• 2021
  Fischer S, Gillis J, , How many markers are needed to robustly determine a cell’s type?, iScience 2021 Nov; 24(11): 103292.
• 2021
  Muñoz-Castañeda R, Zingg B, Matho KS, Chen X, Wang Q, Foster NN, Li A, Narasimhan A, Hirokawa KE, Huo B, Bannerjee S, Korobkova L, Park CS, Park YG, Bienkowski MS, Chon U, Wheeler DW, Li X, Wang Y, Naeemi M, Xie P, Liu L, Kelly K, An X, Attili SM, Bowman I, Bludova A, Cetin A, Ding L, Drewes R, D'Orazi F, Elowsky C, Fischer S, Galbavy W, Gao L, Gillis J, Groblewski PA, Gou L, Hahn JD, Hatfield JT, Hintiryan H, Huang JJ, Kondo H, Kuang X, Lesnar P, Li X, Li Y, Lin M, Lo D, Mizrachi J, Mok S, Nicovich PR, Palaniswamy R, Palmer J, Qi X, Shen E, Sun YC, Tao HW, Wakemen W, Wang Y, Yao S, Yuan J, Zhan H, Zhu M, Ng L, Zhang LI, Lim BK, Hawrylycz M, Gong H, Gee JC, Kim Y, Chung K, Yang XW, Peng H, Luo Q, Mitra PP, Zador AM, Zeng H, Ascoli GA, Josh Huang Z, Osten P, Harris JA, Dong HW, , Cellular anatomy of the mouse primary motor cortex., Nature 2021 10; 598(7879): 159-166.
• 2021
  Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, Bertagnolli D, Casper T, Castanon RG, Crichton K, Daigle TL, Dalley R, Dee N, Dembrow N, Diep D, Ding SL, Dong W, Fang R, Fischer S, Goldman M, Goldy J, Graybuck LT, Herb BR, Hou X, Kancherla J, Kroll M, Lathia K, van Lew B, Li YE, Liu CS, Liu H, Lucero JD, Mahurkar A, McMillen D, Miller JA, Moussa M, Nery JR, Nicovich PR, Niu SY, Orvis J, Osteen JK, Owen S, Palmer CR, Pham T, Plongthongkum N, Poirion O, Reed NM, Rimorin C, Rivkin A, Romanow WJ, Sedeño-Cortés AE, Siletti K, Somasundaram S, Sulc J, Tieu M, Torkelson A, Tung H, Wang X, Xie F, Yanny AM, Zhang R, Ament SA, Behrens MM, Bravo HC, Chun J, Dobin A, Gillis J, Hertzano R, Hof PR, Höllt T, Horwitz GD, Keene CD, Kharchenko PV, Ko AL, Lelieveldt BP, Luo C, Mukamel EA, Pinto-Duarte A, Preissl S, Regev A, Ren B, Scheuermann RH, Smith K, Spain WJ, White OR, Koch C, Hawrylycz M, Tasic B, Macosko EZ, McCarroll SA, Ting JT, Zeng H, Zhang K, Feng G, Ecker JR, Linnarsson S, Lein ES, , Comparative cellular analysis of motor cortex in human, marmoset and mouse., Nature 2021 10; 598(7879): 111-119.
• 2021
  Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI, Ament SA, Bartlett A, Behrens MM, Van den Berge K, Bertagnolli D, de Bézieux HR, Biancalani T, Booeshaghi AS, Bravo HC, Casper T, Colantuoni C, Crabtree J, Creasy H, Crichton K, Crow M, Dee N, Dougherty EL, Doyle WI, Dudoit S, Fang R, Felix V, Fong O, Giglio M, Goldy J, Hawrylycz M, Herb BR, Hertzano R, Hou X, Hu Q, Kancherla J, Kroll M, Lathia K, Li YE, Lucero JD, Luo C, Mahurkar A, McMillen D, Nadaf NM, Nery JR, Nguyen TN, Niu SY, Ntranos V, Orvis J, Osteen JK, Pham T, Pinto-Duarte A, Poirion O, Preissl S, Purdom E, Rimorin C, Risso D, Rivkin AC, Smith K, Street K, Sulc J, Svensson V, Tieu M, Torkelson A, Tung H, Vaishnav ED, Vanderburg CR, van Velthoven C, Wang X, White OR, Huang ZJ, Kharchenko PV, Pachter L, Ngai J, Regev A, Tasic B, Welch JD, Gillis J, Macosko EZ, Ren B, Ecker JR, Zeng H, Mukamel EA, , A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex., Nature 2021 10; 598(7879): 103-110.
