Publications

Selected first author (* co-first authors) publications: 2019-2021

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.

Crawley, T. and Palmer III, A.G., 2021. Approximate Representations of Shaped Pulses Using the Homotopy Analysis Method. Magnetic Resonance. In press.

Crawley, T. and Palmer III, A.G., 2021. Bootstrap Aggregation for Model Selection in the Model-free Formalism. Magnetic Resonance. In press.

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.

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. (in press)

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.

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.

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. 

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. 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., …Stockwell, B.R., Ho, D.D. Chavez, A. 2021. Inhibitors of coronavirus 3cl proteases protect cells from protease-mediated cytotoxicity. Journal of Virology. In press

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. 100044. Advance online publication.

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.

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.

Van Alstyne, M., Tattoli, I., Delestree, N., Recinos, Y., Workman, E., Shihabuddin, L.S., Zhang, C., Mentis, G.Z., and Pellizzoni, L. 2021. Gain of toxic function by long-term AAV9-mediated SMN overexpression in the sensorimotor circuit. Nat Neurosci.

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.

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.