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  1. 1.   Widespread distribution of transcriptionally active, clonally expanded, HIV-1 proviruses despite suppressive antiretroviral therapy
  2. Imamichi, Hiromi; Natarajan,Venkatachala; Scrimieri,Francesca; Smith, Mindy; Badralmaa,Yunden; Bosche,Marjorie; Hensien, Jack M; Buerkert, Thomas; Sherman,Brad; Sherman, Brad T; Singh, Kanal; Lane, H Clifford
  3. The Journal of Clinical Investigation. 2025, Apr 22;
  1. 2.   The differential interactomes of the KRAS splice variants identify BIRC6 as a ubiquitin ligase for KRAS4A
  2. Kochen Rossi, Juan; Nuevo-Tapioles, Cristina; O'Keefe, Rachel A; Hunkeler, Moritz; Schmoker, Anna M; Fissore-O'Leary, Mercedes; Su, Wenjuan; Ahearn, Ian M; Branco, Cristina; Cheong, Hakyung; Esposito,Dom; Clotea, Ioana; Ueberheide, Beatrix; Fischer, Eric S; Philips, Mark R
  3. Cell Reports. 2024, Dec 19; 44(1): 115087.
  1. 3.   Attenuating ribosome load improves protein output from mRNA by limiting translation-dependent mRNA decay
  2. Bicknell, Alicia A; Reid, David W; Licata, Marissa C; Jones, Adriana K; Cheng, Yi Min; Li, Mengying; Hsiao, Chiaowen Joyce; Pepin, Christopher S; Metkar, Mihir; Levdansky,Yevgen; Fritz, Brian R; Andrianova, Elizaveta A; Jain, Ruchi; Valkov,Eugene; Köhrer, Caroline; Moore, Melissa J
  3. Cell Reports. 2024, Apr 15; 43(4): 114098.
  1. 4.   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. 5.   Protocol for the saturation and multiplexing of genetic variants using CRISPR-Cas9
  2. Sahu,Sounak; Sullivan,Teresa; Southon,Eileen; Caylor,Dylan; Geh, Josephine; Sharan,Shyam
  3. STAR Protocols. 2023, Nov 08; 4(4): 102702.
  1. 6.   Detection of the DNA binding of transcription factors in situ at the single-cell resolution in cultured cells by proximity ligation assay
  2. Ram,Babul; Dai,Chengkai
  3. STAR Protocols. 2023, Nov 01; 4(4): 102692.
  1. 7.   AP-1/c-Fos supports SIV and HIV-1 latency in CD4 T cells infected in vivo
  2. Cobos Jiménez, Viviana; Geretz, Aviva; Tokarev, Andrey; Ehrenberg, Philip K; Deletsu, Selase; Machmach, Kawthar; Mudvari, Prakriti; Howard, J Natalie; Zelkoski, Amanda; Paquin-Proulx, Dominic; Del Prete,Greg; Subra, Caroline; Boritz, Eli A; Bosque, Alberto; Thomas, Rasmi; Bolton, Diane L
  3. iScience. 2023, Oct 20; 26(10): 108015.
  1. 8.   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. 9.   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. 10.   Promiscuous splicing-derived hairpins are dominant substrates of tailing-mediated defense of miRNA biogenesis in mammals
  2. Lee, Seungjae; Jee, David; Srivastava, Sid; Yang,Acong; Ramidi, Abhinav; Shang, Renfu; Bortolamiol-Becet, Diane; Pfeffer, Sébastien; Gu,Shuo; Wen, Jiayu; Lai, Eric C
  3. Cell Reports. 2023, Feb 16; 42(2): 112111.
  1. 11.   Comprehensive analysis of HIV reservoirs in elite controllers
  2. Kennedy, Brooke D; Blazkova, Jana; Justement, Jesse S; Shi, Victoria; Rai, M Ali; Manning, Maegan R; Praiss, Lauren; Gittens, Kathleen; Wender, Paul A; Patro,Sean; Wu,Xiaolin; Moir, Susan; Chun, Tae-Wook
  3. The Journal of Clinical Investigation. 2023, Feb 01; 133(3): e165446.
  1. 12.   A transient conformation facilitates ligand binding to the adenine riboswitch
  2. Wu, Lin; Chen, Dian; Ding,Jienyu; Liu, Yu
  3. iScience. 2021, Dec 17; 24(12): 103512.
