Publications

Selected first author/co-first author publications

2023

Altorki NK, Walsh ZH, Melms JC, Port JL, Lee BE, Nasar A, Spinelli C, Caprio L, Rogava M, Ho P, Christos PJ, Saxena A, Elemento O, Bhinder B, Ager C, Amin AD, Sanfilippo NJ, Mittal V, Borczuk AC, Formenti SC, Izar B, McGraw TE. (2023). Neoadjuvant durvalumab plus radiation versus durvalumab alone in stages I-III non-small cell lung cancer: survival outcomes and molecular correlates of a randomized phase II trial. Nat Commun. 14(1):8435.  

Bashkirova EV, Klimpert N, Monahan K, Campbell CE, Osinski J, Tan L, Schieren I, Pourmorady A, Stecky B, Barnea G, Xie XS, Abdus-Saboor I, Shykind BM, Marlin BJ, Gronostajski RM, Fleischmann A, Lomvardas S.(2023). Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice.  Elife. 12:RP87445.

Garretti F, Monahan C, Sloan N, Bergen J, Shahriar S, Kim SW, Sette A, Cutforth T, Kanter E, Agalliu D, Sulzer D. (2023).  Interaction of an α-synuclein epitope with HLA-DRB1^∗15:01 triggers enteric features in mice reminiscent of prodromal Parkinson's disease. Neuron. 111(21):3397-3413.

Garretti F, Monahan C, Sette A, Agalliu D, Sulzer D. (2022). T cells, α-synuclein and Parkinson disease. Handb Clin Neurol. 184:439-455.

Griffin AT, Vlahos LJ, Chiuzan C, Califano A. (2023). NaRnEA: An Information Theoretic Framework for Gene Set Analysis. Entropy (Basel). 25(3):542.

Ho P, Melms JC, Rogava M, Frangieh CJ, Poźniak J, Shah SB, Walsh Z, Kyrysyuk O, Amin AD, Caprio L, Fullerton BT, Soni RK, Ager CR, Biermann J, Wang Y, Khosravi-Maharlooei M, Zanetti G, Mu M, Fatima H, Moore EK, Vasan N, Bakhoum SF, Reiner SL, Bernatchez C, Sykes M, Mace EM, Wucherpfennig KW, Schadendorf D, Bechter O, Shah P, Schwartz GK, Marine JC, Izar B. (2023). The CD58-CD2 axis is co-regulated with PD-L1 via CMTM6 and shapes anti-tumor immunity. Cancer Cell. 41(7):1207-1221.e12.

Huang Y,Sheth RU, Zhao S, Cohen LA, Dabaghi K, Moody T, Sun Y, Ricaurte D, Richardson M, Velez-Cortes F, Blazejewski T, Kaufman A, Ronda C, Wang HH. (2023) High-throughput microbial culturomics using automation and machine learning. Nat Biotechnol. 41(10):1424-1433.

Kasbekar M, Mitchell CA, Proven MA, Pssegué E. (2023). Hematopoietic stem cells through the ages: A lifetime of adaptation to organismal demands. Cell Stem Cell. 30(11):1403-1420.

Kesner JS, Chen Z, Shi P, Aparicio AO, Murphy MR, Guo Y, Trehan A, Lipponen JE, Recinos Y, Myeku N, Wu X. (2023). Noncoding translation mitigation. Nature. 617(7960):395 402.

Kim S, Armand J, Safonov A, Zhang M, Soni RK, Schwartz G, McGuinness JE, Hibshoosh H, Razavi P, Kim M, Chandarlapaty S, Yang HW. (2023). Sequential activation of E2F via Rb degradation and c-Myc drives resistance to CDK4/6 inhibitors in breast cancer. Cell Rep. 42(11):113198.

Koss H, Crawley T, Palmer AG 3rd. (2023). Site-based description of R_1ρ relaxation in local reference frames. J Magn Reson. 347:107366.

Lampe GD, Sternberg SH. (2023). Novel recombinases for large DNA insertions. Nat Biotechnol. 41(4):471-472.

Lampe GD, King RT, Halpin-Healy TS, Klompe SE, Hogan MI, Vo PLH, Tang S, Chavez A, Sternberg SH.  (2023). Targeted DNA integration in human cells without double-strand breaks using CRISPR-associated transposases. Nat Biotechnol. 10.1038/s41587-023-01748-1.

Liu L, Casner RG, Guo Y, Wang Q, Iketani S, Chan JF, Yu J, Dadonaite B, Nair MS, Mohri H, Reddem ER, Yuan S, Poon VK, Chan CC, Yuen KY, Sheng Z, Huang Y, Bloom JD, Shapiro L, Ho DD. (2023). Antibodies targeting a quaternary site on SARS-CoV-2 spike glycoprotein prevent viral receptor engagement by conformational locking.  Immunity. 56(10):2442-2455.e8.

Mitchell CA, Verovskaya EV, Calero-Nieto FJ, Olson OC, Swann JW, Wang X, Hérault A, Dellorusso PV, Zhang SY, Svendsen AF, Pietras EM, Bakker ST, Ho TT, Göttgens B, Passegué E.  (2023). Nat Cell Biol. 25(1):30-41.

