Peer-reviewed papers and preprints by our members

Scientific publications 2024

Bioinformatics has become essential to convert biological questions into answers. Discover the breadth of our scientists' work and contributions through their publications. 

 

Source: Europe PMC, latest update: 31.12.2024

Discover the SIB Remarkable Outputs 2023

The Remarkable Outputs are selected by the Award Committee to provide the community with the yearly achievements by SIB Scientists that are particularly deserving attention. From new algorithms to detect disease-related genes to exploring the origins of sexual reproduction, discover this shortlist of publications, software tools, databases and outreach projects.

  1. Abbara A, Pagani L, García-Pareja C, Bitbol AF. Mutant fate in spatially structured populations on graphs: Connecting models to experiments. PLoS Comput Biol 2024;20(9):e1012424
  2. Abkallo HM, Arbuthnot P, Auer TO, Berger DK, Burger J, Chakauya E, Concordet JP, Diabate A, Di Donato V, Groenewald JH, Guindo A, Koekemoer LL, Nazare F, Nolan T, Okumu F, Orefuwa E, Paemka L, Prieto-Godino L, Runo S, Sadler M, Tesfaye K, Tripathi L, Wondji C. Making genome editing a success story in Africa. Nat Biotechnol 2024;42(4):551-554
  3. Adato O, Sloutskin A, Komemi H, Brabb I, Duttke S, Bucher P, Unger R, Juven-Gershon T. ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements.Bioinformatics 2024;40(3):btae110
  4. Ahel J, Pandey A, Schwaiger M, Mohn F, Basters A, Kempf G, Andriollo A, Kaaij L, Hess D, Bühler M. ChAHP2 and ChAHP control diverse retrotransposons by complementary activities 2024
  5. Ahel J, Pandey A, Schwaiger M, Mohn F, Basters A, Kempf G, Andriollo A, Kaaij L, Hess D, Bühler M. ChAHP2 and ChAHP control diverse retrotransposons by complementary activities. Genes Dev 2024;38(11-12):554-568
  6. Akarsu H, Liljander AM, Lacasta A, Ssajjakambwe P, Brodard I, Cherbuin JDR, Torres-Puig S, Perreten V, Kuhnert P, Labroussaa F, Jores J. Canine Staphylococcaceae circulating in a Kenyan animal shelter. Microbiol Spectr 2024;12(2):e0292423
  7. Albani M, Fassi EMA, Moretti RM, Garofalo M, Montagnani Marelli M, Roda G, Sgrignani J, Cavalli A, Grazioso G. Computational Design of Novel Cyclic Peptides Endowed with Autophagy-Inhibiting Activity on Cancer Cell Lines. Int J Mol Sci 2024;25(9):4622
  8. Alexandre A, Abbara A, Fruet C, Loverdo C, Bitbol AF. Bridging Wright-Fisher and Moran models. J Theor Biol 2025;599:112030
  9. Allen BJ, Hill DJ, Burke AM, Clark M, Marchant R, Stringer LC, Williams DR, Lyon C. Projected future climatic forcing on the global distribution of vegetation types. Philos Trans R Soc Lond B Biol Sci 2024;379(1902):20230011
