Undergraduate Publications

One of the most valuable aspects of a Brandeis education is the opportunity to carry out cutting-edge research in collaboration with faculty, graduate students and postdocs. There are many research opportunities in laboratories in the science departments at Brandeis. Many students begin working in labs as early as their first semester, while others may start as juniors. Often, the research leads up to publication of a Senior Honors Thesis. Since 2003, Brandeis undergraduates have been co-authors on approximately 400 peer-reviewed research publications in scientific journals.

Graph showing undergraduate publications 2003 to 2018

Names of undergraduate students from Brandeis are indicated below in bold face


  1. Roy A, Wang S, Meschede-Krasa B, Breffle J, Van Hooser SD. An early phase of instructive plasticity before the typical onset of sensory experience. Nat Commun. 2020;11(1):11.
  2. Donelson NC, Dixit R, Pichardo-Casas I, Chiu EY, Ohman RT, Slawson JB, Klein M, Fulga TA, Van Vactor D, Griffith LC. MicroRNAs Regulate Multiple Aspects of Locomotor Behavior in Drosophila. G3 (Bethesda). 2020;10(1):43-55.
  3. Greppi C (*), Laursen WJ (*), Budelli G, Chang EC, Daniels AM, van Giesen L, Smidler AL, Catteruccia F, Garrity PA. Mosquito heat seeking is driven by an ancestral cooling receptor. Science. 2020;367(6478):681-4.
  4. Enes J, Haburcak M, Sona S, Gerard N, Mitchell AC, Fu W, Birren SJ. Satellite glial cells modulate cholinergic transmission between sympathetic neurons. PLoS One. 2020;15(2):e0218643.
  5. Lowensohn J, Hensley A, Perlow-Zelman M, Rogers WB. Self-assembly and crystallization of DNA-coated colloids via linker-encoded interactions. Langmuir. 2020.
  6. Hadzipasic A, Wilson C, Nguyen V, Kern N, Kim C, Pitsawong W, Villali J, Zheng Y, Kern D. Ancient origins of allosteric activation in a Ser-Thr kinase. Science. 2020;367(6480):912-7.
  7. He H, Guo J, Lin X, Xu B. Enzyme-Instructed Assemblies Enable Mitochondria Localization of Histone H2B in Cancer Cells. Angew Chem Int Ed Engl. 2020.
  8. Li X, Lee JK, Lu Y, Gerkman MA, Kengmana ES, Fonseca MV, Warner JH, Han GGD. Precursor Design for High Density Single Pt Atom Sites on MoS2: Enhanced Stability at Elevated Temperatures and Reduced 3D Clustering. Chem Mater. 2020.
  9. Gonzalez A, Kengmana ES, Fonseca MV, Han GGD. Solid-state photoswitching molecules: structural design for isomerization in condensed phase. Materials Today Advances. 2020;6.
  10. Tatavarty V, Torrado Pacheco A, Groves Kuhnle C, Lin H, Koundinya P, Miska NJ, Hengen KB, Wagner FF, Van Hooser SD, Turrigiano GG. Autism-Associated Shank3 Is Essential for Homeostatic Compensation in Rodent V1. Neuron. 2020.
  11. Klaric JA, Perr EL, Lovett ST. Identifying Small Molecules That Promote Quasipalindrome-Associated Template-Switch Mutations in Escherichia coli. G3 (Bethesda). 2020.


  1. Kushinsky D, Morozova EO, Marder E. In vivo effects of temperature on the heart and pyloric rhythms in the crab, Cancer borealis. J Exp Biol. 2019.
  2. Blankenship ML, Grigorova M, Katz DB, Maier JX. Retronasal Odor Perception Requires Taste Cortex, but Orthonasal Does Not. Curr Biol. 2019;29(1):62-9 e3
  3. Wang J, Zhou J, He H, Wu D, Du X, Xu B. Cell-compatible Nanoprobes for Imaging Intracellular Phosphatase Activities. Chembiochem : a European journal of chemical biology. 2019;20(4):526-31.
  4. Rajab TK, Beyene MW, Yazdchi F, Menard MT. Aortic Aneurysm Eroding into the Spine. Aorta (Stamford). 2019.
  5. Yu R, Kim Y, Maltseva N, Braunstein P, Joachimiak A, Hedstrom L. Oxanosine monophosphate is a covalent inhibitor of inosine 5′-monophosphate dehydrogenase. Chem Res Toxicol. 2019.
