Scientific publications 2021

Abriata LA, Dal Peraro M. Assessment of transferable forcefields for protein simulations attests improved description of disordered states and secondary structure propensities, and hints at multi-protein systems as the next challenge for optimization. Comput Struct Biotechnol J 2021;19:2626-2636
Abriata LA. How Technologies Assisted Science Learning at Home During the COVID-19 Pandemic. DNA Cell Biol 2021
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
Adolfi MC, Du K, Kneitz S, Cabau C, Zahm M, Klopp C, Feron R, Paixão RV, Varela ES, de Almeida FL, de Oliveira MA, Nóbrega RH, Lopez-Roques C, Iampietro C, Lluch J, Kloas W, Wuertz S, Schaefer F, Stöck M, Guiguen Y, Schartl M. A duplicated copy of id2b is an unusual sex-determining candidate gene on the Y chromosome of arapaima (Arapaima gigas). Sci Rep 2021;11(1):21544
Aguilar-Bultet L, Bagutti C, Egli A, Alt M, Maurer Pekerman L, Schindler R, Furger R, Eichenberger L, Roloff T, Steffen I, Huebner P, Stadler T, Tschudin-Sutter S. Identification of a Cluster of Extended-spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Sequence Type 101 Isolated From Food and Humans. Clin Infect Dis 2021;73(2):332-335
Ahluwalia TS, Prins BP, Abdollahi M, Armstrong NJ, Aslibekyan S, Bain L, Jefferis B, Baumert J, Beekman M, Ben-Shlomo Y, Bis JC, Mitchell BD, de Geus E, Delgado GE, Marek D, Eriksson J, Kajantie E, Kanoni S, Kemp JP, Lu C, Marioni RE, McLachlan S, Milaneschi Y, Nolte IM, Petrelis AM, Porcu E, Sabater-Lleal M, Naderi E, Seppälä I, Shah T, Singhal G, Standl M, Teumer A, Thalamuthu A, Thiering E, Trompet S, Ballantyne CM, Benjamin EJ, Casas JP, Toben C, Dedoussis G, Deelen J, Durda P, Engmann J, Feitosa MF, Grallert H, Hammarstedt A, Harris SE, Homuth G, Hottenga JJ, Jalkanen S, Jamshidi Y, Jawahar MC, Jess T, Kivimaki M, Kleber ME, Lahti J, Liu Y, Marques-Vidal P, Mellström D, Mooijaart SP, Müller-Nurasyid M, Penninx B, Revez JA, Rossing P, Räikkönen K, Sattar N, Scharnagl H, Sennblad B, Silveira A, Pourcain BS, Timpson NJ, Trollor J, CHARGE Inflammation Working Group, van Dongen J, Van Heemst D, Visvikis-Siest S, Vollenweider P, Völker U, Waldenberger M, Willemsen G, Zabaneh D, Morris RW, Arnett DK, Baune BT, Boomsma DI, Chang YC, Deary IJ, Deloukas P, Eriksson JG, Evans DM, Ferreira MA, Gaunt T, Gudnason V, Hamsten A, Heinrich J, Hingorani A, Humphries SE, Jukema JW, Koenig W, Kumari M, Kutalik Z, Lawlor DA, Lehtimäki T, März W, Mather KA, Naitza S, Nauck M, Ohlsson C, Price JF, Raitakari O, Rice K, Sachdev PS, Slagboom E, Sørensen TIA, Spector T, Stacey D, Stathopoulou MG, Tanaka T, Wannamethee SG, Whincup P, Rotter JI, Dehghan A, Boerwinkle E, Psaty BM, Snieder H, Alizadeh BZ. Genome-wide association study of circulating interleukin 6 levels identifies novel loci. Hum Mol Genet 2021;30(5):393-409
Ahrens CH, Wade JT, Champion MM, Langer JD. A Practical Guide to Small Protein Discovery and Characterization using Mass Spectrometry. J Bacteriol 2021:JB0035321