  10. Allentoft ME, Sikora M, Fischer A, Sjögren KG, Ingason A, Macleod R, Rosengren A, Schulz Paulsson B, Jørkov MLS, Novosolov M, Stenderup J, Price TD, Fischer Mortensen M, Nielsen AB, Ulfeldt Hede M, Sørensen L, Nielsen PO, Rasmussen P, Jensen TZT, Refoyo-Martínez A, Irving-Pease EK, Barrie W, Pearson A, Sousa da Mota B, Demeter F, Henriksen RA, Vimala T, McColl H, Vaughn A, Vinner L, Renaud G, Stern A, Johannsen NN, Ramsøe AD, Schork AJ, Ruter A, Gotfredsen AB, Henning Nielsen B, Brinch Petersen E, Kannegaard E, Hansen J, Buck Pedersen K, Pedersen L, Klassen L, Meldgaard M, Johansen M, Uldum OC, Lotz P, Lysdahl P, Bangsgaard P, Petersen PV, Maring R, Iversen R, Wåhlin S, Anker Sørensen S, Andersen SH, Jørgensen T, Lynnerup N, Lawson DJ, Rasmussen S, Korneliussen TS, Kjær KH, Durbin R, Nielsen R, Delaneau O, Werge T, Kristiansen K, Willerslev E. 100 ancient genomes show repeated population turnovers in Neolithic Denmark. Nature 2024;625(7994):329-337
  11. Allentoft ME, Sikora M, Refoyo-Martínez A, Irving-Pease EK, Fischer A, Barrie W, Ingason A, Stenderup J, Sjögren KG, Pearson A, Sousa da Mota B, Schulz Paulsson B, Halgren A, Macleod R, Jørkov MLS, Demeter F, Sørensen L, Nielsen PO, Henriksen RA, Vimala T, McColl H, Margaryan A, Ilardo M, Vaughn A, Fischer Mortensen M, Nielsen AB, Ulfeldt Hede M, Johannsen NN, Rasmussen P, Vinner L, Renaud G, Stern A, Jensen TZT, Scorrano G, Schroeder H, Lysdahl P, Ramsøe AD, Skorobogatov A, Schork AJ, Rosengren A, Ruter A, Outram A, Timoshenko AA, Buzhilova A, Coppa A, Zubova A, Silva AM, Hansen AJ, Gromov A, Logvin A, Gotfredsen AB, Henning Nielsen B, González-Rabanal B, Lalueza-Fox C, McKenzie CJ, Gaunitz C, Blasco C, Liesau C, Martinez-Labarga C, Pozdnyakov DV, Cuenca-Solana D, Lordkipanidze DO, En'shin D, Salazar-García DC, Price TD, Borić D, Kostyleva E, Veselovskaya EV, Usmanova ER, Cappellini E, Brinch Petersen E, Kannegaard E, Radina F, Eylem Yediay F, Duday H, Gutiérrez-Zugasti I, Merts I, Potekhina I, Shevnina I, Altinkaya I, Guilaine J, Hansen J, Aura Tortosa JE, Zilhão J, Vega J, Buck Pedersen K, Tunia K, Zhao L, Mylnikova LN, Larsson L, Metz L, Yepiskoposyan L, Pedersen L, Sarti L, Orlando L, Slimak L, Klassen L, Blank M, González-Morales M, Silvestrini M, Vretemark M, Nesterova MS, Rykun M, Rolfo MF, Szmyt M, Przybyła M, Calattini M, Sablin M, Dobisíková M, Meldgaard M, Johansen M, Berezina N, Card N, Saveliev NA, Poshekhonova O, Rickards O, Lozovskaya OV, Gábor O, Uldum OC, Aurino P, Kosintsev P, Courtaud P, Ríos P, Mortensen P, Lotz P, Persson P, Bangsgaard P, de Barros Damgaard P, Vang Petersen P, Martinez PP, Włodarczak P, Smolyaninov RV, Maring R, Menduiña R, Badalyan R, Iversen R, Turin R, Vasilyev S, Wåhlin S, Borutskaya S, Skochina S, Sørensen SA, Andersen SH, Jørgensen T, Serikov YB, Molodin VI, Smrcka V, Merts V, Appadurai V, Moiseyev V, Magnusson Y, Kjær KH, Lynnerup N, Lawson DJ, Sudmant PH, Rasmussen S, Korneliussen TS, Durbin R, Nielsen R, Delaneau O, Werge T, Racimo F, Kristiansen K, Willerslev E. Population genomics of post-glacial western Eurasia. Nature 2024;625(7994):301-311