  1. 13.   Recapitulation of cell-like KRAS4b membrane dynamics on complex biomimetic membranes
  2. Shrestha,Rebika; Chen,De; Frank,Peter; Nissley,Dwight; Turbyville,Tommy
  3. iScience. 2021, Dec 10; 25(1):
  1. 14.   The Cytokine Receptor IL-7Ra Impairs IL-2 Receptor Signaling and Constrains the In Vitro Differentiation of Foxp3+ Treg Cells
  2. Waickman, Adam T; Keller, Hilary R; Kim, Tae-Hyoun; Luckey, Megan A; Tai, Xuguang; Hong, Changwan; Molina-París, Carmen; Walsh,Scott; Park, Jung-Hyun
  3. iScience. 2020, AUG 21; 23(8): 101421.
  1. 15.   Two-color in situ hybridization of whole-mount mouse embryos
  2. Biris, K. K.; Yamaguchi, T. P.
  3. Methods in molecular biology (Clifton, N.J.). 2014 1092: 17-30.
  1. 16.   Collection and preparation of rodent embryonic samples for transcriptome study
  2. Golubeva, Y.; Symer, D.
  3. Methods in molecular biology (Clifton, N.J.). 2014 1092: 297-356.
  1. 17.   Protein/peptide transduction in metanephric explant culture
  2. Plisov, S.; Wang, H.; Tarasova, N.; Sharma, N.; Perantoni, A. O.
  3. Methods in molecular biology (Clifton, N.J.). 2014 1092: 255-67.
  1. 18.   Short- and long-term changes in gene expression mediated by the activation of TLR9
  2. Klaschik, S.; Tross, D.; Shirota, H.; Klinman, D. M.
  3. Molecular Immunology. 2010, Mar; 47(6): 1317-1324.
  1. 19.   RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases
  2. Shulman-Peleg, A.; Nussinov, R.; Wolfson, H. J.
  3. Nucleic Acids Research. 2009 37(Database issue): D369-D373.
  1. 20.   Global changes in gene expression and synergistic interactions induced by TLR9 and TLR3
  2. Tross, D.; Petrenko, L.; Klaschik, S.; Zhu, Q.; Klinman, D. M.
  3. Molecular Immunology. 2009 46(13): 2557-2564.
  1. 21.   Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins
  2. Ahmad, S.; Keskin, O.; Sarai, A.; Nussinov, R.
  3. Nucleic Acids Research. 2008 36(18): 5922-5932.
  1. 22.   Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition
  2. Akagi, K.; Li, J. F.; Stephens, R. M.; Volfovsky, N.; Symer, D. E.
  3. Genome Research. 2008 18(6): 869-880.
  1. 23.   A microarray analysis for differential gene expression for two cancer cell lines, DU145 non-drug resistant and RC.01 drug-resistant using R & bioconductor
  2. Alvord, W. G.; Roayaei, J. A.; Reinhold, W. C.; Quinones, O. A.; Weinstein, J. N.
  3. Amino Acids. 2008 35(4): 775-776.
  1. 24.   Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design
  2. Bauman, J. D.; Das, K.; Ho, W. C.; Baweja, M.; Himmel, D. M.; Clark, A. D.; Oren, D. A.; Boyer, P. L.; Hughes, S. H.; Shatkin, A. J.; Arnold, E.
  3. Nucleic Acids Research. 2008 36(15): 5083-5092.
  1. 25.   Intracellular interaction of interleukin-15 with its receptor alpha during production leads to mutual stabilization and increased bioactivity
  2. Bergamaschi, C.; Rosati, M.; Jalah, R.; Valentin, A.; Kulkarni, V.; Alicea, C.; Zhang, G. M.; Patel, V.; Felber, B. K.; Pavlakis, G. N.
  3. Journal of Biological Chemistry. 2008 283(7): 4189-4199.
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