2023

[B1] Somatic hypermutation introduces bystander mutations that prepare SARS-CoV-2 antibodies for emerging variants

Korenkov M., Zehner M., Cohen-Dvashi H., Borenstein-Katz A., Kottege L., Janicki H., Vanshylla K., Weber T., Gruell H., Koch M., Diskin R., Kreer C., Klein F., Cell Immunity 1074-7613, 29. November 2023, https://doi.org/10.1016/j.immuni.2023.11.004

[B1] Enhanced SARS-CoV-2 humoral immunity following breakthrough infection builds upon the preexisting memory B cell pool

Weber T., Dähling S., Rose S., Affeldt P., Vanshylla K., Ullrich L., Gieselmann L., Teipel F., Gruell H., Di Cristanziano V., Kim D.S., Georgiou G., Koch M., Kreer C., Klein F., Sci. Immunol.8, eadk5845, 17. November 2023, https://doi.org/10.1126/sciimmunol.adk5845

[B1] Probabilities of developing HIV-1 bNAb sequence features in uninfected and chronically infected individuals

Kreer C., Lupo C, Ercanoglu M.S., Gieselmann L., Spisak N., Grossbach J., Schlotz M., Schommers P., Gruell H., Dold L., Beyer A., Nourmohammad A., Mora T., Walczak A.M., Klein F., Nat Commun 14(7137), 6. November 2023, https://doi.org/10.1038/s41467-023-42906-y

[A5] Genome-wide transformation reveals extensive exchange across closely related Bacillus species

Förster M., Rathman I., Yüksel M., Power J., Maier B., Nucleic Acids Reasearch, 16. November 2023, https://doi.org/10.1093/nar/gkad1074

[B2] Population immunity predicts evolutionary trajectories of SARS-CoV-2

Meijers M., Ruchnewitz D., Eberhardt J., Łuksza M., Lässig M., Cell, 23. October 2023, https://doi.org/10.1016/j.cell.2023.09.022

[B2] Steering and controlling evolution — from bioengineering to fighting pathogens

Lässig M., Mustonen V., Nourmohammad A., Nat Rev Genet, 3. July 2023, https://doi.org/10.1038/s41576-023-00623-8

[A5] Collective polarization dynamics in bacterial colonies signify the occurrence of distinct subpopulations

Hennes M., Bender N., Cronenberg T., Welker A., Maier B., PLOS Biol, 18. January 2023, https://doi.org/10.1371/journal.pbio.3001960

2022

[A1],[A5] Distribution of fitness effects of cross-species transformation reveals potential for fast adaptive evolution

Rathmann I., Förster M., Yüksel M., Horst L., Petrungaro G., Bollenbach T., Maier B., ISME J, 12. October 2022, https://www.nature.com/articles/s41396-022-01325-5

[A3],[A6] Two modes of evolution shape bacterial strain diversity in the mammalian gut for thousands of generations

Frazão N., Konrad A., Amicone M., Seixas E., Güleresi D., Lässig M. and Gordo I., Nature Communications, 23. September 2022, https://doi.org/10.1038/s41467-022-33412-8

[A1],[A4] Growth-mediated negative feedback shapes quantitative antibiotic response

Angermayr S.A., Pang T.Y., Chevereau G., Mitosch K., Lercher M.J., Bollenbach T., Mol Syst Biol., 20. September 2022, https://doi.org/10.15252/msb.202110490

[B1]Pausing methotrexate prevents impairment of Omicron BA.1 and BA.2 neutralisation after COVID-19 booster vaccination

Habermann E., Gieselmann L., Tober-Lau P., Klotsche J., Albach F.N., Ten Hagen A., Zernicke J., Ahmadov E., Arumahandi de Silva A.N., Frommert L.M., Kurth F., Sander L.E., Burmester G.R., Klein F., Biesen R, RMD Open, 12. September 2022, https://doi.org/10.1136/rmdopen-2022-002639

[B1]SARS-CoV-2 Omicron sublineages exhibit distinct antibody escape patterns

Gruell H., Vanshylla K., Korenkov M., Tober-Lau P., Zehner M., Münn F., Janicki H., Augustin M., Schommers P., Sander L.E., Kurth F., Kreer C., Klein F., Cell Host Microbe, 7. July 2022, https://doi.org/10.1016/j.chom.2022.07.002

[B1],[B2] Effective high-throughput RT-qPCR screening for SARS-CoV-2 infections in children

