Student Publications

Squeezed between hours at the bench, early mornings in online classes and the lecture hall, and conferences both near and far, BCMB students have still managed to put pen to paper (or fingertips to keyboard) and publish several fascinating articles in the past few years. Just a few of the more recent papers co-authored by BCMB students include:


  • Wang C, Jacewicz A, Delgado BD, Baradaran R, Long SB. Structures reveal gatekeeping of the mitochondrial Ca2+ uniporter by MICU1-MICU2. Elife. 2020 Jul 15;9:e59991. doi: 10.7554/eLife.59991. Epub ahead of print. PMID: 32667285
  • Abreu N, Levitz J. Optogenetic Techniques for Manipulating and Sensing G Protein-Coupled Receptor Signaling. Methods Mol Biol. 2020;2173:21-51. doi: 10.1007/978-1-0716-0755-8_2. PMID: 32651908
  • Sam J, Mercer EJ, Torregroza I, Banks KM, Evans T. Specificity, redundancy and dosage thresholds among gata4/5/6 genes during zebrafish cardiogenesis. Biol Open. 2020 Jun 24;9(6):bio053611. doi: 10.1242/bio.053611. PMID: 32580940; PMCID: PMC7327998
  • Ngo B, Kim E, Osorio-Vasquez V, et al. Limited Environmental Serine and Glycine Confer Brain Metastasis Sensitivity to PHGDH Inhibition [published online ahead of print, 2020 Jun 22]. Cancer Discov. 2020;CD-19-1228. doi:10.1158/2159-8290.CD-19-1228. PMID: 32571778
  • Han T, Goswami S, Hu Y, et al. Lineage reversion drives WNT independence in intestinal cancer [published online ahead of print, 2020 Jun 16]. Cancer Discov. 2020;CD-19-1536. doi:10.1158/2159-8290.CD-19-1536. PMID: 32546576
  • Wu W, Bhowmick R, Vogel I, Özer Ö, Ghisays F, Thakur RS, Sanchez de Leon E, Richter PH, Ren L, Petrini JH, Hickson ID, Liu Y. RTEL1 suppresses G-quadruplex-associated R-loops at difficult-to-replicate loci in the human genome. Nat Struct Mol Biol. 2020 May;27(5):424-437. doi: 10.1038/s41594-020-0408-6. Epub 2020 May 11. PMID: 32398827
  • Hulton CH, Costa EA, Shah NS, Quintanal-Villalonga A, Heller G, de Stanchina E, et al. Direct genome editing of patient-derived xenografts using CRISPR-Cas9 enables rapid in vivo functional genomics. Nature Cancer. 2020;1(3):359-69. doi: 10.1038/s43018-020-0040-8
  • Christopher H. Hulton, Emily A. Costa, Nisargbhai S. Shah, Alvaro Quintanal-Villalonga, Glenn Heller, Elisa de Stanchina, Charles M. Rudin & John T. Poirier. Direct genome editing of patient-derived xenografts using CRISPR-Cas9 enables rapid in vivo functional genomics. Nature. 2020 Mar 9.
  • Li X, Kim H, Litke JL, Wu J, Jaffrey SR. Fluorophore-Promoted RNA Folding and Photostability Enables Imaging of Single Broccoli-Tagged mRNAs in Live Mammalian Cells.  Angew Chem Int Ed Engl. 2020 Mar 9. PMID:31850609. 
  • Katti A, Foronda M, Zimmerman J, Diaz B, Zafra MP, Goswami S, Dow LE. GO: a functional reporter system to identify and enrich base editing activity. Nucleic Acids Res. 2020 Apr 6. PMID: 32112097
  • Acosta-Ruiz A, Gutzeit VA, Skelly MJ, Meadows S, Lee J, Parekh P, Orr AG, Liston C, Pleil KE, Broichhagen J, Levitz J. Branched Photoswitchable Tethered Ligands Enable Ultra-efficient Optical Control and Detection of G Protein-Coupled Receptors In Vivo. Neuron. 2020 Feb 5;105(3):446-463.e13. doi: 10.1016/j.neuron.2019.10.036. Epub 2019 Nov 26. PMID: 31784287; PMCID: PMC7216301  