Alessandro C, Antoine D, Marta A S P, Olivier M, Vincent Z. SwissBioisostere 2021: updated structural, bioactivity and physicochemical data delivered by a reshaped web interface. Nucleic Acids Res 2021
Alexander LT, Lepore R, Kryshtafovych A, Adamopoulos A, Alahuhta M, Arvin AM, Bomble YJ, Böttcher B, Breyton C, Chiarini V, Chinnam NB, Chiu W, Fidelis K, Grinter R, Gupta GD, Hartmann MD, Hayes CS, Heidebrecht T, Ilari A, Joachimiak A, Kim Y, Linares R, Lovering AL, Lunin VV, Lupas AN, Makbul C, Michalska K, Moult J, Mukherjee PK, Nutt WS, Oliver SL, Perrakis A, Stols L, Tainer JA, Topf M, Tsutakawa SE, Valdivia-Delgado M, Schwede T. Target highlights in CASP14: Analysis of models by structure providers. Proteins 2021
Altenhoff AM, Train CM, Gilbert KJ, Mediratta I, Mendes de Farias T, Moi D, Nevers Y, Radoykova HS, Rossier V, Warwick Vesztrocy A, Glover NM, Dessimoz C. OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more. Nucleic Acids Res 2021;49(d1):D373-D379
Ancey PB, Contat C, Boivin G, Sabatino S, Pascual J, Zangger N, Perentes JY, Peters S, Abel ED, Kirsch DG, Rathmell JC, Vozenin MC, Meylan E. GLUT1 Expression in Tumor-Associated Neutrophils Promotes Lung Cancer Growth and Resistance to Radiotherapy. Cancer Res 2021;81(9):2345-2357
Andreatta M, Carmona SJ. UCell: Robust and scalable single-cell gene signature scoring. Comput Struct Biotechnol J 2021;19:3796-3798
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
Andreatta M, David FPA, Iseli C, Guex N, Carmona SJ. SPICA: Swiss portal for immune cell analysis. Nucleic Acids Res 2021
Annabi N, Baker M, Boettiger A, Chakraborty D, Chen Y, Corbett KS, Correia B, Dahlman J, de Oliveira T, Ertuerk A, Yanik MF, Henaff E, Huch M, Iliev ID, Jacobs T, Junca H, Keung A, Kolodkin-Gal I, Krishnaswamy S, Lancaster M, Macosko E, Martínez-Núñez MA, Miura K, Molloy J, Cruz AO, Platt RJ, Posey AD, Shao H, Simunovic M, Slavov N, Takebe T, Vandenberghe LH, Varshney RK, Wang J. Voices of biotech research. Nat Biotechnol 2021;39(3):281-286
Antonarakis SE, Holoubek A, Rapti M, Rademaker J, Meylan J, Iwaszkiewicz J, Zoete V, Wilson C, Taylor J, Ansar M, Borel C, Menzel O, Kuželová K, Santoni FA. Dominant monoallelic variant in the PAK2 gene causes Knobloch syndrome type 2. Hum Mol Genet 2021;31(1):1-9
Aoki-Kinoshita KF, Lisacek F, Karlsson N, Kolarich D, Packer NH. GlycoBioinformatics. Beilstein J Org Chem 2021;17:2726-2728
Arguello JR, Abuin L, Armida J, Mika K, Chai PC, Benton R. Targeted molecular profiling of rare olfactory sensory neurons identifies fate, wiring, and functional determinants. Elife 2021;10
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
Arnaud M, Chiffelle J, Genolet R, Navarro Rodrigo B, Perez MAS, Huber F, Magnin M, Nguyen-Ngoc T, Guillaume P, Baumgaertner P, Chong C, Stevenson BJ, Gfeller D, Irving M, Speiser DE, Schmidt J, Zoete V, Kandalaft LE, Bassani-Sternberg M, Bobisse S, Coukos G, Harari A. Sensitive identification of neoantigens and cognate TCRs in human solid tumors. Nat Biotechnol 2021