Savage TM, Vincent RL, Rae SS, Huang LH, Ahn A, Pu K, Li F, de Los Santos-Alexis K, Coker C, Danino T, Arpaia N. (2023). Chemokines expressed by engineered bacteria recruit and orchestrate antitumor immunity.Sci Adv. 9(10):eadc9436.

Rybkina K, Bell JN, Bradley MC, Wohlbold T, Scafuro M, Meng W, Korenberg RC, Davis-Porada J, Anderson BR, Weller RJ, Milner JD, Moscona A, Porotto M, Luning Prak ET, Pethe K, Connors TJ, Farber DL. (2023). SARS-CoV-2 infection and recovery in children: Distinct T cell responses in MIS-C compared to COVID-19.  J Exp Med. 220(8):e20221518.

Ressler AK, Goldstein DB.  (2023). Using reported pathogenic variants to identify therapeutic opportunities for genetic diseases. Mol Genet Genomic Med. 11(1):e2097.

Tomlinson KL, Riquelme SA, Baskota SU, Drikic M, Monk IR, Stinear TP, Lewis IA, Prince AS.  (2023). Staphylococcus aureus stimulates neutrophil itaconate production that suppresses the oxidative burst. Cell Rep. 42(2):112064.

Tomlinson KL, Chen YT, Junker A, Urso A, Wong Fok Lung T, Ahn D, Hofstaedter CE, Baskota SU, Ernst RK, Prince A, Riquelme SA. (2023). Ketogenesis promotes tolerance to Pseudomonas aeruginosa pulmonary infection. Cell Metab. 35(10):1767-1781.

von Krusenstiern AN, Robson RN, Qian N, Qiu B, Hu F, Reznik E, Smith N, Zandkarimi F, Estes VM, Dupont M, Hirschhorn T, Shchepinov MS, Min W, Woerpel KA, Stockwell BR.(2023). Identification of essential sites of lipid peroxidation in ferroptosis. Nat Chem Biol. 19(6):719-730.

Wang BZ,Nash TR, Zhang X, Rao J, Abriola L, Kim Y, Zakharov S, Kim M, Luo LJ, Morsink M, Liu B, Lock RI, Fleischer S, Tamargo MA, Bohnen M, Welch CL, Chung WK, Marx SO, Surovtseva YV, Vunjak-Novakovic G, Fine BM. (2023). Engineered cardiac tissue model of restrictive cardiomyopathy for drug discovery. Cell Rep Med. 4(3):100976.

Zagelbaum J, Schooley A, Zhao J, Schrank BR, Callen E, Zha S, Gottesman ME, Nussenzweig A, Rabadan R, Dekker J, Gautier J. (2023). Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization. Nat Struct Mol Biol. 30(1):99-106.

2022

Cho JD, Yang M, Santa-Maria I. (2022). Modeling Alzheimer's disease: considerations for a better translational and replicable mouse model. Neural Regen Res. 17(11):2448-2449.

Chen CW, Potenski AM, Colón Ortiz CK, Avrutsky MI, Troy CM. (2022). In vivo Vascular Injury Readouts in Mouse Retina to Promote Reproducibility. Vis Exp. (182):10.3791/63782.

Cohen AO, Woo SH, Zhang J, Cho J, Ruiz ME, Gong J, Du R, Yarygina O, Jafri DZ, Bachelor MA, Finlayson MO, Soni RK, Hayden MS, Owens DM. (2022). Tbc1d10c is a selective, constitutive suppressor of the CD8 T-cell anti-tumor response. Oncoimmunology. 11(1):2141011.

Colón Ortiz C, Neal AM, Avrutsky MI, Choi M, Smart J, Lawson J, Troy CM. (2022). Neurovascular injury associated non-apoptotic endothelial caspase-9 and astroglial caspase-9 mediate inflammation and contrast sensitivity decline. Cell Death Dis. 13(11):937.

Colón Ortiz CK, Potenski AM, Johnson KV, Chen CW, Snipas SJ, Jean YY, Avrutsky MI, Troy CM. (2022). Quantification of Immunostained Caspase-9 in Retinal Tissue. Vis Exp (185):10.3791/64237.

Flynn, E., and Lappalainen, T. (2022). Functional Characterization of Genetic Variant Effects on Expression. Annu Rev Biomed Data Sci.

Flynn, E.D., Tsu, A.L., Kasela, S., Kim-Hellmuth, S., Aguet, F., Ardlie, K.G., Bussemaker, H.J., Mohammadi, P., and Lappalainen, T. (2022). Transcription factor regulation of eQTL activity across individuals and tissues. PLoS Genet. 18, e1009719.

Giangreco, N.P., Elias, J.E., and Tatonetti, N.P. (2022). No population left behind: Improving paediatric drug safety using informatics and systems biology. Br J Clin Pharmacol. 88, 1464-1470.

Giangreco, N.P.,and Tatonetti, N.P. (2022). A database of pediatric drug effects to evaluate ontogenic mechanisms from child growth and development. Med (N Y). 3(8):579-595.e7

Hobson, B.D., Choi, S.J., Mosharov, E.V., Soni, R.K., Sulzer, D., and Sims, P.A. (2022). Subcellular proteomics of dopamine neurons in the mouse brain. Elife 11.