  12. Allentoft ME, Sikora M, Refoyo-Martínez A, Irving-Pease EK, Fischer A, Barrie W, Ingason A, Stenderup J, Sjögren KG, Pearson A, Sousa da Mota B, Schulz Paulsson B, Halgren A, Macleod R, Jørkov MLS, Demeter F, Sørensen L, Nielsen PO, Henriksen RA, Vimala T, McColl H, Margaryan A, Ilardo M, Vaughn A, Fischer Mortensen M, Nielsen AB, Ulfeldt Hede M, Johannsen NN, Rasmussen P, Vinner L, Renaud G, Stern A, Jensen TZT, Scorrano G, Schroeder H, Lysdahl P, Ramsøe AD, Skorobogatov A, Schork AJ, Rosengren A, Ruter A, Outram A, Timoshenko AA, Buzhilova A, Coppa A, Zubova A, Silva AM, Hansen AJ, Gromov A, Logvin A, Gotfredsen AB, Henning Nielsen B, González-Rabanal B, Lalueza-Fox C, McKenzie CJ, Gaunitz C, Blasco C, Liesau C, Martinez-Labarga C, Pozdnyakov DV, Cuenca-Solana D, Lordkipanidze DO, En'shin D, Salazar-García DC, Price TD, Borić D, Kostyleva E, Veselovskaya EV, Usmanova ER, Cappellini E, Brinch Petersen E, Kannegaard E, Radina F, Eylem Yediay F, Duday H, Gutiérrez-Zugasti I, Merts I, Potekhina I, Shevnina I, Altinkaya I, Guilaine J, Hansen J, Aura Tortosa JE, Zilhão J, Vega J, Buck Pedersen K, Tunia K, Zhao L, Mylnikova LN, Larsson L, Metz L, Yepiskoposyan L, Pedersen L, Sarti L, Orlando L, Slimak L, Klassen L, Blank M, González-Morales M, Silvestrini M, Vretemark M, Nesterova MS, Rykun M, Rolfo MF, Szmyt M, Przybyła M, Calattini M, Sablin M, Dobisíková M, Meldgaard M, Johansen M, Berezina N, Card N, Saveliev NA, Poshekhonova O, Rickards O, Lozovskaya OV, Gábor O, Uldum OC, Aurino P, Kosintsev P, Courtaud P, Ríos P, Mortensen P, Lotz P, Persson P, Bangsgaard P, de Barros Damgaard P, Vang Petersen P, Martinez PP, Włodarczak P, Smolyaninov RV, Maring R, Menduiña R, Badalyan R, Iversen R, Turin R, Vasilyev S, Wåhlin S, Borutskaya S, Skochina S, Sørensen SA, Andersen SH, Jørgensen T, Serikov YB, Molodin VI, Smrcka V, Merts V, Appadurai V, Moiseyev V, Magnusson Y, Kjær KH, Lynnerup N, Lawson DJ, Sudmant PH, Rasmussen S, Korneliussen TS, Durbin R, Nielsen R, Delaneau O, Werge T, Racimo F, Kristiansen K, Willerslev E. Publisher Correction: Population genomics of post-glacial western Eurasia. Nature 2024;626(7997):E3
  13. Altenhoff A, Nevers Y, Tran V, Jyothi D, Martin M, Cosentino S, Majidian S, Marcet-Houben M, Fuentes-Palacios D, Persson E, Walsh T, Lecompte O, Gabaldón T, Kelly S, Hu Y, Iwasaki W, Capella-Gutierrez S, Dessimoz C, Thomas PD, Ebersberger I, Sonnhammer E. New developments for the Quest for Orthologs benchmark service. NAR Genom Bioinform 2024;6(4):lqae167
  14. Altenhoff AM, Warwick Vesztrocy A, Bernard C, Train CM, Nicheperovich A, Prieto Baños S, Julca I, Moi D, Nevers Y, Majidian S, Dessimoz C, Glover NM. OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem. Nucleic Acids Res 2024;52(d1):D513-D521
  15. Anderegg MA, Olinger EG, Bargagli M, Geraghty R, Taylor L, Nater A, Bruggmann R, Sayer JA, Vogt B, Schaller A, Fuster DG. Prevalence and characteristics of genetic disease in adult kidney stone formers. Nephrol Dial Transplant 2024;39(9):1426-1441
  16. Andreatta M, Hérault L, Gueguen P, Gfeller D, Berenstein AJ, Carmona SJ. Semi-supervised integration of single-cell transcriptomics data. Nat Commun 2024;15(1):872
  17. Andreoti TA, Maiolo M, Tuleja A, Döring Y, Schaller A, Vassella E, Boon LM, Baumgartner I, Bernhard SM, Zweier C, Vikkula M, Rössler J. Non-Hotspot PIK3CA Variants Have Higher Variant Allele Frequency and are More Common in Syndromic Vascular Malformations. Am J Med Genet A 2025;197(2):e63883
