Publications


 

Journal covers

 

SAVEMONEY: A Free Algorithm for Cost-Effective Whole-Plasmid Sequencing


Do you want to save 80% or more on your whole-plasmid sequencing costs?

We have developed a free algorithm called SAVEMONEY (“Simple Algorithm for Very Efficient Multiplexing of Oxford Nanopore Experiments for You”) that guides researchers to mix multiple plasmids in a single tube for submission to a commercial whole-plasmid sequencing service (e.g., Plasmidsaurus, Eurofins, etc.) and then subsequently computationally de-mixes the resultant raw sequencing results to provide the sequences. We routinely mix up to six plasmids (that can differ by as little as only a few bases) in a single tube!

To try it out for yourself, go to the SAVEMONEY Google Colab page, which guides you through the entire process. For more background information on SAVEMONEY, check out Masaaki’s publication in eLife.

 

Baskin Lab Publications at Cornell


43. Maio G, Smith M, Bhawal R, Zhang S, Baskin JM, Li J, Lin H. “Interactome analysis identifies the role of BZW2 in promoting endoplasmic reticulum-mitochondrial contact and mitochondrial metabolism.” Mol Cell Proteomics (2023). doi: https://doi.org/10.1016/j.mcpro.2023.100709.

42. Li, X-L, Tei R, Uematsu M, Baskin JM. “Ultralow background membrane editors for spatiotemporal control of lipid metabolism and signaling.” ACS Cent Sci (2024). doi: https://doi.org/10.1021/acscentsci.3c01105.

41. Uematsu M, Baskin JM. “Chemical approaches for measuring and manipulating lipids at the organelle level.” Cold Spring Harb Perspect Biol (2023) doi: 10.1101/cshperspect.a041407.

40. Su YA, Chiu HY, Chang YC, Sung CJ, Chen CW, Tei R, Huang XR, Hsu SC, Lin SS, Wang HC, Lin YC, Hsu JC, Bauer H, Feng Y, Baskin JM, Chang ZF, Liu YW. “NME3 binds to phosphatidic acid and mediates PLD6-induced mitochondrial tethering.” J Cell Biol (2023) 222, 10, e202301091.

39. Uematsu M, Baskin JM. “Barcode-free multiplex plasmid sequencing using Bayesian analysis and nanopore sequencing.” eLife (2023) 12, RP88794.

38. Quirion L, Robert A, Boulais J, Huang S, Kherdjemil Y, Thibault MP, Faubert D, Kmita M, Baskin JM, Gingras AC, Smith MJ, Côté JF. “ARF-family global interactome mapping uncovers spatial organization of cellular signaling pathways.” bioRxiv  (2023). doi: https://doi.org/10.1101/2023.03.01.530598.

37. Sun H, Shami Shah A, Bonfini A, Buchon NS, Baskin JM. “Wnt/β-catenin signaling within multiple cell types dependent upon kramer regulates Drosophila intestinal stem cell proliferation.” bioRxiv (2023). doi: https://doi.org/10.1101/2023.02.21.529411.

36. Liang D, Luan L, Baskin JM. “Imaging interorganelle phospholipid transport by extended synaptotagmins using bioorthogonally tagged lipids.” bioRxiv (2023). doi: https://doi.org/10.1101/2023.02.01.526230.

35. Chiu D-C, Baskin JM. “Imaging and editing the phospholipidome.” Acc Chem Res (2022), 55, 21, 3088–3098.

34. Huang S, Baskin JM. “Adding a chemical biology twist to CRISPR screening.” Isr J Chem. (2023) 63, 1-2, e202200056. (Part of special issue honoring Carolyn Bertozzi). Also available on PubMed Central.

33. Tei R, Bagde SR, Fromme JC, Baskin JM. “Activity-based directed evolution of a membrane editor in mammalian cells.” Nat Chem (2023) 15, 1030–1039. Free link: https://rdcu.be/dcIEc.