Arvaniti E, Fricker KS, Moret M, Rupp N, Hermanns T, Fankhauser C, Wey N, Wild PJ, Rüschoff JH, Claassen M. Author Correction: Automated Gleason grading of prostate cancer tissue microarrays via deep learning. Sci Rep 2021;11(1):23032
Avilla-Royo E, Gegenschatz-Schmid K, Grossmann J, Kockmann T, Zimmermann R, Snedeker JG, Ochsenbein-Kölble N, Ehrbar M. Comprehensive quantitative characterization of the human term amnion proteome. Matrix Biol Plus 2021;12:100084
Azizoglu A, Brent R, Rudolf F. A precisely adjustable, variation-suppressed eukaryotic transcriptional controller to enable genetic discovery. Elife 2021;10
Bai Y, Caussinus E, Leo S, Bosshardt F, Myachina F, Rot G, Robinson MD, Lehner CF. A cis-regulatory element promoting increased transcription at low temperature in cultured ectothermic Drosophila cells. BMC Genomics 2021;22(1):771
Bakker MK, van der Spek RAA, van Rheenen W, Morel S, Bourcier R, Hostettler IC, Alg VS, van Eijk KR, Koido M, Akiyama M, Terao C, Matsuda K, Walters RG, Lin K, Li L, Millwood IY, Chen Z, Rouleau GA, Zhou S, Rannikmäe K, Sudlow CLM, Houlden H, van den Berg LH, Dina C, Naggara O, Gentric JC, Shotar E, Eugène F, Desal H, Winsvold BS, Børte S, Johnsen MB, Brumpton BM, Sandvei MS, Willer CJ, Hveem K, Zwart JA, Verschuren WMM, Friedrich CM, Hirsch S, Schilling S, Dauvillier J, Martin O, HUNT All-In Stroke, China Kadoorie Biobank Collaborative Group, BioBank Japan Project Consortium, ICAN Study Group, CADISP Group, Genetics and Observational Subarachnoid Haemorrhage (GOSH) Study investigators, International Stroke Genetics Consortium (ISGC), Jones GT, Bown MJ, Ko NU, Kim H, Coleman JRI, Breen G, Zaroff JG, Klijn CJM, Malik R, Dichgans M, Sargurupremraj M, Tatlisumak T, Amouyel P, Debette S, Rinkel GJE, Worrall BB, Pera J, Slowik A, Gaál-Paavola EI, Niemelä M, Jääskeläinen JE, von Und Zu Fraunberg M, Lindgren A, Broderick JP, Werring DJ, Woo D, Redon R, Bijlenga P, Kamatani Y, Veldink JH, Ruigrok YM. Author Correction: Genome-wide association study of intracranial aneurysms identifies 17 risk loci and genetic overlap with clinical risk factors. Nat Genet 2021;53(2):254
Bakkeren E, Herter JA, Huisman JS, Steiger Y, Gül E, Newson JPM, Brachmann AO, Piel J, Regoes R, Bonhoeffer S, Diard M, Hardt WD. Pathogen invasion-dependent tissue reservoirs and plasmid-encoded antibiotic degradation boost plasmid spread in the gut. Elife 2021;10
Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A. Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res 2021
Barrat-Charlaix P, Huddleston J, Bedford T, Neher RA. Limited Predictability of Amino Acid Substitutions in Seasonal Influenza Viruses. Mol Biol Evol 2021;38(7):2767-2777
Barrat-Charlaix P, Muntoni AP, Shimagaki K, Weigt M, Zamponi F. Sparse generative modeling via parameter reduction of Boltzmann machines: Application to protein-sequence families. Phys Rev E 2021;104(2-1):024407
