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  1. 1.   How to recover from a bad start: adaptation of HIV-1 transcription start site mutants during serial passaging in culture
  2. Nikolaitchik,Olga; Chameettachal,Akhil; Islam,Mohammad Saiful; Keele,Brandon; Delviks-Frankenberry, Krista; Pathak,Vinay; Hu,Wei-Shau; Cheng,Zetao
  3. Journal of Virology. 2025, May 07; e0015925.
  1. 2.   Developmental onset of planarian whole-body regeneration depends on axis reset
  2. Booth, Clare L T; Stevens, Brian C; Stubbert, Clover A; Kallgren,Neil; Deihl,Ennis; Davies,Erin
  3. Current Biology : CB. 2025, Apr 11;
  1. 3.   Identification of molecular determinants of gene-specific bursting patterns by high-throughput imaging screens
  2. Sood, Varun; Holewinski,Ronald; Andresson,Thorkell; Larson, Daniel R; Misteli, Tom
  3. Molecular Cell. 2025, Feb 11;
  1. 4.   HIV-1 transcription start sites usage and its impact on unspliced RNA functions in people living with HIV
  2. Islam,Mohammad Saiful; Maldarelli,Frank; Nikolaitchik,Olga; Cheng,Zetao; Gorelick,Robert; Nikolaitchik, Maria A; Pathak,Vinay; Hu,Wei-Shau
  3. mBio. 2024, Dec 27; e0357624.
  1. 5.   A KSHV RNA-binding protein promotes FOS to inhibit nuclease AEN and transactivate RGS2 for AKT phosphorylation
  2. Majerciak,Vladimir; Alvarado-Hernandez, Beatriz; Ma, Yanping; Duduskar, Shivalee; Lobanov, Alexei; Cam, Maggie; Zheng,Zhi-Ming
  3. mBio. 2024, Dec 10; e0317224.
  1. 6.   Interleukin-2-mediated NF-kB-dependent mRNA splicing modulates interferon gamma protein production
  2. Van Gelder, Rachel D; Gokhale, Nandan S; Genoyer, Emmanuelle; Omelia, Dylan S; Anderson,Steve; Young,Howard; Savan, Ram
  3. EMBO Reports. 2024, Nov 22;
  1. 7.   Translation of HIV-1 unspliced RNA is regulated by 5' untranslated region structure
  2. Cheng,Zetao; Islam,Mohammad Saiful; Kanlong, Joseph G; Sheppard, Madeline; Seo, Heewon; Nikolaitchik,Olga; Kearse, Michael G; Pathak,Vinay; Musier-Forsyth, Karin; Hu,Wei-Shau
  3. Journal of Virology. 2024, Sep 24; e0116024.
  1. 8.   Novel mechanisms of MITF regulation identified in a mouse suppressor screen
  2. Vu, Hong Nhung; Valdimarsson, Matti Már; Sigurbjörnsdóttir, Sara; Bergsteinsdóttir, Kristín; Debbache, Julien; Bismuth, Keren; Swing, Deborah A; Hallsson, Jón H; Larue, Lionel; Arnheiter, Heinz; Copeland, Neal G; Jenkins, Nancy A; Heidarsson, Petur O; Steingrímsson, Eiríkur
  3. EMBO Reports. 2024, Aug 21;
  1. 9.   Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4
  2. Zhou, Bing-Rui; Feng, Hanqiao; Huang, Furong; Zhu, Iris; Portillo-Ledesma, Stephanie; Shi,Dan; Zaret, Kenneth S; Schlick, Tamar; Landsman, David; Wang, Qianben; Bai, Yawen
  3. Molecular Cell. 2024, Jul 31;
  1. 10.   IRF4 requires ARID1A to establish plasma cell identity in multiple myeloma
  2. Bolomsky, Arnold; Ceribelli, Michele; Scheich, Sebastian; Rinaldi, Kristina; Huang, Da Wei; Chakraborty, Papiya; Pham, Lisette; Wright, George W; Hsiao, Tony; Morris, Vivian; Choi, Jaewoo; Phelan, James D; Holewinski,Ronald; Andresson,Thorkell; Wisniewski, Jan; Riley, Deanna; Pittaluga, Stefania; Hill, Elizabeth; Thomas, Craig J; Muppidi, Jagan; Young, Ryan M