  • Allwein B, Kelly C, Kammoonah S, Mayor T, Cameron DM. Prion-dependent proteome remodeling in response to environmental stress is modulated by prion variant and genetic background. Prion. 2019 Jan 13. PMID: 30773982

  • Li X, Kim H, Litke JL, Wu J, Jaffrey SR. Fluorophore-Promoted RNA Folding and Photostability Enables Imaging of Single Broccoli-Tagged mRNAs in Live Mammalian Cells.  Angew Chem Int Ed Engl. 2020 Mar 9. PMID:31850609.
  • Kim H1, Jaffrey SR2.A Fluorogenic RNA-Based Sensor Activated by Metabolite-Induced RNA Dimerization. Cell Chem Biol. 2019 Dec 19. PMID: 31631009 PMCID: PMC6939632.

  • Jiahui Wu, Sara Zaccara, Deepak Khuperkar, Hyaeyeong Kim, Marvin E. Tanenbaum & Samie R. Jaffrey. Live imaging of mRNA using RNA-stabilized fluorogenic proteins. Nature Methods. 2019 Aug 30. PMID: 31471614 PMCID: PMC6719798.

  • Zheng S, Abreu N, Levitz J, Kruse AC. Structural basis for KCTD-mediated rapid desensitization of GABAB signalling. Nature. 2019 Mar;567(7746):127-131. PubMed PMID: 30814734. Pubmed Central PMCID: PMC6405316.
  • Wu J, Minikes AM, Gao M, Bian H, Li Y, Stockwell BR, Chen ZN, Jiang X. Intercellular interaction dictates cancer cell ferroptosis via NF2-YAP signalling. Nature. 2019 Jul 24. PubMed PMID: 31341276.
  • Vardhana SA, Arnold PK, Rosen BP, Chen Y, Carey BW, Huangfu D, Carmona-Fontaine C, Thompson CB, Finley LWS. Glutamine independence is a selectable feature of pluripotent stem cells. Nature Metabolism. 2019 2019/07/01;1(7):676-687.
  • Munir A, Shuman S. Structure-Function Analysis of the Phosphoesterase Component of the Nucleic Acid End-Healing Enzyme Runella slithyformis HD-Pnk. Journal of bacteriology. 2019 Aug 15;201(16). PubMed PMID: 31160396.
  • Munir A, Abdullahu L, Banerjee A, Damha MJ, Shuman S. NAD(+)-dependent RNA terminal 2' and 3' phosphomonoesterase activity of a subset of Tpt1 enzymes. RNA (New York, NY). 2019 Jul;25(7):783-792. PubMed PMID: 31019096. Pubmed Central PMCID: PMC6573784.
  • Loizou E, Banito A, Livshits G, Ho YJ, Koche RP, Sanchez-Rivera FJ, Mayle A, Chen CC, Kinalis S, Bagger FO, Kastenhuber ER, Durham BH, Lowe SW. A Gain-of-Function p53-Mutant Oncogene Promotes Cell Fate Plasticity and Myeloid Leukemia through the Pluripotency Factor FOXH1. Cancer discovery. 2019 Jul;9(7):962-979. PubMed PMID: 31068365. Pubmed Central PMCID: PMC6606372.
  • Liu Y, Ji W, Shergalis A, Xu J, Delaney AM, Calcaterra A, Pal A, Ljungman M, Neamati N, Rehemtulla A. Activation of the Unfolded Protein Response via Inhibition of Protein Disulfide Isomerase Decreases the Capacity for DNA Repair to Sensitize Glioblastoma to Radiotherapy. Cancer research. 2019 Jun 1;79(11):2923-2932. PubMed PMID: 30996048. Pubmed Central PMCID: PMC6548663.
  • Liu EM, Martinez-Fundichely A, Diaz BJ, Aronson B, Cuykendall T, MacKay M, Dhingra P, Wong EWP, Chi P, Apostolou E, Sanjana NE, Khurana E. Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes. Cell systems. 2019 May 22;8(5):446-455.e448. PubMed PMID: 31078526.