Dewald F., Suárez I., Johnen R., Grossbach J., Moran-Tovar R., Steger G., Joachim A., Rubio G.H., Fries M. , Behr F., Kley J., Lingnau A., Kretschmer A., Gude C., Baeza-Flores G., Laveaga del Valle D., Roblero-Hernandez A., Magana-Cerino J., Hernandez A.T., Ruiz-Quinones J., Schega K., Linne V., Junker L., Wunsch M., Heger E., Knops E., Di Cristanziano V., Meyer M., Hünseler C., Weber L.T., Lüers L.C., Quade G., Wisplinghoff H., Tiemann C., Zotz R., Jomaa H., Pranada A., Herzum I., Cullen P., Schmitz F.J., Philipsen P., Kirchner G., Knabbe C., Hellmich M., Buess M., Wolff A., Kossow A., Niessen J., Jeworutzki S., Schräpler J.-P., Lässig M., Dötsch J., Fätkenheuer D., Kaiser R., Beyer A., Rybniker J., Klein F., Nature Communications, 25. June 2022, https://www.nature.com/articles/s41467-022-30664-2

[B1],[B3] Design of an optimal combination therapy with broadly neutralizing antibodies to suppress HIV-1

LaMont C., Otwinowski J., Vanshylla K., Gruell H., Klein F., Nourmohammad A., eLife, 19. July 2022, https://doi.org/10.7554/eLife.76004

[B1],[B2] Effective high-throughput RT-qPCR screening for SARS-CoV-2 infections in children

Dewald F., Suárez I., Johnen R., Grossbach J., Moran-Tovar R., Steger G., Joachim A., Rubio G.H., Fries M. , Behr F., Kley J., Lingnau A., Kretschmer A., Gude C., Baeza-Flores G., Laveaga del Valle D., Roblero-Hernandez A., Magana-Cerino J., Hernandez A.T., Ruiz-Quinones J., Schega K., Linne V., Junker L., Wunsch M., Heger E., Knops E., Di Cristanziano V., Meyer M., Hünseler C., Weber L.T., Lüers L.C., Quade G., Wisplinghoff H., Tiemann C., Zotz R., Jomaa H., Pranada A., Herzum I., Cullen P., Schmitz F.J., Philipsen P., Kirchner G., Knabbe C., Hellmich M., Buess M., Wolff A., Kossow A., Niessen J., Jeworutzki S., Schräpler J.-P., Lässig M., Dötsch J., Fätkenheuer D., Kaiser R., Beyer A., Rybniker J., Klein F., Nature Communications, 25. June 2022, https://www.nature.com/articles/s41467-022-30664-2

[C2] The impact of genomic variation on protein phosphorylation states and regulatory networks

Grossbach J., Gillet L., Clément-Ziza M., Schmalohr C.L., Schubert O.T., Schütter M., Mawer J.S.P, Barnes C., Bludau I., Weith M., Tessarz P., Graef M., Aebersold R., Beyer A., Molecular Systems Biology, 16. May 2022, https://doi.org/10.15252/msb.202110712

[B1] Cross-Variant Neutralizing Serum Activity after SARS-CoV-2 Breakthrough Infections

Tober-Lau P., Gruell H., Vanshylla K., Koch W.M., Hillus D., Schommers P., Suárez I., Suttorp N., Sander L.E., Klein F., Kurth F., Emerg Infect Dis, 5. May 2022, https://doi.org/10.3201/eid2805.220271

[B1] No substantial preexisting B cell immunity against SARS-CoV-2 in healthy adults

Ercanoglu M.S., Gieselmann L., Dähling S., Poopalasingam N., Detmer S., Koch M., Korenkov M., Halwe S., Klüver M., Di Cristanziano V., Janicki H., Schlotz M., Worczinski J., Gathof B., Gruell H., Zehner M., Becker S., Vanshylla K., Kreer C., Klein F., iScience, 3. March 2022, https://doi.org/10.1016/j.isci.2022.103951

[A2] Population size mediates the contribution of high-rate and large-benefit mutations to parallel evolution

Schenk M.F., Zwart M.P., Hwang S., Ruelens P., Severing E., Krug J., de Visser J.A.G.M., Nat Ecol Evol, 3. March 2022, https://doi.org/10.1038/s41559-022-01669-3

[B4] Extensive age-dependent loss of antibody diversity in naturally short-lived turquoise killifish

Bradshaw W.J., Poeschla M., Placzek A., Kean S., Valenzano D.R., eLife, 7. February 2022, https://doi.org/10.7554/eLife.65117

[B1] Discovery of ultrapotent broadly neutralizing antibodies from SARS-CoV-2 elite neutralizers

