1.) Sheikh SI, Doellman MM, VanKuren NW, Hall P, Kronforst MR (2025 Mar 3). A shared gene but distinct dynamics regulate mimicry polymorphisms in closely related species bioRxiv, (), 2025.03.03.641230. . PMCID: 11908123.
2.) Chowdhary S, Paracha S, Dyer L, Pincus D (2025 Feb 27). Emergent 3D genome reorganization from the stepwise assembly of transcriptional condensates bioRxiv, (), 2025.02.23.639564. . PMCID: 11888319.
3.) Umans BD, Gilad Y (2024 Sep 3). Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids bioRxiv, (), 2024.09.03.611030. . PMCID: 11398411.
4.) Lynch WB, Miracle SA, Goldstein SI, Beierle JA, Bhandari R, Gerhardt ET, Farnan A, Nguyen BM, Wingfield KK, Kazerani I, Saavedra GA, Averin O, Baskin BM, Ferris MT, Reilly CA, Emili A, Bryant CD (2024 Sep 1). Validation studies and multi-omics analysis of Zhx2 as a candidate quantitative trait gene underlying brain oxycodone metabolite (oxymorphone) levels and behavior bioRxiv, (), 2024.08.30.610534. . PMCID: 11383981.
5.) Yang Q, Falahati A, Khosh A, Lastra RR, Boyer TG, Al-Hendy A (2024 Aug 28). Unraveling the Role of Bromodomain and Extra-Terminal Proteins in Human Uterine Leiomyosarcoma. Cells, 13(17), . . PMID: 39273015.
6.) Yuan Y, Bodke VV, Lin C, Gao S, Rehman J, Li J, Khetani SR (2024 Aug 1). Long-term HBV infection of engineered cultures of induced pluripotent stem cell-derived hepatocytes. Hepatology communications, 8(8), . pii: e0506. doi: 10.1097/HC9.0000000000000506. PMID: 39082962.
7.) Yang Q, Falahati A, Khosh A, Vafaei S, Al-Hendy A (2024 Jun 10). Targeting Bromodomain-Containing Protein 9 in Human Uterine Fibroid Cells. Reproductive sciences (Thousand Oaks, Calif.), (), . doi: 10.1007/s43032-024-01608-6. PMID: 38858328.
8.) Liu W, Kurkewich JL, Stoddart A, Khan S, Anandan D, Gaubil AN, Wolfgeher DJ, Jueng L, Kron SJ, McNerney ME (2024 May 28). CUX1 regulates human hematopoietic stem cell chromatin accessibility via the BAF complex. Cell reports, 43(5), 114227. . PMID: 38735044.
9.) Hou Y, Yang K, Wang L, Wang J, Huang X, Piffko A, Luo SZ, Yu X, Rao E, Martinez C, Bugno J, Mack M, Vokes EE, Pitroda SP, Chmura SJ, Weichselbaum RR, Liang HL (2024 May 1). Radiotherapy Enhances Metastasis Through Immune Suppression by Inducing PD-L1 and MDSC in Distal Sites Clinical cancer research : an official journal of the American Association for Cancer Research, 30(9), 1945-1958. . PMCID: 11062826.
10.) Gamble N, Bradu A, Caldwell JA, McKeever J, Bolonduro O, Ermis E, Kaiser C, Kim Y, Parks B, Klemm S, Greenleaf WJ, Crabtree GR, Koh AS (2024 Apr 17). PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape Nature immunology, 25(5), 860-872. . PMCID: 11089574.
11.) Beilinson HA, Erickson SA, Golovkina T (2024 Mar 5). The endogenous Mtv8 locus and the immunoglobulin repertoire Frontiers in Immunology, 15(), 1345467. . PMCID: 10948529.
12.) Parriott G, Hegermiller E, Morman RE, Frank C, Saygin C, Stock W, Bartom ET, Kee BL (2024 Mar). Loss of thymocyte competition underlies the tumor suppressive functions of the E2a transcription factor in T-ALL. Leukemia, 38(3), 491-501. doi: 10.1038/s41375-023-02123-4. PMID: 38155245.
13.) Wang N, Peng YJ, Kang W, Hildreth M, Prabhakar NR, Nanduri J (2024 Feb 27). Transcriptomic Analysis of Postnatal Rat Carotid Body Development. Genes, 15(3), . . PMID: 38540361.