  • Li QV, Dixon G, Verma N, Rosen BP, Gordillo M, Luo R, Xu C, Wang Q, Soh CL, Yang D, Crespo M, Shukla A, Xiang Q, Dundar F, Zumbo P, Witkin M, Koche R, Betel D, Chen S, Massague J, Garippa R, Evans T, Beer MA, Huangfu D. Genome-scale screens identify JNK-JUN signaling as a barrier for pluripotency exit and endoderm differentiation. Nature genetics. 2019 Jun;51(6):999-1010. PubMed PMID: 31110351. Pubmed Central PMCID: PMC6545159.
  • Hamieh M, Dobrin A, Cabriolu A, van der Stegen SJC, Giavridis T, Mansilla-Soto J, Eyquem J, Zhao Z, Whitlock BM, Miele MM, Li Z, Cunanan KM, Huse M, Hendrickson RC, Wang X, Riviere I, Sadelain M. CAR T cell trogocytosis and cooperative killing regulate tumour antigen escape. Nature. 2019 Apr;568(7750):112-116. PubMed PMID: 30918399.
  • Gao M, Yi J, Zhu J, Minikes AM, Monian P, Thompson CB, Jiang X. Role of Mitochondria in Ferroptosis. Molecular cell. 2019 Jan 17;73(2):354-363.e353. PubMed PMID: 30581146. Pubmed Central PMCID: PMC6338496.
  • Cohen SB, Bainter W, Johnson JL, Lin TY, Wong JCY, Wallace JG, Jones J, Qureshi S, Mir F, Qamar F, Cantley LC, Geha RS, Chou J. Human primary immunodeficiency caused by expression of a kinase-dead p110delta mutant. The Journal of allergy and clinical immunology. 2019 Feb;143(2):797-799.e792. PubMed PMID: 30336224. Pubmed Central PMCID: PMC6387453.
  • Boekhout M, Karasu ME, Wang J, Acquaviva L, Pratto F, Brick K, Eng DY, Xu J, Camerini-Otero RD, Patel DJ, Keeney S. REC114 Partner ANKRD31 Controls Number, Timing, and Location of Meiotic DNA Breaks. Molecular cell. 2019 Jun 6;74(5):1053-1068.e1058. PubMed PMID: 31003867. Pubmed Central PMCID: PMC6555648.
  • Banerjee A, Munir A, Abdullahu L, Damha MJ, Goldgur Y, Shuman S. Structure of tRNA splicing enzyme Tpt1 illuminates the mechanism of RNA 2'-PO4 recognition and ADP-ribosylation. Nature communications. 2019 Jan 15;10(1):218. PubMed PMID: 30644400. Pubmed Central PMCID: PMC6333775.
  • Acosta-Ruiz A, Broichhagen J, Levitz J. Optical Regulation of Class C GPCRs by Photoswitchable Orthogonal Remotely Tethered Ligands. Methods in molecular biology (Clifton, NJ). 2019;1947:103-136. PubMed PMID: 30969413. Pubmed Central PMCID: PMC6538505.


  • Zheng Y, Lin TY, Lee G, Paddock MN, Momb J, Cheng Z, Li Q, Fei DL, Stein BD, Ramsamooj S, Zhang G, Blenis J, Cantley LC. Mitochondrial One-Carbon Pathway Supports Cytosolic Folate Integrity in Cancer Cells. Cell. 2018 Nov 29;175(6):1546-1560.e1517. PubMed PMID: 30500537. Pubmed Central PMCID: PMC6568313.
  • Munir A, Banerjee A, Shuman S. NAD+-dependent synthesis of a 5'-phospho-ADP-ribosylated RNA/DNA cap by RNA 2'-phosphotransferase Tpt1. Nucleic acids research. 2018 Oct 12;46(18):9617-9624. PubMed PMID: 30202863. Pubmed Central PMCID: PMC6182162.
  • Munir A, Abdullahu L, Damha MJ, Shuman S. Two-step mechanism and step-arrest mutants of Runella slithyformis NAD(+)-dependent tRNA 2'-phosphotransferase Tpt1. RNA (New York, NY). 2018 Sep;24(9):1144-1157. PubMed PMID: 29884622. Pubmed Central PMCID: PMC6097658.
  • Farrants H, Gutzeit VA, Acosta-Ruiz A, Trauner D, Johnsson K, Levitz J, Broichhagen J. SNAP-Tagged Nanobodies Enable Reversible Optical Control of a G Protein-Coupled Receptor via a Remotely Tethered Photoswitchable Ligand. ACS chemical biology. 2018 Sep 21;13(9):2682-2688. PubMed PMID: 30141622. Pubmed Central PMCID: PMC6620112.