Hobson, B.D., Kong, L., Angelo, M.F., Lieberman, O.J., Mosharov, E.V., Herzog, E., Sulzer, D., and Sims, P.A. (2022). Subcellular and regional localization of mRNA translation in midbrain dopamine neurons. Cell Reports. 38, 110208.

Hoffmann FT, Kim M, Beh LY, Wang J, Vo PLH, Gelsinger DR, George JT, Acree C, Mohabir JT, Fernández IS, Sternberg SH. (2022). Selective TnsC recruitment enhances the fidelity of RNA-guided transposition. Nature. 609(7926):384-393.

Huang, Y., Sheth, R.U., Kaufman, A., and Wang, H.H. (2020). Scalable and cost-effective ribonuclease-based rRNA depletion for transcriptomics. Nucleic Acids Research. 48, e20.

Kanai M, Yeo T, Asua V, Rosenthal PJ, Fidock DA, Mok S. (2022). Comparative Analysis of Plasmodium falciparum Genotyping via SNP Detection, Microsatellite Profiling, and Whole-Genome Sequencing. Antimicrob Agents Chemother. 66(1):e0116321.

Klompe, S.E., Jaber, N., Beh, L.Y., Mohabir, J.T., Bernheim, A., and Sternberg, S.H. (2022). Evolutionary and mechanistic diversity of Type I-F CRISPR-associated transposons. Mol Cell. 82, 616-628 e615.

Li T, Akinade T, Zhou J, Wang H, Tong Q, He S, Rinebold E, Valencia Salazar LE, Bhansali D, Zhong Y, Ruan J, Du J, Dalerba P, Leong KW.  (2022). Therapeutic Nanocarriers Inhibit Chemotherapy-Induced Breast Cancer Metastasis. Adv Sci (Weinh). 9(33):e2203949.

Metz JB, Hornstein NJ, Sharma SD, Worley J, Gonzalez C, Sims PA. (2022). High-throughput translational profiling with riboPLATE-seq.  Sci Rep. 12(1):5718.

Rapp M, Shapiro L, Frank J. (2022). Contributions of single-particle cryoelectron microscopy toward fighting COVID-19. Trends Biochem Sci. 47(2):117-123.

Rybkina K, Davis-Porada J, Farber DL. (2022). Tissue immunity to SARS-CoV-2: Role in protection and immunopathology. Immunol Rev. 309(1):25-39.

Sheng J,Hod EA, Vlad G, Chavez A. (2022). Quantifying protein abundance on single cells using split-pool sequencing on DNA-barcoded antibodies for diagnostic applications. Sci Rep. 12(1):884.

Velez-Cortes F, Wang H. Characterization and Spatial Mapping of the Human Gut Metasecretome. (2022). mSystems. 7(6):e0071722.

Wang, B.Z.,Luo, L.J., and Vunjak-Novakovic, G. (2022). RNA and Protein Delivery by Cell-Secreted and Bioengineered Extracellular Vesicles. Adv Healthc Mater. 11, e2101557.

Wang, P., Casner, R.G., Nair, M.S., Yu, J., Guo, Y., Wang, M., Chan, J.F., Cerutti, G., Iketani, S., Liu, L., et al. (2022). A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. Emerg Microbes Infect. 11, 147-157.

2021

Boyle, L., Rao, L., Kaur, S., Fan, X., Mebane, C., Hamm, L., Thornton, A., Ahrendsen, J.T., Anderson, M.P., Christodoulou, J., Gennerich, A., Shen, Y., Chung, W.K. (2021). Genotype and defects in microtubule-based motility correlate with clinical severity in KIF1A-associated neurological disorder. HGG Adv. 2(2):100026. 

Broyde, J., Simpson, D.R., Murray, D., Paull, E.O., Chu, B. W., Tagore, S., Jones, S.J., Griffin, A.T., Giorgi, F.M., Lachmann, A., Jackson, P., Sweet-Cordero, E.A., Honig, B. and Calfiano, A. (2021). Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses. Nature Biotech. 39:215-224.

Cai SS, Li T, Akinade T, Zhu Y, Leong KW. (2021). Drug delivery carriers with therapeutic functions. Adv Drug Deliv Rev. 76:113884.

Cerutti G, Rapp M, Guo Y, Bahna F, Bimela J, Reddem ER, Yu J, Wang P, Liu L, Huang Y, Ho DD, Kwong PD, Sheng Z, Shapiro L.  (2021). Structural basis for accommodation of emerging B.1.351 and B.1.1.7 variants by two potent SARS-CoV-2 neutralizing antibodies. Structure. 29(7):655-663.e4.

Cho JD, Kim YA, Rafikian EE, Yang M, Santa-Maria I. (2021). Marked Mild Cognitive Deficits in Humanized Mouse Model of Alzheimer's-Type Tau Pathology. Front Behav Neurosci. 15:634157.

Coleman, I., and Korem, T. (2021). Embracing Metagenomic Complexity with a Genome-Free Approach. mSystems. 6, e0081621.

Collins, A., Mitchell, C.A., and Passegue, E. (2021). Inflammatory signaling regulates hematopoietic stem and progenitor cell development and homeostasis. The Journal of Experimental Medicine. 218.