• 2021
  Fischer S, Crow M, Harris BD, Gillis J, , Scaling up reproducible research for single-cell transcriptomics using MetaNeighbor., Nat Protoc 2021 08; 16(8): 4031-4067.
• 2021
  Harris BD, Crow M, Fischer S, Gillis J, , Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain., Cell Syst 2021 07; 12(7): 748-756.e3.
• 2021
  Lu S, Ortiz C, Fürth D, Fischer S, Meletis K, Zador A, Gillis J, , Assessing the replicability of spatial gene expression using atlas data from the adult mouse brain., PLoS Biol 2021 07; 19(7): e3001341.
• 2021
  Sun YC, Chen X, Fischer S, Lu S, Zhan H, Gillis J, Zador AM, , Integrating barcoded neuroanatomy with spatial transcriptional profiling enables identification of gene correlates of projections., Nat Neurosci 2021 06; 24(6): 873-885.
• 2020
  Lehman J, Clune J, Misevic D, Adami C, Altenberg L, Beaulieu J, Bentley PJ, Bernard S, Beslon G, Bryson DM, Cheney N, Chrabaszcz P, Cully A, Doncieux S, Dyer FC, Ellefsen KO, Feldt R, Fischer S, Forrest S, Fŕenoy A, Gagńe C, Le Goff L, Grabowski LM, Hodjat B, Hutter F, Keller L, Knibbe C, Krcah P, Lenski RE, Lipson H, MacCurdy R, Maestre C, Miikkulainen R, Mitri S, Moriarty DE, Mouret JB, Nguyen A, Ofria C, Parizeau M, Parsons D, Pennock RT, Punch WF, Ray TS, Schoenauer M, Schulte E, Sims K, Stanley KO, Taddei F, Tarapore D, Thibault S, Watson R, Weimer W, Yosinski J, , The Surprising Creativity of Digital Evolution: A Collection of Anecdotes from the Evolutionary Computation and Artificial Life Research Communities., Artif Life 2020 ; 26(2): 274-306.
• 2020
  Li S, Kendall J, Park S, Wang Z, Alexander J, Moffitt A, Ranade N, Danyko C, Gegenhuber B, Fischer S, Robinson BD, Lepor H, Tollkuhn J, Gillis J, Brouzes E, Krasnitz A, Levy D, Wigler M, , Copolymerization of single-cell nucleic acids into balls of acrylamide gel., Genome Res 2020 01; 30(1): 49-61.
• 2019
  Chen X, Sun YC, Zhan H, Kebschull JM, Fischer S, Matho K, Huang ZJ, Gillis J, Zador AM, , High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing., Cell 2019 10; 179(3): 772-786.e19.
• 2019
  Bulović A, Fischer S, Dinh M, Golib F, Liebermeister W, Poirier C, Tournier L, Klipp E, Fromion V, Goelzer A, , Automated generation of bacterial resource allocation models., Metab Eng 2019 09; 55(): 12-22.
• 2017
  Henry VJ, Goelzer A, Ferré A, Fischer S, Dinh M, Loux V, Froidevaux C, Fromion V, , The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes., J Biomed Semantics 2017 Nov; 8(1): 53.
• 2014
  Fischer S, Bernard S, Beslon G, Knibbe C, , A model for genome size evolution., Bull Math Biol 2014 Sep; 76(9): 2249-91.