Vanshylla K., Fan C., Wunsch M., Poopalasingam N., Meijers M., Kreer C., Kleipass F., Ruchnewitz D., Ercanoglu M.S., Gruell H., Münn F., Pohl K., Janicki H., Nolden T., Bartl S., Stein S.C., Augustin M., Dewald F., Gieselmann L., Schommers P., Schulz T.F., Sander L.E., Koch M., Łuksza M., Lässig M., Bjorkman P.J., Klein F., Cell Host Microbe, 12. January 2022, https://doi.org/10.1016/j.chom.2021.12.010

2021

[B3] Antigenic evolution of human influenza H3N2 neuraminidase is constrained by charge balancing

Wang Y., Lei R., Nourmohammad A., Wu N.C., eLife 2021;10:e72516, 8. December 2021, https://doi.org/10.7554/eLife.72516

[B6] Stochastic clonal dynamics and genetic turnover in exponentially growing populations

Angaji A., Velling C. and Berg J., J. Stat. Mech. 103502, 26. October 2021, https://doi.org/10.1088/1742-5468/ac257e

[A4] On the optimality of the enzyme–substrate relationship in bacteria

Dourado H., Mori M., Hwa T., Lercher M.J. , PLOS Biol. 19(10): e3001416, 26. October 2021, https://doi.org/10.1371/journal.pbio.3001416

[A4] Deep learning allows genome-scale prediction of Michaelis constants from structural features

Kroll A., Engqvist M.K.M., Heckmann D., Lercher M.J., PLOS Biol. 19(10): e3001402, 19. October 2021, https://doi.org/10.1371/journal.pbio.3001402

[B2] Clinical and Genomic Characterization of SARS CoV-2 infections in mRNA Vaccinated Health Care Personnel in New York City

Robilotti E.V., Whiting K., Lucca A., Poon C., Guest R., McMillen T., Jani K., Solovyov A., Kelson S., Browne K., Freeswick S., Hohl T.M., Korenstein D., Ruchnewitz D., Lässig M., Łuksza M., Greenbaum B., Seshan V.E., Babady N.E., Kamboj M., Clinical Infectious Diseases ciab886, 13. October 2021, https://doi.org/10.1093/cid/ciab886

[B2] Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections

Illingworth C.J.R., Hamilton W.L., Warne B., Routledge M., Popay A., Jackson C., Fieldman T., Meredith L.W., Houldcroft C.J., eLife 10:e67308, 24. August 2021, https://doi.org/10.7554/eLife.67308

[A2] Antibiotic Breakdown by Susceptible Bacteria Enhances the Establishment of β-Lactam Resistant Mutants

Saebelfeld M., Das S.G., Brink J., Hagenbeek A., Krug J., de Visser J.A.G.M., Frontiers in Microbiology, 12: 698970., 19. August 2021, https://doi.org/10.3389/fmicb.2021.698970

[B2] Predicting in vivo escape dynamics of HIV-1 from a broadly neutralizing antibody

Meijers M., Vanshylla K., Gruell H., Klein F., Lässig M., PNAS 118 (30) e2104651118, 27. July 2021, https://doi.org/10.1073/pnas.2104651118

[A2] Choice of β-Lactam Resistance Pathway Depends Critically on Initial Antibiotic Concentration

Ruelens P., de Visser J.A.G.M., Antimicrob. Agents Chemother. 65:e00471-21, 16. July 2021, https://doi.org/10.1128/AAC.00471-21

[B2],[B5] Antigenic waves of virus–immune coevolution

Marchi J., Lässig M., Walczak A.M., Mora T., PNAS 118 (27) e2103398118, 6. July 2021, https://doi.org/10.1073/pnas.2103398118

[B1] Effective high-throughput isolation of fully human antibodies targeting infectious pathogens

Gieselmann L., Kreer C., Ercanoglu M.S., Lehnen N., Zehner M., Schommers P., Potthoff J., Gruell H., Klein F., Nat Protoc, 25. May 2021, https://doi.org/10.1038/s41596-021-00554-w

[B3] Dynamics of B cell repertoires and emergence of cross-reactive responses in patients with different severities of COVID-19

Montague Z., Lv H., Otwinowski J., DeWitt W.S., Isacchini G., Yip G.K., Ng W.W., Tsang O.T.-Y., Yuan M., Liu H., Wilson I.A., Peiris J.S.M., Wu N.C., Nourmohammad A., Ka Pun Mok C, Cell 35(8), 25. May 2021, https://doi.org/10.1016/j.celrep.2021.109173