Crawley, T. and Palmer III, A.G. (2021). Approximate Representations of Shaped Pulses Using the Homotopy Analysis Method. Magnetic Resonance. 2(1):175-186.

Crawley, T. and Palmer III, A.G. (2021). Bootstrap Aggregation for Model Selection in the Model-free Formalism. Magnetic Resonance. 2(1):251-264.

Dhindsa, R.S., Zoghbi, A.W., Krizay, D.K., Vasavda, C., & Goldstein, D.B. (2021). A Transcriptome-Based Drug Discovery Paradigm for Neurodevelopmental Disorders. Annals of Neurology. 89(2), 199-211.

Giangreco, N.P., Lebreton, G., Restaino, S., Jane Farr, M., Zorn, E., Colombo, P.C., Patel, J., Levine, R., Truby, L., Soni, R.K., et al. (2021). Plasma kallikrein predicts primary graft dysfunction after heart transplant. The Journal of Heart and Lung Transplantation: the official publication of the International Society for Heart Transplantation. 40, 1199-1211.

Giangreco, N.P., Lina, S., Qian, J., Kuoame, A., Subbian, V., Boerwinkle, E., Cicek, M., Clark, C.R., Cohen, E., Gebo, K.A., et al. (2021). Pediatric data from the All of Us research program: demonstration of pediatric obesity over time. JAMIA Open. 4, ooab112.

Giangreco, N.P., and Tatonetti, N.P. (2021). Evaluating risk detection methods to uncover ontogenic-mediated adverse drug effect mechanisms in children. BioData Min. 14:34.

Gomez K, Rabadan R. (2021). A persistent look at how tumours evade therapy. Nature. 596(7873):491-493.

Hegewisch-Solloa, E., Seo, S., Mundy-Bosse, B.L., Mishra, A., Waldman, E.H., Maurrasse, S., Grunstein, E., Connors, T.J., Freud, A.G., and Mace, E.M. (2021). Differential Integrin Adhesome Expression Defines Human NK Cell Residency and Developmental Stage. Journal of Immunology. 207, 950-965.

Ho, T.T.*, Dellorusso, P.V.*, Verovskaya E.V.*, Bakker S.T., Flach J., Smith L.K., Ventura P.B., Lansinger O.M., Herault A., Zhang S.Y., Kang Y.A., Mitchell C.A., Villeda S.A., Passegue E. (2021). Aged hematopoietic stem cells are refractory to bloodborne systemic rejuvenation interventions. J Exp Med. 218(7).

Liang, X.*, Qiu, X.*, Dionne, G.*, Cunningham, C.L., Pucak, M.L., Peng, G., Kim, Y.H., Lauer, A., Shapiro, L., and Muller, U. (2021). CIB2 and CIB3 are auxiliary subunits of the mechanotransduction channel of hair cells. Neuron. 109(13):2131-2149.e15

Liu, B., Wang, B., Zhang, X., Lock, R., Nash, T., & Vunjak-Novakovic, G. (2021). Cell type-specific microRNA therapies for myocardial infarction. Science Translational Medicine. 13(580), eabd0914.

Moon C.S., Reglero C., Cortes J.R., Quinn S.A., Alvarez S., Zhao J., Lin W.W., Cooke A.J., Abate F., Soderquist C.R., Fiñana C., Inghirami G., Campo E., Bhagat G., Rabadan R., Palomero T., Ferrando A.A. (2021). FYN-TRAF3IP2 induces NF-κB signaling-driven peripheral T cell lymphoma. Nat Cancer. 2(1):98-113.

Murithi, J.M., Pascal, C., Bath, J., Boulenc, X., Gnadig, N.F., Pasaje, C.F.A., Rubiano, K., Yeo, T., Mok, S., Klieber, S., et al., (2021). The antimalarial MMV688533 provides potential for single-dose cures with a high barrier to Plasmodium falciparum parasite resistance. Science Translational Medicine. 13.

Obradovic, A., Chowdhury, N., Haake, S.M., Ager, C., Wang, V., Vlahos, L., Guo, X.V., Aggen, D.H., Rathmell, W.K., Jonasch, E., et al. (2021). Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages. Cell. 184, 2988-3005 e2916.

Paik, D.H. and Farber, D.L. (2021). Anti-viral protective capacity of tissue resident memory T cells. Current Opinion in Virology. 46, 20–26.

Paik, D.H. and Farber, D.L. (2021). Influenza infection fortifies local lymph nodes to promote lung-resident heterosubtypic immunity. The Journal of Experimental Medicine. 218(1), e20200218.

Park, J., and Wang, H.H. (2021). Systematic dissection of sigma(70) sequence diversity and function in bacteria. Cell Reports. 36, 109590.

Park, J., Yim, S.S., and Wang, H.H. (2021). High-Throughput Transcriptional Characterization of Regulatory Sequences from Bacterial Biosynthetic Gene Clusters. ACS Synth Biol. 10, 1859-1873.

Paull, E.O.*, Aytes, A.*, Jones, S.J.*, Subramaniam, P.S., Giorgi, F.M., Douglass, E.F., Tagore, S., Chu, B., Vasciaveo, A., Zheng, S., Verhaak, R., Abate-Shen, C., Alvarez, M.J., & Califano, A. (2021). A modular master regulator landscape controls cancer transcriptional identity. Cell. 184(2), 334-351.e20. 

