprint server for biology, (), . . PMID: 37205336.
117.) Gocher-Demske AM, Cui J, Szymczak-Workman AL, Vignali KM, Latini JN, Pieklo GP, Kimball JC, Avery L, Cipolla EM, Huckestein BR, Hedden L, Meisel M, Alcorn JF, Kane LP, Workman CJ, Vignali DAA (2023 May). IFNγ-induction of T(H)1-like regulatory T cells controls antiviral responses. Nature immunology, 24(5), 841-854. . PMID: 36928412.
118.) Klein DC, Troy K, Tripplehorn SA, Hainer SJ (2023 Apr 13). The esBAF and ISWI nucleosome remodeling complexes influence occupancy of overlapping dinucleosomes and fragile nucleosomes in murine embryonic stem cells. BMC genomics, 24(1), 201. . PMID: 37055726.
119.) Duan B, Qiu C, Sze SH, Kaplan C (2023 Apr 4). Widespread epistasis shapes RNA Polymerase II active site function and evolution bioRxiv, (), 2023.02.27.530048. . PMCID: 10002619.
120.) Onkar S, Cui J, Zou J, Cardello C, Cillo AR, Uddin MR, Sagan A, Joy M, Osmanbeyoglu HU, Pogue-Geile KL, McAuliffe PF, Lucas PC, Tseng GC, Lee AV, Bruno TC, Oesterreich S, Vignali DAA (2023 Apr). Immune landscape in invasive ductal and lobular breast cancer reveals a divergent macrophage-driven microenvironment. Nature cancer, 4(4), 516-534. doi: 10.1038/s43018-023-00527-w. PMID: 36927792.
121.) Jardine MJA, Dardzinski D, Yu M, Purkayastha A, Chen AH, Chang YH, Engel A, Strocov VN, Hocevar M, Palmstro M C, Frolov SM, Marom N (2023 Mar 29). First-Principles Assessment of CdTe as a Tunnel Barrier at the α-Sn/InSb Interface. ACS applied materials & interfaces, 15(12), 16288-16298. . PMID: 36940162.
122.) Li Y, Fang Y, Chang HC, Gorczyca M, Liu P, Tseng GC (2023 Mar 26). Adaptively Integrative Association between Multivariate Phenotypes and Transcriptomic Data for Complex Diseases. Genes, 14(4), . . PMID: 37107556.
123.) Mao W, Miller CM, Nair VD, Ge Y, Amper MA, Cappuccio A, George M, Goforth CW, Guevara K, Marjanovic N, Nudelman G, Pincas H, Ramos I, Sealfon RS, Soares‐Schanoski A, Vangeti S, Vasoya M, Weir DL, Zaslavsky E, Kim‐Schulze S, Gnjatic S, Merad M, Letizia AG, Troyanskaya OG, Sealfon SC, Chikina M (2023 Mar 15). A methylation clock model of mild SARS‐CoV‐2 infection provides insight into immune dysregulation Molecular Systems Biology, 19(5), e11361. . PMCID: 10167476.
124.) Zuppo DA, Missinato MA, Santana-Santos L, Li G, Benos PV, Tsang M (2023 Mar 14). Foxm1 regulates cardiomyocyte proliferation in adult zebrafish after cardiac injury Development (Cambridge, England), 150(6), dev201163. . PMCID: 10108034.
125.) Chen R, Sanders SM, Ma Z, Paschall J, Chang ES, Riscoe BM, Schnitzler CE, Baxevanis AD, Nicotra ML (2023 Feb 13). XY sex determination in a cnidarian. BMC biology, 21(1), 32. . PMID: 36782149.
126.) Akinyele O, Munir A, Johnson MA, Perez MS, Gao Y, Foley JR, Wu Y, Murray-Stewart T, Casero RA Jr, Bayir H, Kemaladewi DU (2023 Feb 7). Impaired polyamine metabolism causes behavioral and neuroanatomical defects in a novel mouse model of Snyder-Robinson Syndrome. bioRxiv : the preprint server for biology, (), . . PMID: 36711956.
