1. Acinas SG, Sánchez P, Salazar G, Cornejo-Castillo FM, Sebastián M, Logares R, Royo-Llonch M, Paoli L, Sunagawa S, Hingamp P, Ogata H, Lima-Mendez G, Roux S, González JM, Arrieta JM, Alam IS, Kamau A, Bowler C, Raes J, Pesant S, Bork P, Agustí S, Gojobori T, Vaqué D, Sullivan MB, Pedrós-Alió C, Massana R, Duarte CM, Gasol JM. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Commun Biol 2021;4(1):604
  2. Andreatta M, Corria-Osorio J, Müller S, Cubas R, Coukos G, Carmona SJ. Interpretation of T cell states from single-cell transcriptomics data using reference atlases. Nat Commun 2021;12(1):2965
  3. Armstrong EE, Khan A, Taylor RW, Gouy A, Greenbaum G, Thiéry A, Kang JT, Redondo SA, Prost S, Barsh G, Kaelin C, Phalke S, Chugani A, Gilbert M, Miquelle D, Zachariah A, Borthakur U, Reddy A, Louis E, Ryder OA, Jhala YV, Petrov D, Excoffier L, Hadly E, Ramakrishnan U. Recent Evolutionary History of Tigers Highlights Contrasting Roles of Genetic Drift and Selection. Mol Biol Evol 2021;38(6):2366-2379
  4. Bast-Habersbrunner A, Kiefer C, Weber P, Fromme T, Schießl A, Schwalie PC, Deplancke B, Li Y, Klingenspor M. LncRNA Ctcflos orchestrates transcription and alternative splicing in thermogenic adipogenesis. EMBO Rep 2021:e51289
  5. Bloom JD, Chan YA, Baric RS, Bjorkman PJ, Cobey S, Deverman BE, Fisman DN, Gupta R, Iwasaki A, Lipsitch M, Medzhitov R, Neher RA, Nielsen R, Patterson N, Stearns T, van Nimwegen E, Worobey M, Relman DA. Investigate the origins of COVID-19. Science 2021;372(6543):694
  6. Bosi E, Marselli L, De Luca C, Suleiman M, Tesi M, Ibberson M, Eizirik DL, Cnop M, Marchetti P. Correction to 'Integration of single-cell datasets reveals novel transcriptomic signatures of β-cells in human type 2 diabetes'. NAR Genom Bioinform 2021;3(2):lqab053
  7. Chiva C, Mendes Maia T, Panse C, Stejskal K, Douché T, Matondo M, Loew D, Helm D, Rettel M, Mechtler K, Impens F, Nanni P, Shevchenko A, Sabidó E. Quality standards in proteomics research facilities: Common standards and quality procedures are essential for proteomics facilities and their users. EMBO Rep 2021:e52626
  8. Conrad L, Runser SVM, Fernando Gómez H, Lang CM, Dumond MS, Sapala A, Schaumann L, Michos O, Vetter R, Iber D. The biomechanical basis of biased epithelial tube elongation in lung and kidney development. Development 2021;148(9)
  9. Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KR, Donnellan D, Hecht J, Jackson K, Kuchin K, Karasikov M, Lyons A, Mak L, Meleshko D, Mustafa H, Mutai B, Neches RY, Ng A, Nikolayeva O, Nikolayeva T, Png E, Ryon KA, Sanchez JL, Shaaban H, Sierra MA, Thomas D, Young B, Abudayyeh OO, Alicea J, Bhattacharyya M, Blekhman R, Castro-Nallar E, Cañas AM, Chatziefthimiou AD, Crawford RW, De Filippis F, Deng Y, Desnues C, Dias-Neto E, Dybwad M, Elhaik E, Ercolini D, Frolova A, Gankin D, Gootenberg JS, Graf AB, Green DC, Hajirasouliha I, Hastings JJA, Hernandez M, Iraola G, Jang S, Kahles A, Kelly FJ, Knights K, Kyrpides NC, Łabaj PP, Lee PKH, Leung MHY, Ljungdahl PO, Mason-Buck G, McGrath K, Meydan C, Mongodin EF, Moraes MO, Nagarajan N, Nieto-Caballero M, Noushmehr H, Oliveira M, Ossowski S, Osuolale OO, Özcan O, Paez-Espino D, Rascovan N, Richard H, Rätsch G, Schriml LM, Semmler T, Sezerman OU, Shi L, Shi T, Siam R, Song LH, Suzuki H, Court DS, Tighe SW, Tong X, Udekwu KI, Ugalde JA, Valentine B, Vassilev DI, Vayndorf EM, Velavan TP, Wu J, Zambrano MM, Zhu J, Zhu S, Mason CE, International MetaSUB Consortium. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell 2021
  10. Diard M, Bakkeren E, Lentsch V, Rocker A, Bekele NA, Hoces D, Aslani S, Arnoldini M, Böhi F, Schumann-Moor K, Adamcik J, Piccoli L, Lanzavecchia A, Stadtmueller BM, Donohue N, van der Woude MW, Hockenberry A, Viollier PH, Falquet L, Wüthrich D, Bonfiglio F, Loverdo C, Egli A, Zandomeneghi G, Mezzenga R, Holst O, Meier BH, Hardt WD, Slack E. A rationally designed oral vaccine induces immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants. Nat Microbiol 2021