  6. Herzog LE, Pascual LM, Scott SJ, Mathieson ER, Katz DB, Jadhav SP. Interaction of taste and place coding in the hippocampus. The Journal of Neuroscience. 2019.
  7. Waterman DP, Zhou F, Li K, Lee CS, Tsabar M, Eapen VV, Mazzella A, Haber JE. Live cell monitoring of double strand breaks in S. cerevisiae. Plos Genet. 2019;15(3):e1008001.
  8. Opathalage A, Norton MM, Juniper MPN, Langeslay B, Aghvami SA, Fraden S, Dogic Z. Self-organized dynamics and the transition to turbulence of confined active nematics. Proc Natl Acad Sci U S A. 2019.
  9. Horvath V, Kutner DJ, Zeng MD, Epstein IR. Phase-frequency model of strongly pulse-coupled Belousov-Zhabotinsky oscillators. Chaos. 2019;29(2):023128.
  10. Konow C, Somberg NH, Chavez J, Epstein IR, Dolnik M. Turing patterns on radially growing domains: experiments and simulations. Phys Chem Chem Phys. 2019.
  11. Pita-Thomas W, Mahar M, Joshi A, Gan D, Cavalli V. HDAC5 promotes optic nerve regeneration by activating the mTOR pathway. Exp Neurol. 2019.
  12. Long MJC, Lawson AP, Baggio R, Qian Y, Rozhansky L, Fasci D, El Oualid F, Weerapana E, Hedstrom L. Diarylcarbonates are a new class of deubiquitinating enzyme inhibitor. Bioorg Med Chem Lett. 2019;29(2):204-11.
  13. Gerkman M, Yuan S, Duan P, Taufan J, Schmidt-Rohr K, Han GGD. Phase Transition of Spiropyrans: Impact of Isomerization Dynamics at High Temperatures. Chem Commun. 2019.
  14. Royer L, Shangraw K, Herzog JJ, Pouvreau S, Marr MT, Paradis S. The metastasis suppressor protein Nme1 is a concentration dependent modulator of the Ca2+/calmodulin-dependent protein kinase II. Biochemistry. 2019.
  15. Wang J, Cooper DL, Zhan W, Wu D, He H, Sun S, Lovett ST, Xu B. Diglycine Enables Rapid Intrabacterial Hydrolysis for Activating Anbiotics against Gram-negative Bacteria. Angew Chem Int Ed Engl. 2019.
  16. Gutchess A, Alves AN, Paige LE, Rohleder N, Wolf JM. Age differences in the relationship between cortisol and emotional memory. Psychol Aging. 2019.
  17. Zorba A, Nguyen V, Koide A, Hoemberger M, Zheng Y, Kutter S, Kim C, Koide S, Kern D. Allosteric modulation of a human protein kinase with monobodies. Proceedings of the National Academy of Sciences. 2019.
  18. Wang S, Zhao Z, Rodal AA. Higher-order assembly of Sorting Nexin 16 controls tubulation and distribution of neuronal endosomes. J Cell Biol. 2019.
  19. Halpin JC, Jangi R, Street TO. Multi-mapping confounds ribosome profiling analysis: A case-study of the Hsp90 molecular chaperone. Proteins. 2019.
  20. DiTirro D (*), Philbrook A (*), Rubino K, Sengupta P. The C. elegans Tubby homolog dynamically modulates olfactory cilia membrane morphogenesis and phospholipid composition. eLife. 2019;8.
  21. Jackson JD, Luu C, Vigderman A, Leshikar ED, St Jacques PL, Gutchess A. Reduction of the Self-Reference Effect in Younger and Older Adults. Psychol Neurosci. 2019;12(2):257-70.
  22. Memisoglu G, Lanz MC, Eapen VV, Jordan JM, Lee K, Smolka MB, Haber JE. Mec1(ATR) Autophosphorylation and Ddc2(ATRIP) Phosphorylation Regulates DNA Damage Checkpoint Signaling. Cell reports. 2019;28(4):1090-102 e3.