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;22(7):e51289
Bastian FB, Roux J, Niknejad A, Comte A, Fonseca Costa SS, de Farias TM, Moretti S, Parmentier G, de Laval VR, Rosikiewicz M, Wollbrett J, Echchiki A, Escoriza A, Gharib WH, Gonzales-Porta M, Jarosz Y, Laurenczy B, Moret P, Person E, Roelli P, Sanjeev K, Seppey M, Robinson-Rechavi M. The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. Nucleic Acids Res 2021;49(d1):D831-D847
Bates AE, Primack RB, Biggar BS, Bird TJ, Clinton ME, Command RJ, Richards C, Shellard M, Geraldi NR, Vergara V, Acevedo-Charry O, Colón-Piñeiro Z, Ocampo D, Ocampo-Peñuela N, Sánchez-Clavijo LM, Adamescu CM, Cheval S, Racoviceanu T, Adams MD, Kalisa E, Kuuire VZ, Aditya V, Anderwald P, Wiesmann S, Wipf S, Badihi G, Henderson MG, Loetscher H, Baerenfaller K, Benedetti-Cecchi L, Bulleri F, Bertocci I, Maggi E, Rindi L, Ravaglioli C, Boerder K, Bonnel J, Mathias D, Archambault P, Chauvaud L, Braun CD, Thorrold SR, Brownscombe JW, Midwood JD, Boston CM, Brooks JL, Cooke SJ, China V, Roll U, Belmaker J, Zvuloni A, Coll M, Ortega M, Connors B, Lacko L, Jayathilake DRM, Costello MJ, Crimmins TM, Barnett L, Denny EG, Gerst KL, Marsh RL, Posthumus EE, Rodriguez R, Rosemartin A, Schaffer SN, Switzer JR, Wong K, Cunningham SJ, Sumasgutner P, Amar A, Thomson RL, Stofberg M, Hofmeyr S, Suri J, Stuart-Smith RD, Day PB, Edgar GJ, Cooper AT, De Leo FC, Garner G, Des Brisay PG, Schrimpf MB, Koper N, Diamond MS, Dwyer RG, Baker CJ, Franklin CE, Efrat R, Berger-Tal O, Hatzofe O, Eguíluz VM, Rodríguez JP, Fernández-Gracia J, Elustondo D, Calatayud V, English PA, Archer SK, Dudas SE, Haggarty DR, Gallagher AJ, Shea BD, Shipley ON, Gilby BL, Ballantyne J, Olds AD, Henderson CJ, Schlacher TA, Halliday WD, Brown NAW, Woods MB, Balshine S, Juanes F, Rider MJ, Albano PS, Hammerschlag N, Hays GC, Esteban N, Pan Y, He G, Tanaka T, Hensel MJS, Orth RJ, Patrick CJ, Hentati-Sundberg J, Olsson O, Hessing-Lewis ML, Higgs ND, Hindell MA, McMahon CR, Harcourt R, Guinet C, Hirsch SE, Perrault JR, Hoover SR, Reilly JD, Hobaiter C, Gruber T, Huveneers C, Udyawer V, Clarke TM, Kroesen LP, Hik DS, Cherry SG, Del Bel Belluz JA, Jackson JM, Lai S, Lamb CT, LeClair GD, Parmelee JR, Chatfield MWH, Frederick CA, Lee S, Park H, Choi J, LeTourneux F, Grandmont T, de-Broin FD, Bêty J, Gauthier G, Legagneux P, Lewis JS, Haight J, Liu Z, Lyon JP, Hale R, D'Silva D, MacGregor-Fors I, Arbeláez-Cortés E, Estela FA, Sánchez-Sarria CE, García-Arroyo M, Aguirre-Samboní GK, Franco Morales JC, Malamud S, Gavriel T, Buba Y, Salingré S, Lazarus M, Yahel R, Ari YB, Miller E, Sade R, Lavian G, Birman Z, Gury M, Baz H, Baskin I, Penn A, Dolev A, Licht O, Karkom T, Davidzon S, Berkovitch A, Yaakov O, Manenti R, Mori E, Ficetola GF, Lunghi E, March D, Godley BJ, Martin C, Mihaly SF, Barclay DR, Thomson DJM, Dewey R, Bedard J, Miller A, Dearden A, Chapman J, Dares L, Borden L, Gibbs D, Schultz J, Sergeenko