  3. Cancer Cell. 2024, Jul 8; 42(7): 1185-1201.
  1. 11.   The Janus kinase 1 is critical for pancreatic cancer initiation and progression
  2. Shrestha, Hridaya; Rädler, Patrick D; Dennaoui, Rayane; Wicker, Madison N; Rajbhandari, Nirakar; Sun, Yunguang; Peck, Amy R; Vistisen, Kerry; Triplett, Aleata A; Beydoun, Rafic; Sterneck,Esta; Saur, Dieter; Rui, Hallgeir; Wagner, Kay-Uwe
  3. Cell Reports. 2024, May 10; 43(5): 114202.
  1. 12.   Transcriptionally-active "defective" HIV-1 proviruses and their association with immunological non-response to antiretroviral therapy
  2. Scrimieri, Francesca; Bastian, Estella; Smith, Mindy; Rehm, Catherine A; Morse, Caryn; Kuruppu, Janaki; McLaughlin, Mary; Chang,Weizhong; Sereti, Irini; Kovacs, Joseph A; Lane, H Clifford; Imamichi, Hiromi
  3. The Journal of Infectious Diseases. 2024, Jan 16;
  1. 13.   Multifaceted roles for STAT3 in gammaherpesvirus latency revealed through in vivo B cell knockout models
  2. Hogan, Chad H; Owens, Shana M; Reynoso, Glennys V; Liao, Yifei; Meyer,Thomas; Zelazowska, Monika A; Liu, Bin; Li, Xiaofan; Grosskopf, Anna K; Khairallah, Camille; Kirillov, Varvara; Reich, Nancy C; Sheridan, Brian S; McBride, Kevin M; Gewurz, Benjamin E; Hickman, Heather D; Forrest, J Craig; Krug, Laurie T
  3. mBio. 2024, Jan 03; e0299823.
  1. 14.   HIV-1 Transcription Inhibition Using Small RNA-Binding Molecules
  2. Khatkar, Pooja; Mensah, Gifty; Ning, Shangbo; Cowen, Maria; Kim, Yuriy; Williams, Anastasia; Abulwerdi, Fardokht A; Zhao, Yunjie; Zeng, Chen; Le Grice, Stuart F J; Kashanchi, Fatah
  3. Pharmaceuticals (Basel, Switzerland). 2023, Dec 25; 17(1):
  1. 15.   Genome-wide profiling of transcription factor activity in primary liver cancer using single-cell ATAC sequencing
  2. Craig, Amanda J; Silveira, Maruhen A Datsch; Ma, Lichun; Revsine, Mahler; Wang, Limin; Heinrich, Sophia; Rae, Zachary; Ruchinskas, Allison; Dadkhah,Kimia; Do, Whitney; Behrens, Shay; Mehrabadi, Farid R; Dominguez, Dana A; Forgues, Marshonna; Budhu, Anuradha; Chaisaingmongkol, Jittiporn; Hernandez, Jonathan M; Davis, Jeremy L; Tran,Bao; Marquardt, Jens U; Ruchirawat, Mathuros; Kelly, Michael; Greten, Tim F; Wang, Xin W
  3. Cell Reports. 2023, Nov 17; 42(11): 113446.
  1. 16.   Abundant binary promoter switches in lineage-determining transcription factors indicate a digital component of cell fate determination
  2. Li,Hongchuan; Rahman, Md Ahasanur; Ruesch, Michael; Eisele, Caprice D; Anderson,Erik; Wright,Paul; Cao, Jennie; Ratnayake, Shashikala; Chen, Qingrong; Yan, Chunhua; Meerzaman, Daoud; Abraham, Roshini S; Freud, Aharon G; Anderson,Steve