  11. Fuchs Wightman F, Godoy Herz MA, Muñoz JC, Stigliano JN, Bragado L, Moreno NN, Palavecino M, Servi L, Cabrerizo G, Clemente J, Avaro M, Pontoriero A, Benedetti E, Baumeister E, Rudolf F, Remes Lenicov F, Garcia C, Buggiano V, Kornblihtt AR, Srebrow A, de la Mata M, Muñoz MJ, Schor IE, Petrillo E. A DNA intercalating dye-based RT-qPCR alternative to diagnose SARS-CoV-2. RNA Biol 2021:1-8
  12. Gao B, Baudis M. Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes. Front Genet 2021;12:654887
  13. Gerber R, Robinson MD. Censcyt: censored covariates in differential abundance analysis in cytometry. BMC Bioinformatics 2021;22(1):235
  14. Guinat C, Vergne T, Kocher A, Chakraborty D, Paul MC, Ducatez M, Stadler T. What can phylodynamics bring to animal health research? Trends Ecol Evol 2021
  15. Gusyatiner O, Bady P, Pham MDT, Lei Y, Park J, Daniel RT, Delorenzi M, Hegi ME. BET inhibitors repress expression of Interferon-stimulated genes and synergize with HDAC inhibitors in glioblastoma. Neuro Oncol 2021
  16. Heller RA, Seelig J, Crowell HL, Pilz M, Haubruck P, Sun Q, Schomburg L, Daniel V, Moghaddam A, Biglari B. Predicting neurological recovery after traumatic spinal cord injury by time-resolved analysis of monocyte subsets. Brain 2021
  17. Huang R, Soneson C, Germain PL, Schmidt TSB, Mering CV, Robinson MD. treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses. Genome Biol 2021;22(1):157
  18. Khelashvili G, Pillai AN, Lee J, Pandey K, Payne AM, Siegel Z, Cuendet MA, Lewis TR, Arshavsky VY, Broichhagen J, Levitz J, Menon AK. Unusual mode of dimerization of retinitis pigmentosa-associated F220C rhodopsin. Sci Rep 2021;11(1):10536
  19. Lauriola I, Aiolli F, Lavelli A, Rinaldi F. Learning adaptive representations for entity recognition in the biomedical domain. J Biomed Semantics 2021;12(1):10
  20. Liu Y, Nanni L, Sungalee S, Zufferey M, Tavernari D, Mina M, Ceri S, Oricchio E, Ciriello G. Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes. Nat Commun 2021;12(1):2439
  21. Luqman H, Widmer A, Fior S, Wegmann D. Identifying loci under selection via explicit demographic models. Mol Ecol Resour 2021
  22. Makunin A, Korlević P, Park N, Goodwin S, Waterhouse RM, von Wyschetzki K, Jacob CG, Davies R, Kwiatkowski D, St Laurent B, Ayala D, Lawniczak MKN. A targeted amplicon sequencing panel to simultaneously identify mosquito species and Plasmodium presence across the entire Anopheles genus. Mol Ecol Resour 2021
  23. Marques DA, Lucek K, Sousa VC, Excoffier L, Seehausen O. Reply to "Re-evaluating the evidence for facilitation of stickleback speciation by admixture in the Lake Constance basin". Nat Commun 2021;12(1):2807
  24. Mensah AA, Spriano F, Sartori G, Priebe V, Cascione L, Gaudio E, Tarantelli C, Civanelli E, Aresu L, Rinaldi A, Damia G, Lovati E, Zucca E, Stathis A, Pietra C, Bertoni F. Study of the antilymphoma activity of pracinostat reveals different sensitivities of DLBCL cells to HDAC inhibitors. Blood Adv 2021;5(10):2467-2480
  25. Morita K, Wang F, Jahn K, Hu T, Tanaka T, Sasaki Y, Kuipers J, Loghavi S, Wang SA, Yan Y, Furudate K, Matthews J, Little L, Gumbs C, Zhang J, Song X, Thompson E, Patel KP, Bueso-Ramos CE, DiNardo CD, Ravandi F, Jabbour E, Andreeff M, Cortes J, Bhalla K, Garcia-Manero G, Kantarjian H, Konopleva M, Nakada D, Navin N, Beerenwinkel N, Futreal PA, Takahashi K. Author Correction: Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics. Nat Commun 2021;12(1):2823