  • Song W, Filonov GS, Kim H, Hirsch M, Li X, Moon JD, Jaffrey SR. Imaging RNA polymerase III transcription using a photostable RNA-fluorophore complex. Nat Chem Biol. 2017 Nov 1. PMID: 28945233  

  • Poran A*, Nötzel C*, Aly O, Mencia-Trinchant N, Harris CT, Guzman ML, Hassane DC, Elemento O, Kafsack BF. Single-cell RNA sequencing reveals a signature of sexual commitment in malaria parasites. Nature. 2017 09/25/online; advance online publication. doi: 10.1038/nature24280. *authors contributed equally. Link to PubMed.
  • Poulos MG, Ramalingam P, Gutkin MC, Llanos P, Gilleran K, Rabbany SY, Butler JM. Endothelial transplantation rejuvenates aged hematopoietic stem cell function. J Clin Invest. 2017 Oct 16. pii: 93940. doi: 10.1172/JCI93940. [Epub ahead of print] PubMed PMID: 29035282.
  • Ramalingam P, Poulos MG, Butler JM. Regulation of the hematopoietic stem cell lifecycle by the endothelial niche. Curr Opin Hematol. 2017 Jul;24(4):289-299. doi: 10.1097/MOH.0000000000000350. Review. PubMed PMID: 28594660; PubMed Central PMCID: PMC5554937.
    • Khalaj M, Woolthuis CM, Hu W, Durham BH, Chu SH, Qamar S, Armstrong SA, Park CY. miR-99 regulates normal and malignant hematopoietic stem cell self-renewal. J Exp Med. 2017 Jul 21. pii: jem.20161595. doi: 10.1084/jem.20161595. [Epub ahead of print] PubMed PMID: 28733386; PubMed Central PMCID: PMC5551568.
    • Cook PJ, Thomas R, Kannan R, de Leon ES, Drilon A, Rosenblum MK, Scaltriti M, Benezra R, Ventura A. Somatic chromosomal engineering identifies BCAN-NTRK1 as a potent glioma driver and therapeutic target. Nat Commun. 2017 Jul 11;8:15987. doi: 10.1038/ncomms15987. PubMed PMID: 28695888; PubMed Central PMCID: PMC5508201.
    • Han T, Schatoff EM, Murphy C, Zafra MP, Wilkinson JE, Elemento O, Dow LE. R-Spondin chromosome rearrangements drive Wnt-dependent tumour initiation and maintenance in the intestine. Nat Commun. 2017 Jul 11;8:15945. doi: 10.1038/ncomms15945. PubMed PMID: 28695896
    • Chang AY, Dao T, Gejman RS, Jarvis CA, Scott A, Dubrovsky L, Mathias MD, Korontsvit T, Zakhaleva V, Curcio M, Hendrickson RC, Liu C, Scheinberg DA. A therapeutic T cell receptor mimic antibody targets tumor-associated PRAME peptide/HLA-I antigens. J Clin Invest. 2017 Jun 30;127(7):2705-2718. doi: 10.1172/JCI92335. Epub 2017 Jun 19. PubMed PMID: 28628042; PubMed Central PMCID: PMC5490756.
    • O'Rourke KP, Loizou E, Livshits G, Schatoff EM, Baslan T, Manchado E, Simon J, Romesser PB, Leach B, Han T, Pauli C, Beltran H, Rubin MA, Dow LE, Lowe SW. Transplantation of engineered organoids enables rapid generation of metastatic mouse models of colorectal cancer. Nat Biotechnol. 2017 Jun;35(6):577-582. doi: 10.1038/nbt.3837. Epub 2017 May 1. PubMed PMID: 28459450; PubMed Central PMCID: PMC5462850.