32. Yu W, Baskin JM. “Photoaffinity labeling approaches to elucidate lipid–protein interactions.” Curr Opin Chem Biol (2022) 69, 102173.

31. Chiu D-C, Baskin JM. “Organelle-selective membrane labeling through PLD-mediated transphosphatidylation.” JACS Au (2022) 2, 12, 2703–2713.

30. Cao X, Baskin JM. “Phosphoinositide phosphorylation sans kinase.” Nat Cell Biol (2022), 24, 604–606.

29. Tei R, Baskin JM. “Click chemistry and optogenetic approaches to visualize and manipulate phosphatidic acid signaling.” J Biol Chem (2022) 298, 4, 101810.

28. White BM, Kumar P, Conwell AN*, Wu K*, Baskin JM. “Lipid expansion microscopy.” J Am Chem Soc (2022) 144, 40, 18212–18217. *Equal contribution.

27. Cao X, Shami Shah A, Sanford EJ, Smolka MB, Baskin JM. “Spatial regulation of the anaphase-promoting complex/cyclosome by a microtubule adaptor.” ACS Chem Biol (2022) 17, 9, 2605–2618.

26. Yu W, Lin Z, Woo CM, and Baskin JM. “A chemoproteomics approach to profile phospholipase D-derived phosphatidyl alcohol interactions.” ACS Chem Biol (2022) 17, 12, 3276–3283. Part of Young Investigator special issue.

25. Baskin JM and Seeliger JC. “A look at the lives of lipids.” Curr Opin Chem Biol (2021) 65, A4–A6. Editorial overview of Dec 2021 Mechanistic Biology issue devoted to the chemistry and biology of lipids.

24. Bumpus TW, Huang S, Tei R, and Baskin JM. “Click chemistry–enabled CRISPR screening reveals GSK3 as a regulator of PLD signaling.” Proc Natl Acad Sci USA (2021) 118, 48, e2025265118.

23. Yu W and Baskin JM. “There is a lock for every key.” Nat Chem Biol (2021) 17, 1214–1216.

22. Batrouni AG*, Bag N*†, Phan H, Baird BA, and Baskin JM†. “A palmitoylation code controls PI4KIIIα complex formation and PI(4,5)P2 homeostasis at the plasma membrane.” J Cell Sci (2022) 135, 5, jcs259365. *Equal contribution; †Co-corresponding authors. Part of special issue on Cell Biology of Lipids. 

21. Tei R and Baskin JM. “Induced proximity tools for precise manipulation of lipid signaling.” Curr Opin Chem Biol (2021) 65, 93–100. Part of Mechanistic Biology Issue. 

20. Tei R*, Morstein J*, Shemet A, Trauner D†, and Baskin JM†. “Optical control of phosphatidic acid signaling.” ACS Cent Sci (2021) 7, 7, 1205–1215. *Equal contribution; †Co-corresponding authors.

19. Liang D, Cheloha R, Watanabe T, Gardella TJ, and Baskin JM. “Activity-based, bioorthogonal imaging of phospholipase D reveals spatiotemporal dynamics of GPCR-Gq signaling.” Cell Chem Biol (2021) 28, 1–7.

18. Batrouni AG and Baskin JM. “The Chemistry and Biology of Phosphatidylinositol 4-Phosphate at the Plasma Membrane.” Bioorg Med Chem (2021) 40, 116190. (Invited for special issue honoring Neal Devaraj)

17. Batrouni AG and Baskin JM. “A MAP for PI3K Activation on Endosomes.” Nat Cell Biol (2020) 22, 1292–94.

16. Shami Shah A, Sun H, Baskin JM. “For Wnt Signaling, Fucosylation of LRP6 Is a Bitter Pill.” Cell Chem Biol (2020) 27, 9, 1114–16.

15. Shami Shah A, Cao X, White AC, Baskin JM. “PLEKHA4 Promotes Wnt/β-catenin Signaling-Mediated G1/S Transition and Proliferation in Melanoma.” Cancer Res (2021) 81, 2029–43.