  23. Torrado Pacheco A (*), Tilden EI (*), Grutzner SM (*), Lane BJ, Wu Y, Hengen KB, Gjorgjieva J, Turrigiano GG. Rapid and active stabilization of visual cortical firing rates across light-dark transitions. Proc Natl Acad Sci U S A. 2019.
  24. DiGirolamo MA, Simon JC, Hubley KM, Kopulsky A, Gutsell JN. Clarifying the relationship between trait empathy and action-based resonance indexed by EEG mu-rhythm suppression. Neuropsychologia. 2019:107172.
  25. Morehouse BR (*), Kumar RP (*), Matos JO, Yu Q, Bannister A, Malik K, Temme JS, Krauss IJ, Oprian DD. Direct evidence for an enzyme generated LPP intermediate in (+)-limonene synthase using a fluorinated GPP substrate analog. ACS Chem Biol. 2019.
  26. Raman G, Avendano EE, Chen S, Wang J, Matson J, Gayer B, Novotny JA, Cassidy A. Dietary intakes of flavan-3-ols and cardiometabolic health: systematic review and meta-analysis of randomized trials and prospective cohort studies. The American Journal of Clinical Nutrition. 2019.
  27. Norton MM (*), Tompkins N (*), Blanc B, Cambria MC, Held J, Fraden S. Dynamics of Reaction-Diffusion Oscillators in Star and other Networks with Cyclic Symmetries Exhibiting Multiple Clusters. Physical Review Letters. 2019;123(14).
  28. Schlichting M, Diaz MM, Xin J, Rosbash M. Neuron-specific knockouts indicate the importance of network communication to Drosophila rhythmicity. eLife. 2019;8.
  29. Villalonga MB, Sussman RF, Sekuler R. Feeling the Beat (and Seeing It, Too): Vibrotactile, Visual, and Bimodal Rate Discrimination. Multisens Res. 2019:1-29.
  30. Feng Z, Wang H, Yi M, Lo CY, Sallee A, Hsieh JT, Xu B. Instructed‐assembly of small peptides inhibits drug‐resistant prostate cancer cells. Peptide Science. 2019;n/a(n/a):e24123.
  31. Marcus R, Zhang C, Yu S, Kao G, Papaemmanouil O. NashDB. Proceedings of the VLDB Endowment. 2019;12(12):1830-3.
  32. Heyman JB, Chen C-H, Foxman BM. On the Crystal Structures of Missing Links in the Early History of Solid-State Reactions: The Group IA Acrylates and Methacrylates. Cryst Growth Des. 2019.
  33. Gerkman MA, Lee JK, Li X, Zhang Q, Windley M, Fonseca MV, Lu Y, Warner JH, Han GGD. Direct Imaging of Individual Molecular Binding to Clean Nanopore Edges in 2D Monolayer MoS2. ACS nano. 2019.
  34. Zhang B, Shankara SB, Ye S, Zhang H. Design and analysis of high-risk medical device clinical trials for diabetes monitoring and treatment. Journal of Pancreatology. 2019;2(4):123-30.
  35. Zhang B, Ye S, Shankara SB, Zhang H, Zheng Q. Neutral diagnosis: An innovative concept for medical device clinical trials. Contemp Clin Trials Commun. 2019;16:100436. 
  36. Duan P, Zhi B, Coburn L, Haynes CL, Schmidt-Rohr K. A molecular fluorophore in citric-acid/ethylenediamine carbon dots identified and quantified by multinuclear solid-state NMR. Magn Reson Chem. 2019.
  37. Lowensohn J, Oyarzún B, Narváez Paliza G, Mognetti BM, Rogers WB. Linker-Mediated Phase Behavior of DNA-Coated Colloids. Physical Review X. 2019;9(4).


  1. Litschel T, Norton MM, Tserunyan V, Fraden S. Engineering reaction-diffusion networks with properties of neural tissue. Lab Chip. 2018;18(5):714-22.
  2. Saraidaridis JT, Molina G, Savit LR, Milch H, Mei T, Chin S, Kuo J, Bordeianou L. Pudendal nerve terminal motor latency testing does not provide useful information in guiding therapy for fecal incontinence. Int J Colorectal Dis. 2018.
  3. Roberts DH, Saripalli L, Wang KX, Rao MS, Subrahmanyan R, KleinStern CC, Morii-Sciolla CY, Simpson L. What are “X-shaped” Radio Sources Telling Us? I. Very Large Array Imaging of a Large Sample of Candidate XRGs. Astrophys J. 2018;852(1).