Poon, M.M.L., Rybkina, K., Kato, Y., Kubota, M., Matsumoto, R., Bloom, N.I., Zhang, Z., Hastie, K.M., Grifoni, A., Weiskopf, D., et al. (2021). SARS-CoV-2 infection generates tissue-localized immunological memory in humans. Sci Immunol 6, eabl9105.

Rapp, M., Guo Y., Reddem E.R., Yu J., Liu L., Wang P., Cerutti G., Katsamba P., Bimela J.S., Bahna F.A., Mannepalli S.M., Zhang B., Kwong P.D., Huang Y., Ho D.D., Shapiro L., Sheng Z. (2021). Modular basis for potent SARS-CoV-2 neutralization by a prevalent VH1-2-derived antibody class. Cell Rep. 2021;35(1):108950

Resnick, S.J., Iketani, S., Hong, S.J., Zask, A., Liu, H., Kim, S., Melore, S., Lin, F.Y., Nair, M.S., Huang, Y., et al. (2021). Inhibitors of Coronavirus 3CL Proteases Protect Cells from Protease-Mediated Cytotoxicity. J Virol. 95, e0237420.

Tamargo, M.A., Nash, T.R., Fleischer, S., Kim, Y., Vila, O.F., Yeager, K., Summers, M., Zhao, Y., Lock, R., Chavez, M., et al. (2021). milliPillar: A Platform for the Generation and Real-Time Assessment of Human Engineered Cardiac Tissues. ACS Biomater Sci Eng. 7, 5215-5229.

Tate, T., Xiang, T., Wobker, S.E., Zhou, M., Chen, X., Kim, H., Batourina, E., Lin, C.S., Kim, W.Y., Lu, C., et al. (2021). Pparg signaling controls bladder cancer subtype and immune exclusion. Nature Communications. 12, 6160.

Thomas, D.G., Wei, Y., & Tall, A.R. (2021). Lipid and metabolic syndrome traits in coronary artery disease: a Mendelian randomization study. Journal of Lipid Research. 62:100044

Tomlinson, K.L., Lung, T., Dach, F., Annavajhala, M.K., Gabryszewski, S.J., Groves, R.A., Drikic, M., Francoeur, N.J., Sridhar, S.H., Smith, M.L., Khanal, S., Britto, C.J., Sebra, R., Lewis, I., Uhlemann, A.C., Kahl, B.C., Prince, A.S., & Riquelme, S.A. (2021). Staphylococcus aureus induces an itaconate-dominated immunometabolic response that drives biofilm formation. Nature Communications. 12(1), 1399.

Tomlinson, K.L., Prince, A.S., and Wong Fok Lung, T. (2021). Immunometabolites Drive Bacterial Adaptation to the Airway. Front Immunol. 12, 790574.

Usmanova, D.R., Plata, G., and Vitkup, D. (2021). The Relationship between the Misfolding Avoidance Hypothesis and Protein Evolutionary Rates in the Light of Empirical Evidence. Genome Biol Evol. 13.

Wang, P., Casner, R.G., Nair, M.S., Wang, M., Yu, J., Cerutti, G., Liu, L., Kwong, P.D., Huang, Y., Shapiro, L., et al. (2021). Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization. Cell Host Microbe. 29, 747-751 e744.

2020

Abrams, J., Roybal, D., Chakouri, N., Katchman, A.N., Weinberg, R., Yang, L., Chen, B.X., Zakharov, S.I., Hennessey, J.A., Avula, U., Diaz, J., Wang, C., Wan, E.Y., Pitt, G.S., Ben-Johny, M., & Marx, S.O. 2020. Fibroblast growth factor homologous factors tune arrhythmogenic late NaV1.5 current in calmodulin binding-deficient channels. JCI Insight. 5(19), e141736.

Avrutsky, M.I., Colon Ortiz, C., Johnson, K.V., Potenski, A.M. Chen, C.W., Lawson, J.M., White, A.J., Yuen, S.K., Morales, F.M., Canepa, E., Snipas, S.J., Salvesen, G.S., Jean, Y.J., and Troy, C.M., 2020. Endothelial activation of caspase-9 promotes neurovascular injury in retinal vein occlusion. Nature Communications. 11(1):3173

Blattman, S.B., Jiang, W., Oikonomou, P., and Tavazoie, S., 2020. Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing. Nature Microbiology. 5, 1192-1201

Brandt, M., Gokden, A., Ziosi, M., and Lappalainen, T.A., 2020. Polyclonal allelic expression assay for detecting regulatory effects of transcript variants. Genome Med. 12(1):79.

Chramiec, A., Teles, D., Yeager, K., Marturano-Kruik, A., Pak, J., Chen, T., Hao, L., Wang, M., Lock, R., Tavakol, D.N., Lee, M.B., Kim, J., Ronaldson-Bouchard, K., and Vunjak-Novakovic, G., 2020. Integrated human organ-on-a-chip model for predictive studies of anti-tumor drug efficacy and cardiac safety. Lab on a Chip. 20(23), 4357–4372. 