14. Flores J*, White BM*, Brea RJ, Baskin JM†, Devaraj NK†. “Lipids: chemical tools for their synthesis, modification, and analysis.” Chem Soc Rev (2020) 49, 4602–14. *Equal contribution.

13. Bumpus TW*, Liang D*, and Baskin JM. “IMPACT: Imaging phospholipase D activity with clickable alcohols via transphosphatidylation.” Method Enzymol (2020), 641, 75–94. *Equal contribution.

12. Jorgensen JR, Tei R, Baskin JM, Michel AH, Kornmann B, and Emr SD. “ESCRT-III and ER-PM contacts maintain lipid homeostasis.” Mol Biol Cell (2020) 31, 12, 1302–13.

11. Tei R and Baskin JM. “Spatiotemporal Control of Phosphatidic Acid Signaling with Optogenetic, Engineered Phospholipase Ds.” J Cell Biol (2020) 219, 3, e201907013.

10. Daughtry JL, Cao W, Ye J, and Baskin JM. “Clickable Galactose Analogs for Imaging Glycans in Developing Zebrafish.” ACS Chem Biol (2020) 15, 2, 318–24; also at ChemRxiv (2019).

9. Liang D, Wu K*, Tei R*, Bumpus TW, Ye J, and Baskin JM. “A real-time, click chemistry imaging approach reveals stimulus-specific subcellular locations of phospholipase D activity.” Proc Natl Acad Sci USA (2019), 116, 31, 15453–62. *Equal contribution.

8. Shami Shah A, Batrouni AG, Kim DS, Punyala A, Cao W, Han C, Goldberg ML, Smolka MB, and Baskin JM. “PLEKHA4/kramer Attenuates Dishevelled Ubiquitination to Modulate Wnt and Planar Cell Polarity Signaling.” Cell Rep (2019), 27, 7, 2157–70.

7. Wang DG, Paddock MN, Lundquist MR, Sun JY, Mashadova O, Amadiume S, Bumpus TW, Hodakoski C, Hopkins BD, Fine M, Hill A, Yang TJ, Baskin JM, Dow LE, Cantley LC. “PIP4Ks Suppress Insulin Signaling through a Catalytic-Independent Mechanism.” Cell Rep (2019) 27, 7, 1991–2001.

6. Bumpus TW and Baskin JM. “Getting a grip on greasy molecules.” Trends Biochem Sci (2019), 44, 7, 640–41.

5. Bumpus TW and Baskin JM. “Greasing the wheels of lipid biology with chemical tools.” Trends Biochem Sci (2018) 43, 12, 970–83.

4. Bumpus TW, Liang FJ, and Baskin JM. “Ex Uno Plura: Differential labeling of phospholipid biosynthetic pathways with a single bioorthogonal alcohol.” Biochemistry (2018) 57, 2, 226–30. Featured in the “Future of Biochemistry” special issue.

 

 

3. Bumpus TW and Baskin JM. “Clickable Substrate Mimics Enable Imaging of Phospholipase D Activity.” ACS Cent Sci, 3, 10, 1070-1077 (2017). Featured on the cover.


Synopsis: Simple azidoalcohols enable a click chemistry-based method for imaging
the subcellular localizations of the active pools of phospholipase D signaling enzymes.

2. Knopf KM, Murphy BL, MacMillan SN, Baskin JM, Barr MP, Boros E, and Wilson JJ. “In Vitro Anticancer Activity and in Vivo Biodistribution of Rhenium(I) Tricarbonyl Aqua Complexes.” J Am Chem Soc, 139, 40, 14302-14314 (2017).

1. Bumpus TW and Baskin JM. “A Chemoenzymatic Strategy for Imaging Cellular Phosphatidic Acid Synthesis.” Angew Chem Int Ed, 55, 13155-13158 (2016).