  18. Anglada-Girotto M, Ciampi L, Bonnal S, Head SA, Miravet-Verde S, Serrano L. In silico RNA isoform screening to identify potential cancer driver exons with therapeutic applications. Nat Commun 2024;15(1):7039
  19. Antonazzo G, Gaudet P, Lovering RC, Attrill H. Representation of non-coding RNA-mediated regulation of gene expression using the Gene Ontology. RNA Biol 2024;21(1):36-48
  20. Arias-Sánchez FI, Vessman B, Haym A, Alberti G, Mitri S. Artificial selection improves pollutant degradation by bacterial communities. Nat Commun 2024;15(1):7836
  21. Arribas AJ, Napoli S, Cascione L, Barnabei L, Sartori G, Cannas E, Gaudio E, Tarantelli C, Mensah AA, Spriano F, Zucchetto A, Rossi FM, Rinaldi A, Castro de Moura M, Jovic S, Bordone Pittau R, Stathis A, Stussi G, Gattei V, Brown JR, Esteller M, Zucca E, Rossi D, Bertoni F. ERBB4-Mediated Signaling Is a Mediator of Resistance to PI3K and BTK Inhibitors in B-cell Lymphoid Neoplasms. Mol Cancer Ther 2024;23(3):368-380
  22. Arribas AJ, Napoli S, Gaudio E, Herbaux C, Cannas E, Tarantelli C, Bordone-Pittau R, Cascione L, Munz N, Aresu L, Sgrignani J, Rinaldi A, Kwee I, Rossi D, Cavalli A, Zucca E, Stussi G, Stathis A, Sloss C, Davids MS, Bertoni F. PI3Kδ activation, IL-6 overexpression, and CD37 loss cause resistance to naratuximab emtansine in lymphomas. Blood Adv 2024;8(24):6268-6281
  23. Askary A, Chen W, Choi J, Du LY, Elowitz MB, Gagnon JA, Schier AF, Seidel S, Shendure J, Stadler T, Tran M. The lives of cells, recorded. Nat Rev Genet 2024
  24. Ataman M, Mittal N, Tintignac L, Schmidt A, Ham DJ, González A, Ruegg MA, Zavolan M. Calorie restriction and rapamycin distinctly mitigate aging-associated protein phosphorylation changes in mouse muscles. Commun Biol 2024;7(1):974
  25. Attafi OA, Clementel D, Kyritsis K, Capriotti E, Farrell G, Fragkouli SC, Castro LJ, Hatos A, Lenaerts T, Mazurenko S, Mozaffari S, Pradelli F, Ruch P, Savojardo C, Turina P, Zambelli F, Piovesan D, Monzon AM, Psomopoulos F, Tosatto SCE. DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology. Gigascience2024;13:giae094
  26. Aureli S, Bellina F, Rizzi V, Gervasio FL. Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study. J Chem Inf Model2024;64(22):8595-8603
  27. Auwerx C, Jõeloo M, Sadler MC, Tesio N, Ojavee S, Clark CJ, Mägi R, Estonian Biobank Research Team, Reymond A, Kutalik Z. Rare copy-number variants as modulators of common disease susceptibility. Genome Med 2024;16(1):5
  28. Auwerx C, Kutalik Z, Reymond A. The pleiotropic spectrum of proximal 16p11.2 CNVs. Am J Hum Genet 2024;111(11):2309-2346
  29. Auwerx C, Moix S, Kutalik Z, Reymond A. Disentangling mechanisms behind the pleiotropic effects of proximal 16p11.2 BP4-5 CNVs. Am J Hum Genet 2024;111(11):2347-2361
  30. Azizoglu A, Bijman EY, Stelling J, Brent R. Evolverator: An engineeredin celluloyeast system to drive rapid continuous evolution of proteins 2024
  31. Baciu-Drăgan MA, Beerenwinkel N. Oncotree2vec - a method for embedding and clustering of tumor mutation trees. Bioinformatics 2024;40(suppl 1):i180-i188