Costabile, B.K., Kim, Y.K., Chen, Y., Clarke, O.B., Quadro, L., Mancia, F., 2020. Sample preparation for structural and functional analyses of the STRA6 receptor for retinol-binding protein. Methods Enzymol. 637:95-117.

Fan, J., Du, W., Kim-Muller, J. Y., Son, J., Kuo, T., Larrea, D., Garcia, C., Kitamoto, T., Kraakman, M.J., Owusu-Ansah, E., Cirulli, V., & Accili, D. 2020. Cyb5r3 links FoxO1-dependent mitochondrial dysfunction with β-cell failure. Molecular Metabolism. 34, 97–111.

Georgieva, D., Liu, Q., Wang, K., and Egli, D. 2020. Detection of base analogs incorporated during DNA replication by nanopore sequencing. Nucleic Acids
Research. 48, e88.

Giangreco, N.P., Elias, J.E., and Tatonetti, N.P. 2020. No population left behind: Improving paediatric drug safety using informatics and systems biology. Br J Clin Pharmacol. Dec 17. doi: 10.1111/bcp.14705. Online ahead of print.

Goodman, J.H. and Ferrante, A.W., Jr 2020. Fighting for Fat: Gluttonous Tumors and Starved T Cells. Cell. 183(7), 1739–1741.

Halpin-Healy, T.S., Klompe, S.E., Sternberg, S.H., and Fernández, I.S. 2020. Structural basis of DNA targeting by a transposon-encoded CRISPR–Cas system. Nature. 577(7789), 271-274.

Hill, V.M., O'Connor, R.M., & Shirasu-Hiza, M. 2020. Tired and stressed: Examining the need for sleep. The European Journal of Neuroscience. 51(1), 494–508.

Hobson, B.D., Kong, L., Hartwick, E.W., Gonzalez, R.L., & Sims, P.A. 2020. Elongation inhibitors do not prevent the release of puromycylated nascent polypeptide chains from ribosomes. eLife. 9, e60048.

Huang, Y., Sheth, R.U., Kaufman, A., and Wang, H.H. 2020. Scalable and cost-effective ribonuclease-based rRNA depletion for transcriptomics. Nucleic Acids Research 48, e20.

Ji, B.W.*, Sheth, R.U.*, Dixit, P.D., Tchourine, K., & Vitkup, D. 2020. Macroecological dynamics of gut microbiota. Nature Microbiology. 5(5), 768–775.

Huang, Y., Sheth, R.U., Kaufman, A., and Wang, H.H., 2020. Scalable and cost-effective ribonuclease-based rRNA depletion for transcriptomics. Nucleic Acids Res. 48(4):e20.

Liu, C.*, Tate, T.*, Batourina E., Truschel S.T., Potter S., Adam M., Xiang, T., Picard, M., Reiley, M., Schneider, K., Tamargo, M., Lu, C., Chen, X., He, J., Kim, H., Mendelsohn, C.L. 2020. Pparg promotes differentiation and regulates mitochondrial gene expression in bladder epithelial cells. Nat Commun.

Liu, Z., Yuan, J., Lasorella, A., Iavarone, A., Bruce, J.N., Canoll, P., and Sims, P.A. 2020. Integrating single-cell RNA-seq and imaging with SCOPE-seq2. Scientific Reports. 10, 19482.

Luo, K.L., Underwood, R. S., & Greenwald, I. 2020. Positive autoregulation of lag-1 in response to LIN-12 activation in cell fate decisions during C. elegans reproductive system development. Development (Cambridge, England). 147(18), dev193482.

Murithi, J.M., Owen, E.S., Istvan, E.S., Lee, M.C.S., Ottilie, S., Chibale, K., Goldberg, D.E., Winzeler, E.A., Llinás, M., Fidock, D.A., Vanaerschot, M., 2020. Combining Stage Specificity and Metabolomic Profiling to Advance Antimalarial Drug Discovery. Cell Chemical Biology. 27, 2, 158-171.e3.

Obradovic, A.Z., Dallos, M.C., Zahurak, M.L., Partin, A.W., Schaeffer, E.M., Ross, A.E., Allaf, M.E., Nirschl, T.R., Liu, D., Chapman, C.G., O'Neal, T., Cao, H., Durham, J.N., Guner, G., Baena-Del Valle, J.A., Ertunc, O., De Marzo, A.M., Antonarakis, E.S., & Drake, C.G. 2020. T-Cell Infiltration and Adaptive Treg Resistance in Response to Androgen Deprivation With or Without Vaccination in Localized Prostate Cancer. Clinical Cancer Research: an official journal of the American Association for Cancer Research. 26(13), 3182–3192.

Price, J.C., Azizi, E., Naiche, L.A., Parvani, J.G., Shukla, P., Kim, S., Slack-Davis, J.K., Pe'er, D., & Kitajewski, J. K. 2020. Notch3 signaling promotes tumor cell adhesion and progression in a murine epithelial ovarian cancer model. PloS One. 15(6), e0233962.

Tan, Y.Z. and Carragher, B. 2020. Seeing Atoms: Single-Particle Cryo-EM Breaks the Atomic Barrier. Mol Cell. 80, 938-939.