14.) Yang Q, Vafaei S, Falahati A, Khosh A, Bariani MV, Omran MM, Bai T, Siblini H, Ali M, He C, Boyer TG, Al-Hendy A (2024 Jan 11). Bromodomain-Containing Protein 9 Regulates Signaling Pathways and Reprograms the Epigenome in Immortalized Human Uterine Fibroid Cells International Journal of Molecular Sciences, 25(2), 905. . PMCID: 10815284.
15.) Li Y, Girard R, Srinath A, Cruz DV, Ciszewski C, Chen C, Lightle R, Romanos S, Sone JY, Moore T, DeBiasse D, Stadnik A, Lee JJ, Shenkar R, Koskimäki J, Lopez-Ramirez MA, Marchuk DA, Ginsberg MH, Kahn ML, Shi C, Awad IA (2024 Jan 9). Transcriptomic signatures of individual cell types in cerebral cavernous malformation Cell Communication and Signaling : CCS, 22(), 23. . PMCID: 10775676.
16.) VanKuren NW, Sheikh SI, Massardo D, Lu W, Kronforst MR (2024 Jan 9). Supergene evolution via gain of auto-regulation bioRxiv, (), 2024.01.09.574839. . PMCID: 10802445.
17.) Huggins RJ, Greene GL (2023 Nov 30). ERα/PR crosstalk is altered in the context of the ERα Y537S mutation and contributes to endocrine therapy-resistant tumor proliferation. NPJ breast cancer, 9(1), 96. . PMID: 38036546.
18.) Morgan RC, Frank C, Greger M, Attaway M, Sigvardsson M, Bartom ET, Kee BL (2023 Nov 1). TGF-β Promotes the Postselection Thymic Development and Peripheral Function of IFN-γ-Producing Invariant NKT cells. Journal of immunology (Baltimore, Md. : 1950), 211(9), 1376-1384. . PMID: 37702745.
19.) Yukawa K, Yamamoto-Mcguire S, Cafaro L, Hong C, Kamme F, Ikezu T, Ikezu S (2023 Oct 19). Antisense oligonucleotide-based targeting of Tau-tubulin kinase 1 prevents hippocampal accumulation of phosphorylated tau in PS19 tauopathy mice Acta Neuropathologica Communications, 11(), 166. . PMCID: 10585748.
20.) Pang L, Dunterman M, Guo S, Khan F, Liu Y, Taefi E, Bahrami A, Geula C, Hsu WH, Horbinski C, James CD, Chen P (2023 Oct). Kunitz-type protease inhibitor TFPI2 remodels stemness and immunosuppressive tumor microenvironment in glioblastoma. Nature immunology, 24(10), 1654-1670. . PMID: 37667051.
21.) Frazier K, Manzoor S, Carroll K, DeLeon O, Miyoshi S, Miyoshi J, St. George M, Tan A, Chrisler EA, Izumo M, Takahashi JS, Rao MC, Leone VA, Chang EB (2023 Sep 15). Gut microbes and the liver circadian clock partition glucose and lipid metabolism The Journal of Clinical Investigation, 133(18), e162515. . PMCID: 10503806.
22.) Bariani MV, Cui YH, Ali M, Bai T, Grimm SL, Coarfa C, Walker CL, He YY, Yang Q, Al-Hendy A (2023 Sep 9). TGFβ signaling links early life endocrine-disrupting chemicals exposure to suppression of nucleotide excision repair in rat myometrial stem cells Cellular and Molecular Life Sciences, 80(10), 288. . PMCID: 10492698.
23.) VanKuren NW, Doellman MM, Sheikh SI, Palmer Droguett DH, Massardo D, Kronforst MR (2023 Sep 5). Acute and Long-Term Consequences of Co-opted doublesex on the Development of Mimetic Butterfly Color Patterns Molecular Biology and Evolution, 40(9), msad196. . PMCID: 10498343.
24.) Devany J, Falk MJ, Holt LJ, Murugan A, Gardel ML (2023 Aug 21). Epithelial tissue confinement inhibits cell growth and leads to volume-reducing divisions. Developmental cell, 58(16), 1462-1476.e8. . PMID: 37339629.
25.) Bariani MV, Cui YH, Ali M, Bai T, Grimm SL, Coarfa C, Walker CL, He YY, Yang Q, Al-Hendy A (2023 Jun 7). TGFβ signaling links early-life endocrine-disrupting chemicals exposure to suppression of nucleotide excision repair in rat myometrial stem cells Research Square, (), rs.3.rs-3001855. . PMCID: 10274956.