[B1] Kinetics and correlates of the neutralizing antibody response to SARS-CoV-2 infection in humans

Vanshylla K., Di Cristanziano V., Kleipass F., Dewald F., Schommers P., Gieselmann L., Gruell H., Schlotz M., Ercanoglu M.S., Stumpf R., Mayer P., Zehner M., Heger E., Johannis W., Horn C., Suárez I., Jung N., Salomon S., Eberhardt K.A., Gathof B., Fätkenheuer G., Pfeifer N., Eggeling R., Augustin M., Lehmann C., Klein F., Cell Host Microbe, 28. April 2021, https://doi.org/10.1016/j.chom.2021.04.015

[B3] Optimal evolutionary decision-making to store immune memory

Schnaack O.H., Nourmohammad A., eLife 10:e61346, 28. April 2021, https://doi.org/10.7554/eLife.61346

[B3],[B5] Deep generative selection models of T and B cell receptor repertoires with soNNia

Isacchini G., Walczak A.M., Mora T., Nourmohammad A., PNAS 118 (14) e2023141118, 6. April 2021, https://doi.org/10.1073/pnas.2023141118

[B1] Evaluation of a New Spike (S)-Protein-Based Commercial Immunoassay for the Detection of Anti-SARS-CoV-2 IgG

Eberhardt K.A., Dewald F., Heger E., Gieselmann L., Vanshylla K., Wirtz M., Kleipass F., Johannis W., Schommers P., Gruell H., Brensing K.A., Müller R.U., Augustin M., Lehmann C., Koch M., Klein F., Di Cristanziano V., Microorganisms, 31. March 2021, https://doi.org/10.3390/microorganisms9040733

[A3] Metabolic fitness landscapes predict the evolution of antibiotic resistance

Pinheiro, F., Warsi, O., Andersson, D.I., Lässig M., Nat Ecol Evol, 4. March 2021, https://doi.org/10.1038/s41559-021-01397-0

[A3],[A5] Adaptive evolution of hybrid bacteria by horizontal gene transfer

Power J.J., Pinheiro F., Pompei S., Kovacova V., Yüksel M., Rathmann I., Förster M., Lässig M., Maier B., PNAS 11, 118 (10), 9. March 2021, https://doi.org/10.1073/pnas.2007873118

[B3] Optimal Evolutionary Control for Artificial Selection on Molecular Phenotypes

Nourmohammad A. & Eksin C., Phys. Rev. X 11, 011044, 4. March 2021, https://doi.org/10.1103/PhysRevX.11.011044

[B1] CD34T+ Humanized Mouse Model to Study Mucosal HIV-1 Transmission and Prevention

Vanshylla K., Held K., Eser T.M., Gruell H., Kleipass F., Stumpf R., Jain K., Weiland D., Münch J., Grüttner B., Geldmacher C., Klein F., Vaccines (Basel) 9(3):198, 27. February 2021, https://doi.org/10.3390/vaccines9030198

[A2] Clonal Interference and Mutation Bias in Small Bacterial Populations in Droplets

Ruelens P., de Visser J.A.G.M., Genes 2021, 12(2), 223, 4. February 2021, https://doi.org/10.3390/genes12020223

[A2] The fitness landscapes of translation

Josupeit M., Krug J., Physica A 569, 125768 (2021), 18. January 2021, https://doi.org/10.1016/j.physa.2021.125768

[A1] Minimal biophysical model of combined antibiotic action

Kavči B., Tkačik G., Bollenbach T., PLoS Comput Biol 17(1): e1008529, 7. January 2021, https://doi.org/10.1371/journal.pcbi.1008529

[B5] Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection

Minervina A.A., Komech E.A., Titov A., Koraichi M.B., Rosati E., Mamedov I.Z., Franke A., Efimov G.A., Chudakov D.M., Mora T., Walczak A.M., Lebedev Y.B., Pogorelyy M.V., eLife 2021;10:e63502, 5. January 2021, https://doi.org/10.7554/eLife.63502

2020

[B5] Learning the heterogeneous hypermutation landscape of immunoglobulins from high-throughput repertoire data

Spisak N., Walczak A.M., Mora T., Nucleic Acids Research, Volume 48, Issue 19, Pages 10702–10712, 4 November 2020, https://doi.org/10.1093/nar/gkaa825

[B7] Convergent network effects along the axis of gene expression during prostate cancer progression