N, Francis F, Weltman A, Moity N, Ramírez-González J, Mucientes G, Alonso-Fernández A, Namir I, Bar-Massada A, Chen R, Yedvab S, Okey TA, Oppel S, Arkumarev V, Bakari S, Dobrev V, Saravia-Mullin V, Bounas A, Dobrev D, Kret E, Mengistu S, Pourchier C, Ruffo A, Tesfaye M, Wondafrash M, Nikolov SC, Palmer C, Sileci L, Rex PT, Lowe CG, Peters F, Pine MK, Radford CA, Wilson L, McWhinnie L, Scuderi A, Jeffs AG, Prudic KL, Larrivée M, McFarland KP, Solis R, Hutchinson RA, Queiroz N, Furtado MA, Sims DW, Southall E, Quesada-Rodriguez CA, Diaz-Orozco JP, Rodgers KS, Severino SJL, Graham AT, Stefanak MP, Madin EMP, Ryan PG, Maclean K, Weideman EA, Şekercioğlu ÇH, Kittelberger KD, Kusak J, Seminoff JA, Hanna ME, Shimada T, Meekan MG, Smith MKS, Mokhatla MM, Soh MCK, Pang RYT, Ng BXK, Lee BPY, Loo AHB, Er KBH, Souza GBG, Stallings CD, Curtis JS, Faletti ME, Peake JA, Schram MJ, Wall KR, Terry C, Rothendler M, Zipf L, Ulloa JS, Hernández-Palma A, Gómez-Valencia B, Cruz-Rodríguez C, Herrera-Varón Y, Roa M, Rodríguez-Buriticá S, Ochoa-Quintero JM, Vardi R, Vázquez V, Requena-Mesa C, Warrington MH, Taylor ME, Woodall LC, Stefanoudis PV, Zhang X, Yang Q, Zukerman Y, Sigal Z, Ayali A, Clua EEG, Carzon P, Seguine C, Corradini A, Pedrotti L, Foley CM, Gagnon CA, Panipakoochoo E, Milanes CB, Botero CM, Velázquez YR, Milchakova NA, Morley SA, Martin SM, Nanni V, Otero T, Wakeling J, Abarro S, Piou C, Sobral AFL, Soto EH, Weigel EG, Bernal-Ibáñez A, Gestoso I, Cacabelos E, Cagnacci F, Devassy RP, Loretto MC, Moraga P, Rutz C, Duarte CM. Global COVID-19 lockdown highlights humans as both threats and custodians of the environment. Biol Conserv 2021;263:109175
Baumgaertner P, Sankar M, Herrera F, Benedetti F, Barras D, Thierry AC, Dangaj D, Kandalaft LE, Coukos G, Xenarios I, Guex N, Harari A. Unsupervised Analysis of Flow Cytometry Data in a Clinical Setting Captures Cell Diversity and Allows Population Discovery. Front Immunol 2021;12:633910
Bauzile B, Sicard G, Guinat C, Andraud M, Rose N, Hammami P, Durand B, Paul MC, Vergne T. Unravelling direct and indirect contact patterns between duck farms in France and their association with the 2016-2017 epidemic of Highly Pathogenic Avian Influenza (H5N8). Prev Vet Med 2021;198:105548
Beber ME, Gollub MG, Mozaffari D, Shebek KM, Flamholz AI, Milo R, Noor E. eQuilibrator 3.0: a database solution for thermodynamic constant estimation. Nucleic Acids Res 2021
Begum T, Robinson-Rechavi M. Special Care Is Needed in Applying Phylogenetic Comparative Methods to Gene Trees with Speciation and Duplication Nodes. Mol Biol Evol 2021;38(4):1614-1626
Bellenberg S, Salas B, Ganji S, Jorquera-Román C, Valenzuela ML, Buetti-Dinh A, Unelius CR, Dopson M, Vera M. Diffusible signal factor signaling controls bioleaching activity and niche protection in the acidophilic, mineral-oxidizing leptospirilli. Sci Rep 2021;11(1):16275