26.) Apiz Saab JJ, Dzierozynski LN, Jonker PB, AminiTabrizi R, Shah H, Menjivar RE, Scott AJ, Nwosu ZC, Zhu Z, Chen RN, Oh M, Sheehan C, Wahl DR, Pasca di Magliano M, Lyssiotis CA, Macleod KF, Weber CR, Muir A (2023 May 31). Pancreatic tumors exhibit myeloid-driven amino acid stress and upregulate arginine biosynthesis eLife, 12(), e81289. . PMCID: 10260022.
27.) Yang Q, Al-Hendy A (2023 Apr 27). The Functional Role and Regulatory Mechanism of FTO m6A RNA Demethylase in Human Uterine Leiomyosarcoma International Journal of Molecular Sciences, 24(9), 7957. . PMCID: 10178470.
28.) Parriott G, Hegermiller E, Morman RE, Frank C, Saygin C, Stock W, Bartom ET, Kee BL (2023 Apr 25). Loss of thymocyte competition underlies the tumor suppressive functions of the E2a transcription factor in T lymphocyte acute lymphoblastic leukemia. bioRxiv : the preprint server for biology, (), . . PMID: 37163059.
29.) Firpo MR, LoMascolo NJ, Petit MJ, Shah PS, Mounce BC (2023 Apr 18). Polyamines and eIF5A hypusination facilitate SREBP2 synthesis and cholesterol production leading to enhanced enterovirus attachment and infection PLOS Pathogens, 19(4), e1011317. . PMCID: 10146511.
30.) Changrob S, Halfmann PJ, Liu H, Torres JL, McGrath JJC, Ozorowski G, Li L, Wilbanks GD, Kuroda M, Maemura T, Huang M, Zheng NY, Turner HL, Erickson SA, Fu Y, Yasuhara A, Singh G, Monahan B, Mauldin J, Srivastava K, Simon V, Krammer F, Sather DN, Ward AB, Wilson IA, Kawaoka Y, Wilson PC (2023 Apr 17). Site of vulnerability on SARS-CoV-2 spike induces broadly protective antibody against antigenically distinct Omicron subvariants. The Journal of clinical investigation, 133(8), . . PMID: 36862518.
31.) McCann M, Li Y, Baccouche B, Kazlauskas A (2023 Mar 29). VEGF Induces Expression of Genes That Either Promote or Limit Relaxation of the Retinal Endothelial Barrier International Journal of Molecular Sciences, 24(7), 6402. . PMCID: 10094353.
32.) An N, Khan S, Imgruet MK, Jueng L, Gurbuxani S, McNerney ME (2023 Mar). Oncogenic RAS promotes leukemic transformation of CUX1-deficient cells. Oncogene, 42(12), 881-893. . PMID: 36725889.
33.) Beadell AV, Zhang Z, Capuano AW, Bennett DA, He C, Zhang W, Arvanitakis Z (2023). Genome-wide Mapping Implicates 5-Hydroxymethylcytosines in Diabetes Mellitus and Alzheimer’s Disease Journal of Alzheimer's disease : JAD, 93(3), 1135-1151. . PMCID: 10490934.
34.) Beadell AV, Zhang Z, Capuano AW, Bennett DA, He C, Zhang W, Arvanitakis Z (2023). Genome-Wide Mapping Implicates 5-Hydroxymethylcytosines in Diabetes Mellitus and Alzheimer's Disease. Journal of Alzheimer's disease : JAD, 93(3), 1135-1151. . PMID: 37182870.
35.) Klunk J, Vilgalys TP, Demeure CE, Cheng X, Shiratori M, Madej J, Beau R, Elli D, Patino MI, Redfern R, DeWitte SN, Gamble JA, Boldsen JL, Carmichael A, Varlik N, Eaton K, Grenier JC, Golding GB, Devault A, Rouillard JM, Yotova V, Sindeaux R, Ye CJ, Bikaran M, Dumaine A, Brinkworth JF, Missiakas D, Rouleau GA, Steinrücken M, Pizarro-Cerdá J, Poinar HN, Barreiro LB (2022 Oct 19). Evolution of immune genes is associated with the Black Death Nature, 611(7935), 312-319. . PMCID: 9580435.