Jeremy’s Publications Prior to Cornell


27. Lees JA, Zhang Y, Oh MS, Schauder CM, Yu X, Baskin JM, Dobbs K, Notarangelo LD, De Camilli P, Walz T, Reinisch KM. “Architecture of the human PI4KIIIα lipid kinase complex.”  Proc Natl Acad Sci USA, 114, 13720–25 (2017).

26. *Baskin JM, *Wu X, Christiano R, Oh MS, Schauder CM, Gazzerro E, Messa M, Baldassari S, Assereto S, Biancheri R, Zara F, Minetti C, Raimondi A, Simons M, Walther TC, Reinisch KM, De Camilli P. “The leukodystrophy protein FAM126A (hyccin) regulates PtdIns(4)P synthesis at the plasma membrane.” Nat Cell Biol, 18, 132-38 (2016). Featured in Yale News and the Yale Daily News.

25. Chung J, Nakatsu F, Baskin JM, De Camilli P. “Plasticity of PI4KIIIα interactions at the plasma membrane.” EMBO Rep, 16, 312-20 (2015).

24. Wu X, Chi RJ, Baskin JM, Lucast L, Burd CG, De Camilli P, Reinisch KM. “Structural insights into assembly and regulation of the plasma membrane phosphatidylinositol 4-kinase complex.” Dev Cell, 28, 19–29 (2014). Featured in Faculty of 1000.

23. Gupta AR, Pirruccello M, Cheng F, Kang HJ, Fernandez TV, Baskin JM, Choi M, Liu L, Ercan-Sencicek AG, Murdoch JD, Klei L, Neale BM, Sanders SJ, Daly MJ, Lifton RP, De Camilli P, Zhao H, Sestan N, State MW. “Rare deleterious mutations in the gene EFR3A are associated with autism spectrum disorders.” Mol Autism, 5, 31 (2014).

22. *Nakatsu F, *Baskin JM, Chung J, Tanner LB, Shui G, Lee SY, Pirruccello M, Hao M, Ingolia NT, Wenk MR, De Camilli P. “PtdIns4P synthesis by PI4KIIIα at the plasma membrane and its impact on plasma membrane identity.” J Cell Biol, 199, 1003–16 (2012). *Equal contribution. Featured in Faculty of 1000.

21. Dehnert KW, Baskin JM, Laughlin ST, Beahm BJ, Naidu NN, Amacher SL, Bertozzi CR. “Imaging the sialome during zebrafish development with copper-free click chemistry.” ChemBioChem, 13, 353–57 (2012).

20. Yao JZ, Uttamapinant C, Poloukhtine A, Baskin JM, Codelli JA, Sletten EM, Bertozzi CR, Popik VV, Ting AY. “Fluorophore targeting to cellular proteins via enzyme-mediated azide ligation and strain-promoted cycloaddition.” J Am Chem Soc, 134, 3720–28 (2012).

19. Dehnert KW, Beahm BJ, Huynh TT, Baskin JM, Laughlin ST, Wang W, Wu P, Amacher SL, Bertozzi CR. “Metabolic labeling of fucosylated glycans in developing zebrafish.” ACS Chem Biol, 6, 547–52 (2011).

18. *Baskin JM, *Dehnert KW, *Laughlin ST, Amacher SL, Bertozzi CR. “Visualizing enveloping layer glycans during zebrafish early embryogenesis.” Proc Natl Acad Sci USA, 107, 10360–65 (2010). Featured in Faculty of 1000. *Equal contribution.

17. Baskin JM and Bertozzi CR. “Copper-free click chemistry: Bioorthogonal reagents for tagging azides.” Aldrichimica Acta, 43, 15–23 (2010).

16. Beatty KE, Fisk JD, Smart BP, Lu YY, Szychowski J, Hangauer MJ, Baskin JM, Bertozzi CR, Tirrell DA. “Live-cell imaging of cellular proteins by a strain-promoted cycloaddition.” ChemBioChem, 11, 2092–95 (2010).