  4. Lorson LC, Tai O, Foxman BM. Use of Topotactic Phase Transformations to Obtain Solutions of the Crystal Structures of Highly Disordered Materials. Cryst Growth Des. 2018;18(1):409-15.
  5. Zhou J, Du X, Chen X, Wang J, Zhou N, Wu D, Xu B. Enzymatic Self-Assembly Confers Exceptionally Strong Synergism with NF-kB Targeting for Selective Necroptosis of Cancer Cells. J Am Chem Soc. 2018.
  6. Turman DL, Cheloff AZ, Corrado AD, Nathanson JT, Miller C. Molecular Interactions between a Fluoride Ion Channel and Synthetic Protein Blockers. Biochemistry. 2018.
  7. Pochapsky TC, Wong N, Zhuang Y, Futcher J, Pandelia M-E, Teitz DR, Colthart AM. NADH reduction of nitroaromatics as a probe for residual ferric form high-spin in a cytochrome P450. Biochim Biophys Acta. 2018;1866(1):126-33.
  8. Zhou J, Du X, Berciu C, Del Signore SJ, Chen X, Yamagata N, Rodal AA, Nicastro D, Xu B. Cellular Uptake of A Taurine-Modified, Ester Bond-Decorated D-Peptide Derivative via Dynamin-Based Endocytosis and Macropinocytosis. Mol Ther. 2018.
  9. Lisman J, Cooper K, Sehgal M, Silva AJ. Memory formation depends on both synapse-specific modifications of synaptic strength and cell-specific increases in excitability. Nat Neurosci. 2018.
  10. Reiner BR, Mucha NT, Rothstein A, Temme JS, Duan P, Schmidt-Rohr K, Foxman BM, Wade CR. Zirconium Metal-Organic Frameworks Assembled from Pd and Pt P(N)N(N)P Pincer Complexes: Synthesis, Postsynthetic Modification, and Lewis Acid Catalysis. Inorg Chem. 2018.
  11. Wang H, Feng Z, Qin Y, Wang J, Xu B. Nucleopeptide Assemblies Selectively Sequester ATP in Cells. Angew Chem Int Ed Engl. 2018.
  12. Norton MM, Baskaran A, Opathalage A, Langeslay B, Fraden S, Baskaran A, Hagan MF. Insensitivity of active nematic liquid crystal dynamics to topological constraints. Phys Rev E. 2018;97(1-1):012702.
  13. Gaskins DK, Soohoo JS, Dolnik M, Epstein IR. Birth and Death of Invading Standing Waves in the BZ-AOT Reaction-diffusion System. Isr J Chem. 2018.
  14. Leow S-S, Luu A, Shrestha S, Hayes KC, Sambanthamurthi R. Drosophila larvae fed palm fruit juice (PFJ) delay pupation via expression regulation of hormetic stress response genes linked to ageing and longevity. Experimental Gerontology. 2018.
  15. Tu Y, Kreinbring CA, Hill M, Liu C, Petsko GA, McCune CD, Berkowitz DB, Liu D, Ringe D. Crystal Structures of Cystathionine beta-Synthase from Saccharomyces cerevisiae: One Enzymatic Step at a Time. Biochemistry. 2018.
  16. Acker DWM, Wong I, Kang M, Paradis S. Semaphorin 4D promotes inhibitory synapse formation and suppresses seizures in vivo. Epilepsia. 2018.
  17. Moore AR, Richards SE, Kenny K, Royer L, Chan U, Flavahan K, Van Hooser SD, Paradis S. Rem2 stabilizes intrinsic excitability and spontaneous firing in visual circuits. eLife. 2018;7.
  18. Memet E, Hilitsk F, Morris MA, Schwenger WJ, Dogic Z, Mahadevan L. Microtubules soften due to cross-sectional flattening. eLife. 2018;7.
  19. Cai H, Liu M, Russell CJ. Directed evolution of an influenza reporter virus to restore replication and virulence and enhance non-invasive bioluminescence imaging in mice. Journal of virology. 2018.