36.) Gupta PK, Allocco JB, Fraipont JM, McKeague ML, Wang P, Andrade MS, McIntosh C, Chen L, Wang Y, Li Y, Andrade J, Conejo-Garcia JR, Chong AS, Alegre ML (2022 Sep 26). Reduced Satb1 expression predisposes CD4+ T conventional cells to Treg suppression and promotes transplant survival Proceedings of the National Academy of Sciences of the United States of America, 119(40), e2205062119. . PMCID: 9546564.
37.) Nguyen LC, Renner DM, Silva D, Yang D, Parenti NA, Medina KM, Nicolaescu V, Gula H, Drayman N, Valdespino A, Mohamed A, Dann C, Wannemo K, Robinson-Mailman L, Gonzalez A, Stock L, Cao M, Qiao Z, Moellering RE, Tay S, Randall G, Beers MF, Rosner MR, Oakes SA, Weiss SR (2022 Sep 20). SARS-CoV-2 Diverges from Other Betacoronaviruses in Only Partially Activating the IRE1α/XBP1 Endoplasmic Reticulum Stress Pathway in Human Lung-Derived Cells mBio, 13(5), e02415-22. . PMCID: 9600248.
38.) Wang AG, Son M, Kenna E, Thom N, Tay S (2022 Aug 16). NF-κB memory coordinates transcriptional responses to dynamic inflammatory stimuli. Cell reports, 40(7), 111159. doi: 10.1016/j.celrep.2022.111159. PMID: 35977475.
39.) Okoreeh MK, Kennedy DE, Emmanuel AO, Veselits M, Moshin A, Ladd RH, Erickson S, McLean KC, Madrigal B, Nemazee D, Maienschein-Cline M, Mandal M, Clark MR (2022 Aug 5). Asymmetrical forward and reverse developmental trajectories determine molecular programs of B cell antigen receptor editing Science immunology, 7(74), eabm1664. . PMCID: 9636592.
40.) Nguyen LC, Renner DM, Silva D, Yang D, Parenti N, Medina KM, Nicolaescu V, Gula H, Drayman N, Valdespino A, Mohamed A, Dann C, Wannemo K, Robinson-Mailman L, Gonzalez A, Stock L, Cao M, Qiao Z, Moellering RE, Tay S, Randall G, Beers MF, Rosner MR, Oakes SA, Weiss SR (2022 Jun 13). SARS-CoV-2 diverges from other betacoronaviruses in only partially activating the IRE1α/XBP1 ER stress pathway in human lung-derived cells bioRxiv, (), 2021.12.30.474519. . PMCID: 9275661.
41.) Arsala D, Wu X, Yi SV, Lynch JA (2022 May 6). Dnmt1a is essential for gene body methylation and the regulation of the zygotic genome in a wasp PLoS Genetics, 18(5), e1010181. . PMCID: 9075658.
42.) Baeten JT, Liu W, Preddy IC, Zhou N, McNerney ME (2022 May). CRISPR screening in human hematopoietic stem and progenitor cells reveals an enrichment for tumor suppressor genes within chromosome 7 commonly deleted regions. Leukemia, 36(5), 1421-1425. doi: 10.1038/s41375-021-01491-z. PMID: 35034954.
43.) Ly OT, Chen H, Brown GE, Hong L, Wang X, Han YD, Pavel MA, Sridhar A, Maienschein-Cline M, Chalazan B, Ong SG, Abdelhady K, Massad M, Rizkallah LE, Rehman J, Khetani SR, Darbar D (2022 Apr 8). Mutant ANP induces mitochondrial and ion channel remodeling in a human iPSC-derived atrial fibrillation model. JCI insight, 7(7), . . PMID: 35393944.
44.) Catela C, Chen Y, Weng Y, Wen K, Kratsios P (2022 Mar 22). Control of spinal motor neuron terminal differentiation through sustained Hoxc8 gene activity. eLife, 11(), . pii: e70766. doi: 10.7554/eLife.70766. PMID: 35315772.
45.) Nguyen LC, Yang D, Nicolaescu V, Best TJ, Gula H, Saxena D, Gabbard JD, Chen SN, Ohtsuki T, Friesen JB, Drayman N, Mohamed A, Dann C, Silva D, Robinson-Mailman L, Valdespino A, Stock L, Suárez E, Jones KA, Azizi SA, Demarco JK, Severson WE, Anderson CD, Millis JM, Dickinson BC, Tay S, Oakes SA, Pauli GF, Palmer KE, Meltzer DO, Randall G, Rosner MR (2022 Feb 25). Cannabidiol inhibits SARS-CoV-2 replication through induction of the host ER stress and innate immune responses. Science advances, 8(8), eabi6110. doi: 10.1126/sciadv.abi6110. PMID: 35050692.