  3. Cell Reports. 2023, Nov 16; 42(11): 113454.
  1. 17.   The KIR2DL1 intermediate upstream element participates in gene activation
  2. Wright,Paul; Li,Hongchuan; Rahman, Md Ahasanur; Anderson,Erik; Karwan,Megan; Carrell,Jeff; Anderson,Steve
  3. Immunogenetics. 2023, Oct 06;
  1. 18.   Patterns of metastatic progression and association with clinical outcomes in canine osteosarcoma: A necropsy study of 83 dogs
  2. Silver, K I; Patkar, S; Mazcko, C; Berger,Erika; Beck, J A; LeBlanc, A K
  3. Veterinary and Comparative Oncology. 2023, Aug 17;
  1. 19.   HIV-1 usurps transcription start site heterogeneity of host RNA polymerase II to maximize replication fitness
  2. Nikolaitchik,Olga; Islam,Mohammad Saiful; Kitzrow,Jonathan; Duchon,Alice; Cheng,Zetao; Liu, Yang; Rawson, Jonathan M O; Shao,Wei; Nikolaitchik, Maria; Kearney,Mary; Maldarelli,Frank; Musier-Forsyth, Karin; Pathak,Vinay; Hu,Wei-Shau
  3. Proceedings of the National Academy of Sciences of the United States of America. 2023, Jun 06; 120(23): e2305103120.
  1. 20.   Heat shock factor 1 (HSF1) specifically potentiates c-MYC-mediated transcription independently of the canonical heat shock response
  2. Xu, Meng; Lin,Ling; Ram,Babul; Shriwas,Omprakash; Chuang, Kun-Han; Dai, Siyuan; Su, Kuo-Hui; Tang, Zijian; Dai,Chengkai
  3. Cell Reports. 2023, May 23; 42(6): 112557.
  1. 21.   Matrin3 regulates mitotic spindle dynamics by controlling alternative splicing of CDC14B
  2. Muys, Bruna R; Shrestha, Roshan L; Anastasakis, Dimitrios G; Pongor, Lorinc; Li, Xiao Ling; Grammatikakis, Ioannis; Polash, Ahsan; Chari,Raj; Gorospe, Myriam; Harris, Curtis C; Aladjem, Mirit I; Basrai, Munira A; Hafner, Markus; Lal, Ashish
  3. Cell Reports. 2023, Mar 15; 42(3): 112260.
  1. 22.   The fidelity of transcription in human cells
  2. Chung, Claire; Verheijen, Bert M; Zhang, Xinmin; Huang, Biao; Coakley, Aeowynn; McGann, Eric; Wade, Emily; Dinep-Schneider, Olivia; LaGosh, Jessica; Anagnostou, Maria-Eleni; Simpson, Stephen; Thomas, Kelly; Ernst, Mimi; Rattray, Allison; Lynch, Michael; Kashlev,Mikhail; Benayoun, Berenice A; Li, Zhongwei; Strathern,Jeffrey; Gout, Jean-Francois; Vermulst, Marc
  3. Proceedings of the National Academy of Sciences of the United States of America. 2023, Jan 31; 120(5): e2210038120.
  1. 23.   Non-specific and specific DNA binding modes of bacterial histone, HU, separately regulate distinct physiological processes through different mechanisms
  2. Verma, Subhash C; Harned,Adam; Narayan,Kedar; Adhya, Sankar
  3. Molecular Microbiology. 2023, Jan 27;
  1. 24.   Massively parallel reporter assays and variant scoring identified functional variants and target genes for melanoma loci and highlighted cell-type specificity
  2. Long, Erping; Yin, Jinhu; Funderburk, Karen M; Xu, Mai; Feng, James; Kane, Alexander; Zhang, Tongwu; Myers, Timothy; Golden, Alyxandra; Thakur, Rohit; Kong, Hyunkyung; Jessop, Lea; Kim, Eun Young; Jones, Kristine; Chari,Raj; Machiela, Mitchell J; Yu, Kai; Iles, Mark M; Landi, Maria Teresa; Law, Matthew H; Chanock, Stephen J; Brown, Kevin M; Choi, Jiyeon
  3. American Journal of Human Genetics. 2022, Nov 18;
  1. 25.   Single-cell sequencing reveals activation of core transcription factors in PRC2-deficient malignant peripheral nerve sheath tumor
  2. Zhang, Xiyuan; Lou, Hannah E; Gopalan, Vishaka; Liu, Zhihui; Jafarah, Hilda M; Lei, Haiyan; Jones, Paige; Sayers, Carly M; Yohe, Marielle E; Chittiboina, Prashant; Widemann, Brigitte C; Thiele, Carol J; Kelly,Michael; Hannenhalli, Sridhar; Shern, Jack F
  3. Cell Reports. 2022, Sep 20; 40(12): 111363.
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