Charmpi, K., Guo, T., Zhong, Q. et al., Beyer A., Genome Biol 21, 302, 14. December 2020, https://doi.org/10.1186/s13059-020-02188-9

[A4] The protein translation machinery is expressed for maximal efficiency in Escherichia coli

Hu X., Dourado H., Schubert P. & Lercher M. J., Nat Commun 11, 5260, 16. October 2020, https://doi.org/10.1038/s41467-020-18948-x

[B4] Intra-species differences in population size shape life history and genome evolution

Willemsen D., Cui R., Reichard M., Valenzano D.R., eLife 2020;9:e55794, 1. September 2020, https://doi.org/10.7554/eLife.55794

[B3] Information-Geometric Optimization with Natural Selection

Otwinowski J, LaMont C.H., Nourmohammad A. , Entropy 2020, 22(9), 967, 31. August 2020, https://doi.org/10.3390/e22090967

[A2]Distribution of the number of fitness maxima in Fisher's geometric model

Park S.C., Hwang S. and Krug J., J. Phys. A: Math. Theor. 53 385601, 21. August 2020, https://doi.org/10.1088/1751-8121/ab9780

[A2]Longitudinal Isolation of Potent Near-Germline SARS-CoV-2-Neutralizing Antibodies from COVID-19 Patients

Kreer C., Zehner M., Weber T., Ercanoglu M.S., Gieselmann L., Rohde C., Halwe S., Korenkov M., Schommers P., Vanshylla K., Di Cristanziano V., Janicki H., Brinker R., Ashurov A., Krähling V., Kupke A., Cohen-Dvashi H., Koch M, Eckert J.M., Lederer S., Pfeifer N., Wolf T., Vehreschild M.J.G.T., Wendtner C., Diskin R., Gruell H., Becker S., Klein F., Cell 182(4):843-854.e12., 20. August 2020, https://doi.org/10.1016/j.cell.2020.06.044

[B3],[B5] SOS: online probability estimation and generation of T-and B-cell receptors

Isacchini G., Olivares C., Nourmohammad. A, Walczak A.M., Mora T., Bioinformatics, Volume 36, Issue 16, 4510–4512, 15. August 2020, https://doi.org/10.1093/bioinformatics/btaa574

[A1] Mechanisms of drug interactions between translation-inhibiting antibiotics

Kavčič B., Tkačik G. & Bollenbach T., Nat Commun 11, 4013, 11. August 2020, https://doi.org/10.1038/s41467-020-17734-z

[B4] Microbiota–host interactions shape ageing dynamics

Popkes M., Valenzano D.R., Phil. Trans. R. Soc. B 375, 20190596, 10. August 2020, https://doi.org/10.1098/rstb.2019.0596

[B2] Eco-evolutionary control of pathogens

Lässig M., Mustonen V., PNAS:201920263 , 31. July 2020, https://doi.org/10.1073/pnas.1920263117

[B1] Repertoire characterization and validation of gB-specific human IgGs directly cloned from humanized mice vaccinated with dendritic cells and protected against HCMV

Theobald S.J., Kreer C., Khailaie S., Bonifacius A., Eiz-Vesper B., Figueiredo C., Mach M., Backovic M., Ballmaier M., Koenig J., Olbrich H., Schneider A., Volk V., Danisch S., Gieselmann L., Ercanoglu M.S., Messerle M., Kaisenberg C.V., Witte T., Klawonn F., Meyer-Hermann M., Klein F., Stripecke R., Pathog 16(7):e1008560, 15. July 2020, https://doi.org/10.1371/journal.ppat.1008560

[B4] Nothobranchius furzeri (African Turquoise Killifish)

Cui R., Willemsen D., Valenzano D.R., Trends In Genetics, 1. July 2020, https://doi.org/10.1016/j.tig.2020.01.012

[A6] Mutation accumulation and horizontal gene transfer in Escherichia coli colonizing the gut of old mice

Barreto H.C., Frazão N., Sousa A., Konrad A., & Gordo I., Communicative & Integrative Biology, 13:1, 89-96, 24. June 2020, https://doi.org/10.1080/19420889.2020.1783059

[A1] Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance

Lukačišinová M., Fernando B., Bollenbach T., Nat Commun 11, 31051, 19. June 2020, https://doi.org/10.1038/s41467-020-16932-z

[B3],[B5] Generative models of T-cell receptor sequences

Isacchini G., Sethna Z., Elhanati Y., Nourmohammad A., Walczak A.M., Mora T., Phys. Rev. E 101, 062414, 15. June 2020, https://doi.org/10.1103/PhysRevE.101.062414