    • Deng P, Haynes CM. Mitochondrial dysfunction in cancer: Potential roles of ATF5 and the mitochondrial UPR. Semin Cancer Biol. 2017 May 10. pii: S1044-579X(17)30125-6. doi: 10.1016/j.semcancer.2017.05.002. [Epub ahead of print] Review. PubMed PMID: 28499833.
    • Kim IS, Heilmann S, Kansler ER, Zhang Y, Zimmer M, Ratnakumar K, Bowman RL, Simon-Vermot T, Fennell M, Garippa R, Lu L, Lee W, Hollmann T, Xavier JB, White RM. Microenvironment-derived factors driving metastatic plasticity in melanoma. Nat Commun. 2017 Feb 9;8:14343. doi: 10.1038/ncomms14343. PubMed PMID: 28181494; PubMed Central PMCID: PMC5309794.
    • Kang M, Garg V, Hadjantonakis AK. Lineage Establishment and Progression within the Inner Cell Mass of the Mouse Blastocyst Requires FGFR1 and FGFR2. Dev Cell. 2017 Jun 5;41(5):496-510.e5. doi: 10.1016/j.devcel.2017.05.003. Epub 2017 May 25. PubMed PMID: 28552559.
    • Liu Y, Pelham-Webb B, Di Giammartino DC, Li J, Kim D, Kita K, Saiz N, Garg V,  Doane A, Giannakakou P, Hadjantonakis AK, Elemento O, Apostolou E. Widespread Mitotic Bookmarking by Histone Marks and Transcription Factors in Pluripotent Stem Cells. Cell Rep. 2017 May 16;19(7):1283-1293. doi: 10.1016/j.celrep.2017.04.067. PubMed PMID: 28514649; PubMed Central PMCID: PMC5495017.
    • Khalaj M, Park CY. snoRNAs contribute to myeloid leukaemogenesis. Nat Cell Biol. 2017 Jun 29;19(7):758-760. doi: 10.1038/ncb3566. PubMed PMID: 28659642.
    • Yang Z, Peng YC, Gopalan A, Gao D, Chen Y, Joyner AL. Stromal hedgehog signaling maintains smooth muscle and hampers micro-invasive prostate cancer. Dis Model Mech. 2017 Jan 1;10(1):39-52. doi: 10.1242/dmm.027417. Epub 2016 Nov 30. PubMed PMID: 27935821; PubMed Central PMCID: PMC5278527
    • Chung SS, Eng WS, Hu W, Khalaj M, Garrett-Bakelman FE, Tavakkoli M, Levine RL, Carroll M, Klimek VM, Melnick AM, Park CY. CD99 is a therapeutic target on disease stem cells in myeloid malignancies. Sci Transl Med. 2017 Jan 25;9(374). pii: eaaj2025. doi: 10.1126/scitranslmed.aaj2025. PubMed PMID: 28123069
    • Poulos MG, Ramalingam P, Gutkin MC, Kleppe M, Ginsberg M, Crowley MJ, Elemento O, Levine RL, Rafii S, Kitajewski J, Greenblatt MB, Shim JH, Butler JM. Endothelial-specific inhibition of NF-κB enhances functional haematopoiesis. Nat  Commun. 2016 Dec 21;7:13829. doi: 10.1038/ncomms13829. PubMed PMID: 28000664; PubMed Central PMCID: PMC5187502.
    • Wang G, Hauver J, Thomas Z, Darst SA, Pertsinidis A. Single-Molecule Real-Time 3D Imaging of the Transcription Cycle by Modulation Interferometry. Cell. 2016 Dec 15;167(7):1839-1852.e21. doi: 10.1016/j.cell.2016.11.032. PubMed PMID: 27984731; PubMed Central PMCID: PMC5444671.
    • Deng P, Haynes CM. The mitokine quest(ion). Cell Res. 2016 Dec;26(12):1265-1266. doi: 10.1038/cr.2016.138. Epub 2016 Nov 25. PubMed PMID: 27886169; PubMed Central PMCID: PMC5143424