Tan, Y.Z., Rodrigues, J., Keener, J.E., Zheng, R.B., Brunton, R., Kloss, B., Giacometti, S.I., Rosario, A.L., Zhang, L., Niederweis, M., et al. (2020a). Cryo-EM structure of arabinosyltransferase EmbB from Mycobacterium smegmatis. Nature Communications. 11, 3396.

Tan, Y.Z., Zhang, L., Rodrigues, J., Zheng, R.B., Giacometti, S.I., Rosario, A.L., Kloss, B., Dandey, V.P., Wei, H., Brunton, R., et al. (2020b). Cryo-EM Structures and Regulation of Arabinofuranosyltransferase AftD from Mycobacteria. Mol Cell. 78, 683-699 e611.

Tenen, C.C. and Greenwald, I. (2019). Cell Non-autonomous Function of daf-18/PTEN in the Somatic Gonad Coordinates Somatic Gonad and Germline Development in C. elegans Dauer Larvae. Current Biology. 29(6), 1064–1072.e8.

Thangaraj, P.M., Kummer, B.R., Lorberbaum, T., Elkind, M., & Tatonetti, N.P. 2020. Comparative analysis, applications, and interpretation of electronic health record-based stroke phenotyping methods. BioData Mining. 13(1), 21.

Thomas, D.G., Wei, Y., & Tall, A.R. 2020. Lipid and Metabolic Syndrome Traits in Coronary Artery Disease: A Mendelian Randomization Study. Journal of Lipid Research. jlr.P120001000. Advance online publication.

Wu, F., Strand, A., Ober, C., Wall, J.D., Moorjani, P., and Przeworski, M., 2020. A comparison of humans and baboons suggests germline mutations do not track cell divisions. PloS Biology. 18:e3000838

Yang, J. and Tavazoie, S. 2020. Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress. PloS One. 15(11), e0239528.

2019

Bashkirova E. and Lomvardas S. 2019. Olfactory receptor genes make the case for inter-chromosomal interactions. Curr Opin Genet Dev. 55:106-113.

Chramiec, A. and Vunjak-Novakovic, G. 2019. Tissue engineered models of healthy and malignant human bone marrow. Advanced Drug Delivery Reviews. 140, 78–92. 

Das Sharma, S.*, Metz, J.*, Li, H., Hobson, B.D., Hornstein, N., Sulzer, D., Tang, G., and Sims, P.A. 2019. Widespread Alterations in Translation Elongation in the Brain of Juvenile Fmr1 Knockout Mice. Cell Rep. 26:3313-3322 e3315.

Dieck, C.L. and Ferrando, A. 2019. Genetics and mechanisms of NT5C2-driven chemotherapy resistance in relapsed ALL. Blood. 133:2263-2268

Eberle-Singh, J.A., Sagalovskiy, I., Maurer, H.C., Sastra, S.A., Palermo, C.F., Decker, A.R., Kim, M.J., Sheedy, J., Mollin, A., Cao, L., Hu, J., Branstrom, A., Weetal, M., and Olive, K.P., 2019. Effective delivery of a microtubule polymerization inhibitor synergizes with standard regimens in models of pancreatic ductal adenocarcinoma. Clin Cancer Res. 25(18): 5545-5560

Eckels, E.C., Haldar, S., Tapia-Rojo, R., Rivas-Pardo, J.A., and Fernandez, J.M. 2019. The Mechanical Power of Titin Folding. Cell Rep. 27:1836-1847 e1834.

Fu, Z., Indrisiunaite, G., KaledhonkarS., Shah, B., Sun, M., Chen, B., Grassucci, R.A., Ehrenberg, M., and Frank, J. 2019. The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy. Nat Commun. 10:2579.

Groopman, E.E., Goldstein, D.B., and Gharavi, A.G. 2019. Diagnostic Utility of Exome Sequencing for Kidney Disease. Reply. N Engl J Med. 380:2080-2081.

Groopman, E.E. and Gharavi, A.G. 2019. Expanding opportunities and emerging challenges: broadening the scope of genetic testing in nephrology. Kidney Int. 95:743-746.

Groopman, E.E., Marasa, M., Cameron-Christie, S., …, Platt, A., Goldstein, D.B., and Gharavi, A.G. 2019. Diagnostic Utility of Exome Sequencing for Kidney Disease. N Engl J Med. 380:142-151.

Hobson, B.D. and Sims, P.A. 2019. Critical Analysis of Particle Detection Artifacts in Synaptosome Flow Cytometry. eNeuro. 6.

Ji, B.W.*, Sheth, R.U.*, Dixit, P.D., Huang, Y., Kaufman, A., Wang, H.H., and Vitkup, D., 2019. Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling. Nature Methods. 16(8):731-736.

Kaledhonkar, S.*, Fu, Z.*, Caban, K., Li, W., Chen, B., Sun, M., Gonzalez, Jr., R.L., and Frank, J. 2019. Late steps in bacterial translation initiation visualized using time-resolved cryo-EM. Nature. 570:400-404. 

Klompe, S. E., Vo, P.L., Halpin-Healy, T.S., and Sternberg, S.H. 2019. Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration. Nature. 571(7764), 219-225.