[A2] Predictable properties of fitness landscapes induced by adaptational tradeoffs

Das S.G., Direito S.O.L., Waclaw B., Allen R.J., Krug J., elife 9, e55155 (2020), 19. May 2020, https://doi.org/10.7554/eLife.55155

[B4] Low mutational load and high mutation rate variation in gut commensal bacteria

Bradshaw W.J., Valenzano D.R., Proc. R. Soc. B.28720200489, 13. May 2020, https://doi.org/10.1098/rspb.2020.0489

[A6] Low mutational load and high mutation rate variation in gut commensal bacteria

Ramiro R.S., Durão P., Bank C., Gordo I., PLoS Biol 18 (3): e3000617. , 10. May 2020, https://doi.org/10.1371/journal.pbio.3000617

[B7] Pyruvate kinase variant of fission yeast tunes carbon metabolism, cell regulation, growth and stress resistance

Kamrad S., Grossbach J., Rodríguez‐López M., Mülleder M., Townsend S.J, Cappelletti V., Stojanovski G., Correia‐Melo C., Picotti P., Beyer A., Ralser M., Bähler J., Mol Syst Biol (2020)16:e9270, 1. April 2020, https://doi.org/10.15252/msb.20199270

[B1] Structural Basis for a Convergent Immune Response against Ebola Virus

Cohen-Dvashi H., Zehner M., Ehrhardt S., Katz M., Elad N., Klein F., Diskin R., Cell Host Microbe. 27(3):418-427.e4., 11. March 2020, https://doi.org/10.1016/j.chom.2020.01.007

[B3] Major antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape

Wu N. C., Otwinowski J., Thompson A. J., Nycholat C. M. Nourmohammad A and Wilson I. A., Nat Commun 11, 1233, 6. March 2020, https://doi.org/10.1038/s41467-020-15102-5

[A4] An analytical theory of balanced cellular growth

Dourado H., and Lercher M. J., Nat Commun 11, 1226, 6. March 2020, https://doi.org/10.1038/s41467-020-14751-w

[B5] Primary and secondary anti-viral response captured by the dynamics and phenotype of individual T cell clones

Minervina A.A., Pogorelyy M.V, Komech E.A., Karnaukhov V.K., Bacher P. , Rosat E. , Franke A., Chudakov D.M., Mamedov I.Z., Lebedev Y.B., Mora T., Walczak A.M., eLife2020;9:e53704, 21. February 2020, https://doi.org/10.7554/eLife.53704

[B3] The size of the immune repertoire of bacteria

Bradde S., Nourmohammad A., Goyal S., and Balasubramanian V., PNAS:201903666, 18. February 2020, https://doi.org/10.1073/pnas.1903666117

[B1] Antibody Teamwork against Ebola Virus Disease

Zehner M., Klein F., Immunity. 52(2):217-219, 18. February 2020, https://doi.org/10.1016/j.immuni.2020.01.016

[B1] Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody

Schommers P., Gruell H., Abernathy M.E., Tran M.K., Dingens A.S., Gristick H.B., Barnes C.O., Schoofs T., Schlotz M., Vanshylla K., Kreer C., Weiland D., Holtick U., Scheid C., Valter M.M., van Gils M.J., Sanders R.W., Vehreschild J.J., Cornely O.A., Lehmann C., Fätkenheuer G., Seaman M.S., Bloom J.D., Bjorkman P.J., Klein F., Cell 180(3):471-489.e22, 6. February 2020, https://doi.org/10.1016/j.cell.2020.01.010

[B1] openPrimeR for multiplex amplification of highly diverse templates

Kreer C., Döring M., Lehnen N., Ercanoglu M.S., Gieselmann L., Luca D., Jain K., Schommers P., Pfeifer N., Klein F., J Immunol Methods. 480:112752, 25. January 2020, https://doi.org/10.1016/j.jim.2020.112752

[B1],[B5] Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies

Kreer C., Gruell H., Mora T., Walczak A.M., Klein F., Vaccines 8(1) 13, 1. January 2020, https://doi.org/10.3390/vaccines8010013

2019

[A1]Emergent Gene Expression Responses to Drug Combinations Predict Higher-Order Drug Interactions

Lukačišin M., Bollenbach T.,Cell Systems 9(5), P423-433.E3, 13. November 2019, https://doi.org/10.1016/j.cels.2019.10.004

[B1]Polyclonal and convergent antibody response to Ebola virus vaccine rVSV-ZEBOV