  20. Goodwin PR, Meng A, Moore J, Hobin M, Fulga TA, Van Vactor D, Griffith LC. MicroRNAs Regulate Sleep and Sleep Homeostasis in Drosophila. Cell reports. 2018;23(13):3776-86.
  21. McDermott JE, Goldblatt D, Paradis S. Class 4 Semaphorins and Plexin-B receptors regulate GABAergic and glutamatergic synapse development in the mammalian hippocampus. Molecular and Cellular Neuroscience. 2018.
  22. Garabedian MV, Stanishneva-Konovalova T, Lou C, Rands TJ, Pollard LW, Sokolova OS, Goode BL. Integrated control of formin-mediated actin assembly by a stationary inhibitor and a mobile activator. J Cell Biol. 2018.
  23. Royer L, Herzog JJ, Kenny K, Tzvetkova B, Cochrane JC, Marr MT, 2nd, Paradis S. The Ras-like GTPase Rem2 is a potent inhibitor of calcium/calmodulin-dependent kinase II activity. J Biol Chem. 2018.
  24. Cao Z, Wu S, Wang C, Wang L, Soares JC, He SC, Zhang XY. Serotonin transporter gene (5-HTT) rs6354 polymorphism, job-related stress, and their interaction in burnout in healthcare workers in a Chinese hospital. Psychopharmacology. 2018.
  25. Wong NR, Liu X, Lloyd H, Colthart AM, Ferrazzoli AE, Cooper DL, Zhuang Y, Esquea P, Futcher J, Pochapsky TM, Matthews JM, Pochapsky TC. A new approach to understanding structure-function relationships in cytochromes P450 by targeting terpene metabolism in the wild. J Inorg Biochem. 2018;188:96-101.
  26. Maharjan DM, Dai YY, Glantz EH, Jadhav SP. Disruption of dorsal hippocampal – prefrontal interactions using chemogenetic inactivation impairs spatial learning. Neurobiol Learn Mem. 2018.
  27. Li J, Zhan ZQ, Du XW, Wang JQ, Hong BD, Xu B. Selection of Secondary Structures of Heterotypic Supramolecular Peptide Assemblies by an Enzymatic Reaction. Angew Chem Int Edit. 2018;57(36):11716-21.
  28. Flores VL, Parmet T, Mukherjee N, Nelson S, Katz DB, Levitan D. The role of the gustatory cortex in incidental experience-evoked enhancement of later taste learning. Learn Mem. 2018;25(11):587-600.
  29. Gaskins DK, Soohoo JS, Epstein IR, Dolnik M. Turing-Hopf front invasion: Rings and shells. Phys Rev E. 2018;98(4).
  30. Johnston AB, Hilton DM, McConnell P, Johnson B, Harris MT, Simone A, Amarasinghe GK, Cooper JA, Goode BL. A novel mode of Capping Protein-regulation by Twinfilin. eLife. 2018;7.
  31. Wirth JD, Boucher JI, Jacobowitz JR, Classen S, Theobald DL. Functional and structural resilience of the active site loop in the evolution of Plasmodium lactate dehydrogenase. Biochemistry. 2018.
  32. Aizenman AM, Gold JM, Sekuler R. Multisensory Integration in Short-term Memory: Musicians do Rock. Neuroscience. 2018;389:141-51.
  33. Gorur-Shandilya S, Hoyland A, Marder E. Xolotl: An Intuitive and Approachable Neuron and Network Simulator for Research and Teaching. Front Neuroinform. 2018.
  34. Laranjo LT (*), Klaric JA (*), Pearlman LR, Lovett ST. Stimulation of Replication Template-Switching by DNA-Protein Crosslinks. Genes (Basel). 2018;10(1).
  35. Roy A, Christie IK, Escobar GM, Osik JJ, Popovic M, Ritter NJ, Stacy AK, Wang S, Fiser J, Miller P, Van Hooser SD. Does experience provide a permissive or instructive influence on the development of direction selectivity in visual cortex? Neural Dev. 2018;13(1):16.
  36. Stamoulis C, Connolly J, Axeen E, Kaulas H, Bolton J, Dorfman K, Halford JJ, Duffy FH, Treves ST, Pearl PL. Non-invasive Seizure Localization with Ictal Single-Photon Emission Computed Tomography is Impacted by Preictal/Early Ictal Network Dynamics. IEEE Trans Biomed Eng. 2018.

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