Lee, H., Bao, S., Qian, Y., Geula, S., Leslie, J., Zhang, C., Hanna, J. H., & Ding, L. (2019). Stage-specific requirement for Mettl3-dependent m6A mRNA methylation during haematopoietic stem cell differentiation. Nature Cell Biology. 21(6), 700–709.

Levitin, H.M., Yuan, J., Cheng, Y.L., Ruiz, F.J., Bush, E.C., Bruce, J.N., Canoll, P., Iavarone, A., Lasorella, A., Blei, D.M., and Sims, P.A.,2019. De novo gene signature identification from single-cell RNA-seq with hierarchical Poisson factorization. Mol Syst Biol. 15(2):e8557.

Liu, Q.*, Georgieva, D.C.*, Egli, D., and Wang, K. 2019. NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data. BMC Genomics. 20:78.

McCurdy E.P., Chung, K.M., Benitez-Agosto, C.R., and Hengst U., 2019. Promotion of Axon Growth by the Secreted End of a Transcription Factor. Cell Rep. 29(2):363-77 e5.

McGoldrick, L.L., Singh A.K., Demirkhanyan, L., Lin, T-Y., Casner, R. G., Zakharian, E. and Sobolevsky, A.I., 2019. Structure of the Thermo-Sensitive TRP Channel TRP1 from the Alga Chlamydomonas Reinhardtii. Nature Communications. 10 (1): 4180.

Sheth, R.U., Li, M., Jiang, W., Sims, P.A., Leong, K.W., and Wang, H.H., 2019. Spatial metagenomic characterization of microbial biogeography in the gut. Nature Biotechnol, 37(8):877-883

Singer, R.A., Arnes, L., Cui, Y., Wang, J., Gao, Y., Guney, M.A., Burnum-Johnson, K.E., Rabadan, R., Ansong, C., Orr, G., and Sussel, L. 2019. The Long Noncoding RNA Paupar Modulates PAX6 Regulatory Activities to Promote Alpha Cell Development and Function. Cell Metab. 30(6):1091-1106.e8.

Singh, A.K., McGoldrick, L.L.*, and Sobolevsky, A.I. 2019. Expression, Purification, and Crystallization of the Transient Receptor Potential Channel TRPV6. Methods Mol Biol. 1987:23-37.

Steinbach, N., Hasson, D., Mathur, D., Stratikopoulos, E.E., Sachidanandam, R., Bernstein, E., and Parsons, R.E. 2019. PTEN interacts with the transcription machinery on chromatin and regulates RNA polymerase II-mediated transcription. Nucleic Acids Res. 47:5573-5586.

Steinfeld, J.B., Belan, O., Kwon, Y., Terakawa, T., Al-Zain, A., Smith, M.J., Crickard, J.B., Qi, Z., Zhao, W.,  Rothstein, R., Symington, L.S., Sung, P., Boulton, S.J., and Greene, E.C. 2019. Defining the influence of Rad51 and Dmc1 lineage-specific amino acids on genetic recombination. Genes Dev.

Su, S., Begum, S., & Ezratty, E. J. 2020. An IFT20 mechanotrafficking axis is required for integrin recycling, focal adhesion dynamics, and polarized cell migration. Molecular Biology of the Cell. 31(17), 1917–1930.

Szymanski J.R. and Yuste R. Mapping the Whole-Body Muscle Activity of Hydra vulgaris. Curr Biol. 2019;29(11):1807-17 e3.

Tapia-Rojo, R.*, Eckels, E.C.*, and Fernandez, J.M. 2019. Ephemeral states in protein folding under force captured with a magnetic tweezers design. Proc Natl Acad Sci USA. 116:7873-7878.

Taveras, C., Liu, C., and Mao, Y. 2019. A tension-independent mechanism reduces Aurora B-mediated phosphorylation upon microtubule capture by CENP-E at the kinetochore. Cell Cycle. 18(12):1349-63.

Tenen, C.C. and Greenwald, I. 2019. Cell Non-autonomous Function of daf-18/PTEN in the Somatic Gonad Coordinates Somatic Gonad and Germline Development in C. elegans Dauer Larvae. Curr Biol. 29:1064-1072 e1068.

Thomas, D.G., Doran, A.C., Fotakis, P., Westerterp, M., Antonson, P., Jiang, H., Jiang, X.C., Gustafsson, J.A., Tabas, I., and Tall, A.R. 2018. LXR Suppresses Inflammatory Gene Expression and Neutrophil Migration through cis-Repression and Cholesterol Efflux. Cell Rep. 25:3774-3785 e3774.

Twomey, E.C., Yelshanskaya, M.V., and Sobolevsky, A.I., 2019. Structural and functional insights into transmembrane AMPA receptor regulatory protein complexes. Journal of General Physiology. 151: 1347-1356.

Wang, E.C.E., Da, Z.i, Ferrante, A.W., Drake, C.G., and Christiano, A.M. 2019. A Subset of TREM2(+) Dermal Macrophages Secretes Oncostatin M to Maintain Hair Follicle Stem Cell Quiescence and Inhibit Hair Growth. Cell Stem Cell. 24:654-669 e656.

Zhao, J.*, Chen, A.X.*, Gartrell, R.D., …, Sonabend, A.M., and Rabadan, R. 2019. Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma. Nat Med. 25:462-469.