Ehrhardt S.A., Zehner M., Krähling V., Cohen-Dvashi H., Kreer C., Elad N., Gruell H., Ercanoglu M.S., Schommers P., Gieselmann L., Eggeling R., Dahlke C., Wolf T., Pfeifer N., Addo M.M., Diskin R., Becker S., Klein F., Nat Med. 25(10):1589-1600., 7. October 2019, https://doi.org/10.1038/s41591-019-0602-4

[A3][A6] Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut

Frazão N., Sousa A., Lässig M., and Gordo I., PNAS:201906958, 20. August 2019, https://doi.org/10.1073/pnas.1906958116

[A2]Recombination and mutational robustness in neutral fitness landscapes

Klug A., Park S.C, Krug J., PLoS Comput Biol 15(8): e1006884., 15. August 2019, https://doi.org/10.1371/journal.pcbi.1006884

[B1] Modeling the Amplification of Immunoglobulins through Machine Learning on Sequence-Specific Features

Döring M., Kreer C., Lehnen N., Klein F., Pfeifer N., Sci Rep. 9(1):10748., 24. July 2019, https://doi.org/10.1038/s41598-019-47173-w

[B3] Fierce Selection and Interference in B-Cell Repertoire Response to Chronic HIV-1

Nourmohammad A., Otwinowski J., Łuksza M., Mora T., M. Walczak A., Molecular Biology and Evolution, msz143, 18. June 2019, https://doi.org/10.1093/molbev/msz143

[B5] Multi-Lineage Evolution in Viral Populations Driven by Host Immune Systems

Nourmohammad A., Otwinowski J., Łuksza M., Mora T., Walczak A.M. , Molecular Biology and Evolution 36(10) 2184-2194, 29. July 2019, https://doi.org/10.3390/pathogens8030115

[B4] Relaxed Selection Limits Lifespan by Increasing Mutation Load

Cui R., Medeiros T., Willemsen D., Iasi L.N.M, Collier G.R., Graef M., Reichard M., Valenzano D.R., Cell 11;178(2):385-399.e20, 27. June 2019, 10.1016/j.cell.2019.06.004

[B2] Survival of the simplest in microbial evolution

Held T., Klemmer D., Lässig M., Nature Communications 10: 2472, 6. June 2019, https://doi.org/10.1038/s41467-019-10413-8

[A1] Temporal order and precision of complex stress responses in individual bacteria

Mitosch K., Rieckh G., Bollenbach T., Mol Syst Biol (2019)15:e8470, 14. February 2019, https://doi.org/10.15252/msb.20188470

2018

[A4] Each of 3,323 metabolic innovations in the evolution of E. coli arose through the horizontal transfer of a single DNA segment

Pang T. J., Lercher M. J., PNAS, 18. December 2018, https://doi.org/10.1073/pnas.1718997115

[A4] Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

Heckmann D., Lloyd C. J., Mih N., Ha Y., Zielinski D. C., Haiman Z. B., Desouki A. A., Lercher M. J., Palsson B. O., Nature Communications 9: 5252, 7. December 2018, https://doi.org/10.1038/s41467-018-07652-6

[A4] Alleles of a gene differ in pleiotropy, often mediated through currency metabolite production, in E. coli and yeast metabolic simulations

Alzoubi D., Desouki A. A., Lercher M. J., Scientific Reports 8: 17252, 22. November 2018, https://doi.org/10.1038/s41598-018-35092-1

[A3] Gene expression variability across cells and species shapes innate immunity

Hagai T., Chen X., Miragaia R. J., Rostom R., Gomes T., Kunowska N., Henriksson J., Park J.-E., Proserpio V., Donati G., Bossini-Castillo L., Vieira Braga F. A., Naamati G., Fletcher J., Stephenson E., Vegh P., Trynka G., Kondova I., Dennis M., Haniffa M., Nourmohammad A., Lässig M., Teichmann S. A., Nature 563: 197 - 202, 24. October 2018, https://doi.org/10.1038/s41586-018-0657-2

[B8] Genomic Characterization of TP53–Wild-Type Esophageal Carcinoma1

Quaas A., Heydt C., Gebauer F., Alakus H., Loeser H., Büttner R., Hillmer A., Bruns C., Merkelbach-Bruse S., Zander T., Frommolt P., Transl Oncol. 12: 154-161, 11. October 2018, https://doi.org/10.1016/j.tranon.2018.09.007

[B8] Impact of TP53 mutation status on systemic treatment outcome in ALK-rearranged non-small-cell lung cancer