  32. Bak M, van Nimwegen E, Kouzel IU, Gur T, Schmidt R, Zavolan M, Gruber AJ. MAPP unravels frequent co-regulation of splicing and polyadenylation by RNA-binding proteins and their dysregulation in cancer. Nat Commun 2024;15(1):4110
  33. Bakker OB, Claringbould A, Westra HJ, Wiersma H, Boulogne F, Võsa U, Urzúa-Traslaviña CG, Mulcahy Symmons S, Zidan MMM, Sadler MC, Kutalik Z, Jonkers IH, Franke L, Deelen P.Identification of rare disease genes as drivers of common diseases through tissue-specific gene regulatory networks. Sci Rep 2024;14(1):30206
  34. Bao K, Silbereisen A, Grossmann J, Nanni P, Gehrig P, Emingil G, Erguz M, Karapinar DY, Pekpinarli B, Belibasakis GN, Tsilingaridis G, Zaura E, Bostanci N. Protein Network Alterations in G-CSF Treated Severe Congenital Neutropenia Patients and Beneficial Effects of Oral Health Intervention. Proteomics Clin Appl 2024;18(6):e202400064
  35. Barras D, Ghisoni E, Chiffelle J, Orcurto A, Dagher J, Fahr N, Benedetti F, Crespo I, Grimm AJ, Morotti M, Zimmermann S, Duran R, Imbimbo M, de Olza MO, Navarro B, Homicsko K, Bobisse S, Labes D, Tsourti Z, Andriakopoulou C, Herrera F, Pétremand R, Dummer R, Berthod G, Kraemer AI, Huber F, Thevenet J, Bassani-Sternberg M, Schaefer N, Prior JO, Matter M, Aedo V, Dromain C, Corria-Osorio J, Tissot S, Kandalaft LE, Gottardo R, Pittet M, Sempoux C, Michielin O, Dafni U, Trueb L, Harari A, Laniti DD, Coukos G. Response to tumor-infiltrating lymphocyte adoptive therapy is associated with preexisting CD8+ T-myeloid cell networks in melanoma. Sci Immunol 2024;9(92):eadg7995
  36. Barrat-Charlaix P, Neher RA. Eco-evolutionary dynamics of adapting pathogens and host immunity. Elife 2024;13:RP97350
  37. Baumann KBL, Mazzoli A, Salazar G, Ruscheweyh HJ, Müller B, Niederdorfer R, Sunagawa S, Lever MA, Lehmann MF, Bürgmann H. Metagenomic and -transcriptomic analyses of microbial nitrogen transformation potential, and gene expression in Swiss lake sediments. ISME Commun 2024;4(1):ycae110
  38. Baykal PI, Łabaj PP, Markowetz F, Schriml LM, Stekhoven DJ, Mangul S, Beerenwinkel N. Genomic reproducibility in the bioinformatics era. Genome Biol 2024;25(1):213
  39. Beavogui A, Lacroix A, Wiart N, Poulain J, Delmont TO, Paoli L, Wincker P, Oliveira PH. The defensome of complex bacterial communities. Nat Commun 2024;15(1):2146
  40. Bejarano L, Kauzlaric A, Lamprou E, Lourenco J, Fournier N, Ballabio M, Colotti R, Maas R, Galland S, Massara M, Soukup K, Lilja J, Brouland JP, Hottinger AF, Daniel RT, Hegi ME, Joyce JA.Interrogation of endothelial and mural cells in brain metastasis reveals key immune-regulatory mechanisms. Cancer Cell 2024;42(3):378-395.e10
  41. Beltrao P, Van Den Bossche T, Gabriels R, Holstein T, Kockmann T, Nameni A, Panse C, Schlapbach R, Lautenbacher L, Mattanovich M, Nesvizhskii A, Van Puyvelde B, Scheid J, Schwämmle V, Strauss M, Susmelj AK, The M, Webel H, Wilhelm M, Winkelhardt D, Wolski WE, Xi M. Proceedings of the EuBIC-MS developers meeting 2023. J Proteomics 2024;305:105246
  42. Beltrao P. The power of scientific collaborations and the future of structural biology. Nat Struct Mol Biol 2024;31(9):1309-1310