46.) Carr T, McGregor S, Dias S, Verykokakis M, Le Beau MM, Xue HH, Sigvardsson M, Bartom ET, Kee BL (2022). Oncogenic and Tumor Suppressor Functions for Lymphoid Enhancer Factor 1 in E2a-/- T Acute Lymphoblastic Leukemia. Frontiers in immunology, 13(), 845488. doi: 10.3389/fimmu.2022.845488. PMID: 35371057.
47.) Changrob S, Fu Y, Guthmiller JJ, Halfmann PJ, Li L, Stamper CT, Dugan HL, Accola M, Rehrauer W, Zheng NY, Huang M, Wang J, Erickson SA, Utset HA, Graves HM, Amanat F, Sather DN, Krammer F, Kawaoka Y, Wilson PC (2021 Dec 21). Cross-Neutralization of Emerging SARS-CoV-2 Variants of Concern by Antibodies Targeting Distinct Epitopes on Spike. mBio, 12(6), e0297521. doi: 10.1128/mBio.02975-21. PMID: 34781736.
48.) Randolph HE, Fiege JK, Thielen BK, Mickelson CK, Shiratori M, Barroso-Batista J, Langlois RA, Barreiro LB (2021 Nov 26). Genetic ancestry effects on the response to viral infection are pervasive but cell type specific. Science (New York, N.Y.), 374(6571), 1127-1133. . PMID: 34822289.
49.) Shah A, Mittleman BE, Gilad Y, Li YI (2021 Oct 14). Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation. Genome biology, 22(1), 291. doi: 10.1186/s13059-021-02502-z. PMID: 34649612.
50.) Imgruet MK, Lutze J, An N, Hu B, Khan S, Kurkewich J, Martinez TC, Wolfgeher D, Gurbuxani SK, Kron SJ, McNerney ME (2021 Sep 2). Loss of a 7q gene, CUX1, disrupts epigenetically driven DNA repair and drives therapy-related myeloid neoplasms. Blood, 138(9), 790-805. . PMID: 34473231.
51.) Wilson P, Changrob S, Fu Y, Guthmiller J, Halfmann P, Li L, Stamper C, Dugan H, Accola M, Rehrauer W, Zheng NY, Huang M, Wang J, Erickson S, Utset H, Graves H, Amanat F, Sather DN, Krammer F, Kawaoka Y (2021 Jul 19). Cross neutralization of emerging SARS-CoV-2 variants of concern by antibodies targeting distinct epitopes on spike. Research square, (), . pii: rs.3.rs-678247. doi: 10.21203/rs.3.rs-678247/v1. PMID: 34312615.
52.) Dugan HL, Stamper CT, Li L, Changrob S, Asby NW, Halfmann PJ, Zheng NY, Huang M, Shaw DG, Cobb MS, Erickson SA, Guthmiller JJ, Stovicek O, Wang J, Winkler ES, Madariaga ML, Shanmugarajah K, Jansen MO, Amanat F, Stewart I, Utset HA, Huang J, Nelson CA, Dai YN, Hall PD, Jedrzejczak RP, Joachimiak A, Krammer F, Diamond MS, Fremont DH, Kawaoka Y, Wilson PC (2021 Jun 8). Profiling B cell immunodominance after SARS-CoV-2 infection reveals antibody evolution to non-neutralizing viral targets. Immunity, 54(6), 1290-1303.e7. . PMID: 34022127.
53.) Nguyen LC, Yang D, Nicolaescu V, Best TJ, Ohtsuki T, Chen SN, Friesen JB, Drayman N, Mohamed A, Dann C, Silva D, Gula H, Jones KA, Millis JM, Dickinson BC, Tay S, Oakes SA, Pauli GF, Meltzer DO, Randall G, Rosner MR (2021 Mar 10). Cannabidiol Inhibits SARS-CoV-2 Replication and Promotes the Host Innate Immune Response. bioRxiv : the preprint server for biology, (), . pii: 2021.03.10.432967. doi: 10.1101/2021.03.10.432967. PMID: 33758843.