15. Chang PV, Prescher JA, Sletten EM, Baskin JM, Miller IA, Agard NJ, Lo A, Bertozzi CR. “Copper-free click chemistry in living animals.” Proc Natl Acad Sci USA, 107, 1821–26 (2010). Featured in Faculty of 1000.

14. Baskin JM and Bertozzi CR. “Copper-free click chemistry.” In Click Chemistry for Biotechnology and Materials Science. Ed. J. Lahann. pp. 25–51, Wiley (2009).

13. Nessen MA, Kramer G, Back J, Baskin JM, Smeenk LE, de Koning LJ, van Maarseveen JH, de Jong L, Bertozzi CR, Hiemstra H, de Koster CG. “Selective enrichment of azide-containing peptides from complex mixtures.” J Proteome Res, 8, 3702–11 (2009).

12. Hur GH, Meier JL, Baskin J, Codelli JA, Bertozzi CR, Marahiel MA, Burkart MD. “Crosslinking studies of protein-protein interaction in nonribosomal peptide biosynthesis.” Chem Biol, 16, 372–81 (2009).

11. *Laughlin ST, *Baskin JM, Amacher SL, Bertozzi CR. “In vivo imaging of membrane-associated glycans in developing zebrafish. Science, 320, 664–67 (2008). *Equal contribution. Featured in the New York Times, C&E News, Nat Chem Biol, Nat Reports Stem Cells, ACS Chem Biol, Science Daily, Chemistry World.

10. Johnson JA, Baskin JM, Bertozzi CR, Koberstein JT, Turro NJ. “Copper-free click chemistry for the in situ crosslinking of photodegradable star polymers.” Chem Commun, 3064–66 (2008).

9. Codelli JA, Baskin JM, Agard NJ, Bertozzi CR. “Second-generation difluorinated cyclooctynes for copper-free click chemistry.” J Am Chem Soc, 130, 11486–93 (2008).

8. Baskin JM, Prescher JA, Laughlin ST, Agard NJ, Chang PV, Miller IA, Lo A, Codelli JA, Bertozzi CR. “Copper-free click chemistry for dynamic in vivo imaging.” Proc Natl Acad Sci USA, 104, 16793–97 (2007). Featured on the cover and in Nature, C&E News, Biophotonics InternationalScience Daily.

7. Baskin JM and Bertozzi CR. “Bioorthogonal click chemistry: Covalent labeling in living systems.” QSAR Comb Sci, 26, 1211–19 (2007).

6. Fernández-Suárez M, Baruah H, Martínez-Hernández L, Xie KT, Baskin JM, Bertozzi CR, Ting AY. “Redirecting lipoic acid ligase for cell surface protein labeling with small-molecule probes.” Nat Biotechnol, 25, 1483–87 (2007).

5. *Agard NJ, *Baskin JM, Prescher JA, Lo A, Bertozzi CR. “A comparative study of bioorthogonal reactions with azides.” ACS Chem Biol, 1, 644–48 (2006). *Equal contribution. Featured on the cover and in Faculty of 1000.

4. Laughlin ST, Agard NJ, Baskin JM, Carrico IS, Chang PV, Ganguli AS, Hangauer MJ, Lo A, Prescher JA, Bertozzi CR. “Metabolic labeling of glycans with azido sugars for visualization and glycoproteomics.” Methods Enzymol, 415, 230–50 (2006).

3. Antilla JC, Baskin JM, Barder TE, Buchwald SL. “Copper-diamine-catalyzed N-arylation of pyrroles, pyrazoles, indazoles, imidazoles, and triazoles.” J Org Chem, 69, 5578–87 (2004).

2. Baskin JM and Wang Z. “An efficient copper catalyst for the formation of sulfones from sulfinic acid salts and aryl iodides.” Org Lett, 4, 4423–25 (2002).

1. Baskin JM and Wang Z. “A mild, convenient synthesis of sulfinic acid salts and sulfonamides from alkyl and aryl halides.” Tetrahedron Lett, 43, 8479–83 (2002).

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