Benet S, Gálvez C, Drobniewski F, Kontsevaya I, Arias L, Monguió-Tortajada M, Erkizia I, Urrea V, Ong RY, Luquin M, Dupont M, Chojnacki J, Dalmau J, Cardona P, Neyrolles O, Lugo-Villarino G, Vérollet C, Julián E, Furrer H, Günthard HF, Crocker PR, Tapia G, Borràs FE, Fellay J, McLaren PJ, Telenti A, Cardona PJ, Clotet B, Vilaplana C, Martinez-Picado J, Izquierdo-Useros N. Dissemination of Mycobacterium tuberculosis is associated to a SIGLEC1 null variant that limits antigen exchange via trafficking extracellular vesicles. J Extracell Vesicles 2021;10(3):e12046
Bibert S, Guex N, Lourenco J, Brahier T, Papadimitriou-Olivgeris M, Damonti L, Manuel O, Liechti R, Götz L, Tschopp J, Quinodoz M, Vollenweider P, Pagani JL, Oddo M, Hügli O, Lamoth F, Erard V, Voide C, Delorenzi M, Rufer N, Candotti F, Rivolta C, Boillat-Blanco N, Bochud PY, RegCOVID Study Group. Transcriptomic Signature Differences Between SARS-CoV-2 and Influenza Virus Infected Patients. Front Immunol 2021;12:666163
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
Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Necci M, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A, Finn RD. The InterPro protein families and domains database: 20 years on. Nucleic Acids Res 2021;49(d1):D344-D354
Boareto M, Tomka T, Iber D. Positional information encoded in the dynamic differences between neighboring oscillators during vertebrate segmentation. Cells Dev 2021:203737
Bock C, Moor M, Jutzeler CR, Borgwardt K. Machine Learning for Biomedical Time Series Classification: From Shapelets to Deep Learning. Methods Mol Biol 2021;2190:33-71
Boehm E, Kronig I, Neher RA, Eckerle I, Vetter P, Kaiser L, Geneva Centre for Emerging Viral Diseases. Novel SARS-CoV-2 variants: the pandemics within the pandemic. Clin Microbiol Infect 2021;27(8):1109-1117
Bolis M, Bossi D, Vallerga A, Ceserani V, Cavalli M, Impellizzieri D, Di Rito L, Zoni E, Mosole S, Elia AR, Rinaldi A, Pereira Mestre R, D'Antonio E, Ferrari M, Stoffel F, Jermini F, Gillessen S, Bubendorf L, Schraml P, Calcinotto A, Corey E, Moch H, Spahn M, Thalmann G, Kruithof-de Julio M, Rubin MA, Theurillat JP. Dynamic prostate cancer transcriptome analysis delineates the trajectory to disease progression. Nat Commun 2021;12(1):7033
Bonnardel F, Haslam SM, Dell A, Feizi T, Liu Y, Tajadura-Ortega V, Akune Y, Sykes L, Bennett PR, MacIntyre DA, Lisacek F, Imberty A. Proteome-wide prediction of bacterial carbohydrate-binding proteins as a tool for understanding commensal and pathogen colonisation of the vaginal microbiome. NPJ Biofilms Microbiomes 2021;7(1):49
Bonnardel F, Mariethoz J, Pérez S, Imberty A, Lisacek F. LectomeXplore, an update of UniLectin for the discovery of carbohydrate-binding proteins based on a new lectin classification. Nucleic Acids Res 2021;49(d1):D1548-D1554
Börsch A, Ham DJ, Mittal N, Tintignac LA, Migliavacca E, Feige JN, Rüegg MA, Zavolan M. Molecular and phenotypic analysis of rodent models reveals conserved and species-specific modulators of human sarcopenia. Commun Biol 2021;4(1):194