  26. Porcu E, Sjaarda J, Lepik K, Carmeli C, Darrous L, Sulc J, Mounier N, Kutalik Z. Causal Inference Methods to Integrate Omics and Complex Traits. Cold Spring Harb Perspect Med 2021;11(5)
  27. Sahadevan S, Hembach KM, Tantardini E, Pérez-Berlanga M, Hruska-Plochan M, Megat S, Weber J, Schwarz P, Dupuis L, Robinson MD, De Rossi P, Polymenidou M. Synaptic FUS accumulation triggers early misregulation of synaptic RNAs in a mouse model of ALS. Nat Commun 2021;12(1):3027
  28. Santos-Moreno J, Tasiudi E, Stelling J, Schaerli Y. Author Correction: Multistable and dynamic CRISPRi-based synthetic circuits. Nat Commun 2021;12(1):3119
  29. Schmidt T, Samaras P, Dorfer V, Panse C, Kockmann T, Bichmann L, van Puyvelde B, Perez-Riverol Y, Deutsch EW, Kuster B, Wilhelm M. Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison. J Proteome Res 2021
  30. Song S, Cao C, Choukrallah MA, Tang F, Christofori G, Kohler H, Wu F, Fodor BD, Frederiksen M, Willis SN, Jackson JT, Nutt SL, Dirnhofer S, Stadler MB, Matthias P. OBF1 and Oct factors control the germinal center transcriptional program. Blood 2021;137(21):2920-2934
  31. Stevens CA, Bachtiger F, Kong XD, Abriata LA, Sosso GC, Gibson MI, Klok HA. A minimalistic cyclic ice-binding peptide from phage display. Nat Commun 2021;12(1):2675
  32. Sungalee S, Liu Y, Lambuta RA, Katanayeva N, Donaldson Collier M, Tavernari D, Roulland S, Ciriello G, Oricchio E. Histone acetylation dynamics modulates chromatin conformation and allele-specific interactions at oncogenic loci. Nat Genet 2021;53(5):650-662
  33. Träger S, Tamò G, Aydin D, Fonti G, Audagnotto M, Dal Peraro M. CLoNe: automated clustering based on local density neighborhoods for application to biomolecular structural ensembles. Bioinformatics 2021;37(7):921-928
  34. van Gestel J, Wagner A. Cryptic surface-associated multicellularity emerges through cell adhesion and its regulation. PLoS Biol 2021;19(5):e3001250
  35. Vogels CBF, Breban MI, Ott IM, Alpert T, Petrone ME, Watkins AE, Kalinich CC, Earnest R, Rothman JE, Goes de Jesus J, Morales Claro I, Magalhães Ferreira G, Crispim MAE, Brazil-UK CADDE Genomic Network, Singh L, Tegally H, Anyaneji UJ, Network for Genomic Surveillance in South Africa, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JR, Grubaugh ND. Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. PLoS Biol 2021;19(5):e3001236
  36. Voisin N, Schnur RE, Douzgou S, Hiatt SM, Rustad CF, Brown NJ, Earl DL, Keren B, Levchenko O, Geuer S, Verheyen S, Johnson D, Zarate YA, Hančárová M, Amor DJ, Bebin EM, Blatterer J, Brusco A, Cappuccio G, Charrow J, Chatron N, Cooper GM, Courtin T, Dadali E, Delafontaine J, Del Giudice E, Doco M, Douglas G, Eisenkölbl A, Funari T, Giannuzzi G, Gruber-Sedlmayr U, Guex N, Heron D, Holla ØL, Hurst ACE, Juusola J, Kronn D, Lavrov A, Lee C, Lorrain S, Merckoll E, Mikhaleva A, Norman J, Pradervand S, Prchalová D, Rhodes L, Sanders VR, Sedláček Z, Seebacher HA, Sellars EA, Sirchia F, Takenouchi T, Tanaka AJ, Taska-Tench H, Tønne E, Tveten K, Vitiello G, Vlčková M, Uehara T, Nava C, Yalcin B, Kosaki K, Donnai D, Mundlos S, Brunetti-Pierri N, Chung WK, Reymond A. Variants in the degron of AFF3 are associated with intellectual disability, mesomelic dysplasia, horseshoe kidney, and epileptic encephalopathy. Am J Hum Genet 2021;108(5):857-873
  37. Žegarac A, Winkelbach L, Blöcher J, Diekmann Y, Krečković Gavrilović M, Porčić M, Stojković B, Milašinović L, Schreiber M, Wegmann D, Veeramah KR, Stefanović S, Burger J. Ancient genomes provide insights into family structure and the heredity of social status in the early Bronze Age of southeastern Europe. Sci Rep 2021;11(1):10072
  38. Zhang Q, Ree RH, Salamin N, Xing Y, Silvestro D. Fossil-informed models reveal a Boreotropical origin and divergent evolutionary trajectories in the walnut family (Juglandaceae). Syst Biol 2021