127.) Fan P, Zeng L, Ding Y, Kofler J, Silverstein J, Krivinko J, Sweet RA, Wang L (2023 Jan 28). Combination of Antidepressants and Antipsychotics as A Novel Treatment Option for Psychosis in Alzheimer's Disease. medRxiv : the preprint server for health sciences, (), . . PMID: 36747620.
128.) Xue X, Zong W, Huo Z, Ketchesin KD, Scott MR, Petersen KA, Logan RW, Seney ML, McClung C, Tseng G (2023 Jan 19). DiffCircaPipeline: a framework for multifaceted characterization of differential rhythmicity Bioinformatics, 39(1), btad039. . PMCID: 9889843.
129.) Zhu B, Liu S (2023). Preservation of ∼12-h ultradian rhythms of gene expression of mRNA and protein metabolism in the absence of canonical circadian clock. Frontiers in physiology, 14(), 1195001. . PMID: 37324401.
130.) DeMoya RA, Forman-Rubinsky RE, Fontaine D Jr, Shin J, Watkins SC, Lo CW, Tsang M (2023). Sin3a associated protein 130 kDa, sap130, plays an evolutionary conserved role in zebrafish heart development. Frontiers in cell and developmental biology, 11(), 1197109. . PMID: 37711853.
131.) Fan P, Kofler J, Ding Y, Marks M, Sweet RA, Wang L (2022 Nov 19). Efficacy difference of antipsychotics in Alzheimer's disease and schizophrenia: explained with network efficiency and pathway analysis methods. Briefings in bioinformatics, 23(6), . . PMID: 36151774.
132.) Carew NT, Schmidt HM, Yuan S, Galley JC, Hall R, Altmann HM, Hahn SA, Miller MP, Wood KC, Gabris B, Stapleton MC, Hartwick S, Fazzari M, Wu YL, Trebak M, Kaufman BA, McTiernan CF, Schopfer FJ, Navas P, Thibodeau PH, McNamara DM, Salama G, Straub AC (2022 Sep 15). Loss of cardiomyocyte CYB5R3 impairs redox equilibrium and causes sudden cardiac death. The Journal of clinical investigation, 132(18), . . PMID: 36106636.
133.) Wang X, Xu Z, Hu H, Zhou X, Zhang Y, Lafyatis R, Chen K, Huang H, Ding Y, Duerr RH, Chen W (2022 Sep). SECANT: a biology-guided semi-supervised method for clustering, classification, and annotation of single-cell multi-omics. PNAS nexus, 1(4), pgac165. . PMID: 36157595.
134.) Miranda O, Fan P, Qi X, Yu Z, Ying J, Wang H, Brent DA, Silverstein JC, Chen Y, Wang L (2022 Mar 24). DeepBiomarker: Identifying Important Lab Tests from Electronic Medical Records for the Prediction of Suicide-Related Events among PTSD Patients. Journal of personalized medicine, 12(4), . . PMID: 35455640.
135.) Spiegel JO, Van Houten B, Durrant JD (2021 Jul). PARP1: Structural insights and pharmacological targets for inhibition. DNA repair, 103(), 103125. . PMID: 33940558.
136.) Cassidy KC, Šefčík J, Raghav Y, Chang A, Durrant JD (2020 Mar). ProteinVR: Web-based molecular visualization in virtual reality. PLoS computational biology, 16(3), e1007747. . PMID: 32231351.
137.) Cheng W, Ng CA (2019 Dec 3). Using Machine Learning to Classify Bioactivity for 3486 Per- and Polyfluoroalkyl Substances (PFASs) from the OECD List. Environmental science & technology, 53(23), 13970-13980. doi: 10.1021/acs.est.9b04833. PMID: 31661253.
138.) Liu S, Zhou L, Wang P, Zhang F, Yu S, Shao Z, Yi B (2014 Mar 12). Ionic-liquid-based proton conducting membranes for anhydrous H2/Cl2 fuel-cell applications. ACS applied materials & interfaces, 6(5), 3195-200. doi: 10.1021/am404645c. PMID: 24490850.