  43. Benvenga V, Cuénod A, Purushothaman S, Dasen G, Weisser M, Bassetti S, Roloff T, Siegemund M, Heininger U, Bielicki J, Wehrli M, Friderich P, Frei R, Widmer A, Herzog K, Fankhauser H, Nolte O, Bodmer T, Risch M, Dubuis O, Pranghofer S, Calligaris-Maibach R, Graf S, Perreten V, Seth-Smith HMB, Egli A. Historic methicillin-resistant Staphylococcus aureus: expanding current knowledge using molecular epidemiological characterization of a Swiss legacy collection. Genome Med 2024;16(1):23
  44. Bibekar P, Krapp L, Peraro MD. PeSTo-Carbs: Geometric Deep Learning for Prediction of Protein-Carbohydrate Binding Interfaces. J Chem Theory Comput 2024;20(8):2985-2991
  45. Bibert S, Quinodoz M, Perriot S, Krebs FS, Jan M, Malta RC, Collinet E, Canales M, Mathias A, Faignart N, Roulet-Perez E, Meylan P, Brouillet R, Opota O, Lozano-Calderon L, Fellmann F, Guex N, Zoete V, Asner S, Rivolta C, Du Pasquier R, Bochud PY. Herpes simplex encephalitis due to a mutation in an E3 ubiquitin ligase. Nat Commun 2024;15(1):3969
  46. Bilous M, Hérault L, Gabriel AA, Teleman M, Gfeller D. Building and analyzing metacells in single-cell genomics data. Mol Syst Biol 2024;20(7):744-766
  47. Bilous M, Hérault L, Gabriel AA, Teleman M, Gfeller D. Building and analyzing metacells in single-cell genomics data 2024
  48. Boder-Pasche S, Demir M, Heub S, Garzuel M, Ischer R, Migliozzi D, Graf S, Schmid N, Atakan HB, Gudkova D, Alpern D, Dainese R, Deplancke B, Weder G. Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing. Biomed Microdevices 2024;26(2):18
  49. Boersma B, Puddinu V, Huard A, Fauteux-Daniel S, Wirapati P, Guedri S, Tille JC, McKee T, Pittet M, Palmer G, Bourquin C. GSDMD is associated with survival in human breast cancer but does not impact anti-tumor immunity in a mouse breast cancer model. Front Immunol 2024;15:1396777
  50. Bontonou G, Saint-Leandre B, Kafle T, Baticle T, Hassan A, Sánchez-Alcañiz JA, Arguello JR. Evolution of chemosensory tissues and cells across ecologically diverse Drosophilids. Nat Commun 2024;15(1):1047
  51. Borsatto A, Gianquinto E, Rizzi V, Gervasio FL. SWISH-X, an Expanded Approach to Detect Cryptic Pockets in Proteins and at Protein-Protein Interfaces. J Chem Theory Comput2024;20(8):3335-3348
  52. Bourguignon L, Lukas LP, Guest JD, Geisler FH, Noonan V, Curt A, Brüningk SC, Jutzeler CR. Studying missingness in spinal cord injury data: challenges and impact of data imputation. BMC Med Res Methodol 2024;24(1):5
  53. Bourguignon L, Lukas LP, Kondiles BR, Tong B, Lee JJ, Gomes T, Tetzlaff W, Kramer JLK, Walter M, Jutzeler CR. Impact of commonly administered drugs on the progression of spinal cord injury: a systematic review. Commun Med (Lond) 2024;4(1):213
  54. Bozzi D, Neuenschwander S, Cruz Dávalos DI, Sousa da Mota B, Schroeder H, Moreno-Mayar JV, Allentoft ME, Malaspinas AS. Towards predicting the geographical origin of ancient samples with metagenomic data. Sci Rep 2024;14(1):21794