Kron A., Alidousty C., Scheffler M., Merkelbach-Bruse S., Seidel D., Riedel R., Ihle M. A., Michels S., Nogova L., Fassunke J., Heydt C., Kron F., Ueckeroth F., Serke M., Krüger S., Grohe C., Koschel D., Benedikter J., Kaminsky B., Schaaf B., Braess J., Sebastian M., Kambartel K. O., Thomas R., Zander T., Schultheis A. M., Büttner R., Wolf J., Ann Oncol. 29: 2068-2075, 1. October 2018, https://doi.org/10.1093/annonc/mdy333

[A2] Rare beneficial mutations cannot halt Muller's ratchet in spatial populations           

Park S.-C., Klatt P., Krug J., EPL 123: 48001, 3. September 2018, http://stacks.iop.org/0295-5075/123/i=4/a=48001

[A2] The utility of fitness landscapes and big data for predicting evolution

de Visser, J. A. G. M., Santiago F. E., Fragata I., Matuszewski S., Heredity 121: 401–405, 20. August 2018, https://doi.org/10.1038/s41437-018-0128-4

[A2] Ecology dictates evolution? About the importance of genetic and ecological constraints in adaptation

de Vos M. G. J., Schoustra S. E., de Visser J. A. G. M., EPL 122: 58002, 17. July 2018, http://stacks.iop.org/0295-5075/122/i=5/a=58002

[A2] Unraveling the causes of adaptive benefits of synonymous mutations in TEM-1 β-lactamase

Zwart M. P., Schenk M. F., Hwang S., Koopmanschap B., de Lange N., van de Pol L., Nga T. T. T., Szendro I. G., Krug J., de Visser J. A. G. M., Heredity 121: 406–421, 2. July 2018, https://doi.org/10.1038/s41437-018-0104-z

[B8] Genetic instability and recurrent MYC amplification in ALK‐translocated NSCLC: a central role of TP53 mutations

Alidousty C., Baar T., Martelotto L. G., Heydt C., Wagener S., Fassunke J., Duerbaum N., Scheel A. H., Frank S., Holz B., Binot E., Kron A., Merkelbach-Bruse S., Ihle M. A., Wolf J., Büttner R., Schultheis A.M., J Pathol. 246: 67-76, 9. June 2018, https://doi.org/10.1002/path.5110

[B7] Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers

Guo T., Li L., Zhong Q., Rupp N.J., Charmpi K., Wong C.E., Wagner U., Rueschoff J.H., Jochum W., Fankhauser C.D., Saba K., Poyet C., Wild P.J., Aebersold R., Beyer A., Life Science Alliance, 29. May 2018, https://doi.org/10.26508/lsa.201800042

[B5] Method for identification of condition-associated public antigen receptor sequences

Pogorelyy M.V., Minervina A.A., Chudakov D.M., Mamedov I.Z., Lebedev Y.B., Mora T., Walczak A.M., eLife 2018;7:e33050, 13. May 2018,               https://doi.org/10.7554/eLife.33050

[B4] The short-lived African turquoise killifish (Nothobranchius furzeri): a new model system for research on ageing.
In Conn's Handbook of Models of Human Aging

Muck J., Kean S., Valenzano D.R.,Academic Press, 2. May 2018, ISBN: 9780128113530

[B4] A Protocol for Laboratory Housing of Turquoise Killifish (Nothobranchius furzeri)

Dodzian J., Kean S., Seidel J., Valenzano D.R., J. Vis. Exp. (134) e57073, 11. April 2018, https://doi.org/10.3791/57073

[A2] Universality Classes of Interaction Structures for NK Fitness Landscapes

Hwang S., Schmiegelt B., Ferretti L., Krug J., J Stat Phys 172: 226, 13. February 2018, https://doi.org/10.1007/s10955-018-1979-z

[B5] High-throughput immune repertoire analysis with IGoR

Marcou Q., Mora T., Walczak A.M., Nature Communications Volume 9:561, 8. February 2018, https://doi.org/10.1038/s41467-018-02832-w

[B7] regNet: an R package for network-based propagation of gene expression alterations

Seifert M., Beyer A., Bioinformatics Volume 34 Issue 2:308–311, 15. January 2018, https://doi.org/10.1093/bioinformatics/btx544

[A2] Local Fitness Landscapes Predict Yeast Evolutionary Dynamics in Directionally Changing Environments

Gorter F. A., Aarts M. G. M, Zwaan B. J., de Visser J. A. G. M., Genetics 208: 307-322, 1. January 2018, https://doi.org/10.1534/genetics.117.300519