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
Bourguignon L, Vo AK, Tong B, Geisler F, Mach O, Maier D, Kramer JLK, Grassner L, Jutzeler CR. Natural Progression of Routine Laboratory Markers after Spinal Trauma: A Longitudinal, Multi-Cohort Study. J Neurotrauma 2021;38(15):2151-2161
Brandt A, Tran Van P, Bluhm C, Anselmetti Y, Dumas Z, Figuet E, François CM, Galtier N, Heimburger B, Jaron KS, Labédan M, Maraun M, Parker DJ, Robinson-Rechavi M, Schaefer I, Simion P, Scheu S, Schwander T, Bast J. Haplotype divergence supports long-term asexuality in the oribatid mite Oppiella nova. Proc Natl Acad Sci U S A 2021;118(38)
Breda J, Zavolan M, van Nimwegen E. Bayesian inference of gene expression states from single-cell RNA-seq data. Nat Biotechnol 2021;39(8):1008-1016
Brewer TE, Wagner A. Translation stalling proline motifs are enriched in slow-growing, thermophilic, and multicellular bacteria. ISME J 2021
Brkic S, Stivala S, Santopolo A, Szybinski J, Jungius S, Passweg JR, Tsakiris D, Dirnhofer S, Hutter G, Leonards K, Lischer HEL, Dettmer MS, Neel BG, Levine RL, Meyer SC. Dual targeting of JAK2 and ERK interferes with the myeloproliferative neoplasm clone and enhances therapeutic efficacy. Leukemia 2021;35(10):2875-2884
Bruand M, Barras D, Mina M, Ghisoni E, Morotti M, Lanitis E, Fahr N, Desbuisson M, Grimm A, Zhang H, Chong C, Dagher J, Chee S, Tsianou T, Dorier J, Stevenson BJ, Iseli C, Ronet C, Bobisse S, Genolet R, Walton J, Bassani-Sternberg M, Kandalaft LE, Ren B, McNeish I, Swisher E, Harari A, Delorenzi M, Ciriello G, Irving M, Rusakiewicz S, Foukas PG, Martinon F, Dangaj Laniti D, Coukos G. Cell-autonomous inflammation of BRCA1-deficient ovarian cancers drives both tumor-intrinsic immunoreactivity and immune resistance via STING. Cell Rep 2021;36(3):109412
Brümmer A, Dreos R, Marques AC, Bergmann S. Analysis of eukaryotic lincRNA sequences indicates signatures of hindered translation linked to selection pressure. Mol Biol Evol 2021
Buetti-Dinh A, Ruinelli M, Czerski D, Scapozza C, Martignier A, Roman S, Caminada A, Tonolla M. Geochemical and metagenomics study of a metal-rich, green-turquoise-coloured stream in the southern Swiss Alps. PLoS One 2021;16(3):e0248877
Burri D, Zavolan M. Shortening of 3' UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism. RNA 2021;27(12):1459-1470
Burton-Pimentel KJ, Pimentel G, Hughes M, Michielsen CC, Fatima A, Vionnet N, Afman LA, Roche HM, Brennan L, Ibberson M, Vergères G. Discriminating Dietary Responses by Combining Transcriptomics and Metabolomics Data in Nutrition Intervention Studies. Mol Nutr Food Res 2021;65(4):e2000647
Cacciatore S, Wium M, Licari C, Ajayi-Smith A, Masieri L, Anderson C, Salukazana AS, Kaestner L, Carini M, Carbone GM, Catapano CV, Loda M, Libermann TA, Zerbini LF. Inflammatory metabolic profile of South African patients with prostate cancer. Cancer Metab 2021;9(1):29
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