  55. Brewer TE, Wagner A. Horizontal Gene Transfer of a key Translation Factor and its Role in Polyproline Proteome Evolution. Mol Biol Evol 2024;41(9):msae180
  56. Bruschi M, Angeletti A, Prunotto M, Meroni PL, Ghiggeri GM, Zeus consortium, Moroni G, Sinico RA, Franceschini F, Fredi M, Vaglio A, Cavalli A, Scapozza L, Patel JJ, Tan JC, Lo KC, Cavagna L, Petretto A, Pratesi F, Migliorini P, Locatelli F, Pazzola G, Pesce G, Giannese D, Manfredi A, Ramirez GA, Esposito P, Murdaca G, Negrini S, Bui F, Trezzi B, Emmi G, Cavazzana I, Binda V, Fenaroli P, Pisan I, Montecucco C, Santoro D, Scolari F, Mescia F, Volpi S, Mosca M, Tincani A, Ravelli A, Murtas C, Candiano G, Caridi G, La Porta E, Verrina E. A critical view on autoantibodies in lupus nephritis: Concrete knowledge based on evidence. Autoimmun Rev 2024;23(5):103535
  57. Brümmer A, Bergmann S. Disentangling genetic effects on transcriptional and post-transcriptional gene regulation through integrating exon and intron expression QTLs. Nat Commun2024;15(1):3786
  58. Brüningk SC, Bourguignon L, Lukas LP, EMSCI study group, Maier D, Abel R, Weidner N, Rupp R, Geisler F, Kramer JLK, Guest J, Curt A, Jutzeler CR. Prediction of segmental motor outcomes in traumatic spinal cord injury: Advances beyond sum scores. Exp Neurol 2024;380:114905
  59. Bugnon M, Röhrig UF, Goullieux M, Perez MAS, Daina A, Michielin O, Zoete V. SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina.Nucleic Acids Res 2024;52(w1):W324-W332
  60. Burgermeister S, Stoykova S, Krebs F, Zoete V, Mbefo M, Egervari K, Reinhard A, Bisig B, Hewer E. Methylation-Based Characterization of a New IDH2 Mutation in Sinonasal Undifferentiated Carcinoma Int J Mol Sci 2024;25(12)
  61. Burgermeister S, Stoykova S, Krebs FS, Zoete V, Mbefo M, Egervari K, Reinhard A, Bisig B, Hewer E. Methylation-Based Characterization of a New IDH2 Mutation in Sinonasal Undifferentiated Carcinoma. Int J Mol Sci 2024;25(12):6518
  62. Cacciatore A, Shinde D, Musumeci C, Sandrini G, Guarrera L, Albino D, Civenni G, Storelli E, Mosole S, Federici E, Fusina A, Iozzo M, Rinaldi A, Pecoraro M, Geiger R, Bolis M, Catapano CV, Carbone GM. Epigenome-wide impact of MAT2A sustains the androgen-indifferent state and confers synthetic vulnerability in ERG fusion-positive prostate cancer. Nat Commun2024;15(1):6672
  63. Caduff M, Eckel R, Leuenberger C, Wegmann D. Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data. Mol Ecol Resour2024;24(3):e13913
  64. Cai P, Robinson MD, Tiberi S. DESpace: spatially variable gene detection via differential expression testing of spatial clusters. Bioinformatics 2024;40(2):btae027
  65. Cailleau G, Junier T, Paul C, Fatton M, Corona-Ramirez A, Gning O, Beck K, Vidal J, Bürgmann H, Junier P. Temporal and spatial changes in the abundance of antibiotic resistance gene markers in a wastewater treatment plant. Water Environ Res 2024;96(8):e11104
  66. Calderón Del Cid C, Villalobos F, Dobrovolski R, Carrillo JD, Silvestro D, Vilela B. The Clade Replacement Theory: a framework to study age-dependent extinction. J Evol Biol 2024;37(3):290-301
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