Browse by Research Team

Advanced Science

Efficient recovery of complete gut viral genomes by combined short- and long-read sequencing.
Chen, J., Sun, C., Dong, Y., Jin, M., Lai, S., Jia, L., Zhao, X., Wang, H., Gao, N.L., Bork, P., Liu, Z., Chen, W.H. and Zhao, X.M.
Advanced Science 11 (13): 2305818. 3 April 2024

Long-read sequencing reveals extensive DNA methylations in human gut phagenome contributed by prevalently phage-encoded methyltransferases.
Sun, C., Chen, J., Jin, M., Zhao, X., Li, Y., Dong, Y., Gao, N., Liu, Z., Bork, P., Zhao, X.M. and Chen, W.H.
Advanced Science 10 (25): 2302159. 5 September 2023

Advances in Experimental Medicine and Biology

Analysis of marker genes contributing to coeliac disease susceptibility.
Roschmann, E., Wienker, T.F., Gerok, W. and Volk, A.
Advances in Experimental Medicine and Biology 371 B : 1339-1343. 1 January 1995

Advances in Protein Chemistry

Sequence analysis of multidomain proteins: Past perspectives and future directions.
Copley, R.R., Ponting, C.P., Schultz, J. and Bork, P.
Advances in Protein Chemistry 61 : 75-98. 2002

Evolution of domain families.
Ponting, C.P., Schultz, J., Copley, R., Andrade, M.A. and Bork, P.
Advances in Protein Chemistry 54 : 185-244. 1 January 2000

Gene and context: Integrative approaches to genome analysis.
Huynen, M.A. and Snel, B.
Advances in Protein Chemistry 54 : 345-379. 1 January 2000

Preface: Protein sequence analysis.
Bork, P.
Advances in Protein Chemistry 54 : xi-xv. 1 January 2000

Individual variation in protein-coding sequences of human genome.
Sunyaev, S., Hanke, J., Brett, D., Aydin, A., Zastrow, I., Lathe, W., Bork, P. and Reich, J.
Advances in Protein Chemistry 54 : 409-437. 2000

Alternatives to Laboratory Animals

Using in vitro prediction models instead of the rabbit eye irritation test to classify and label new chemicals: a post hoc data analysis of the international EC/HO validation study.
Moldenhauer, F.
Alternatives to Laboratory Animals 31 (1): 31-46. January 2003

A compartment model to calculate time-dependent concentration profiles of topically applied chemical compounds in the anterior compartments of the rabbit eye.
Pospisil, H. and Holzhuetter, H.G.
Alternatives to Laboratory Animals 29 : 347-365. 3 May 2001

American Journal of Cardiology

Angiotensin converting enzyme and heart chymase gene polymorphisms in hypertrophic cardiomyopathy.
Pfeufer, A., Osterziel, K.J., Urata, H., Borck, G., Schuster, H., Wienker, T.F., Dietz, R. and Luft, F.C.
American Journal of Cardiology 78 : 362-364. 1 January 1996

An angiotensin-converting enzyme gene variant is associated with acute myocardial infarction in women but not in men.
Schuster, H., Wienker, T.F., Stremmler, U., Noll, B., Steinmetz, A. and Luft, F.C.
American Journal of Cardiology 76 (8): 601-603. 1 January 1995

American Journal of Human Genetics

The effect of single-nucleotide polymorphism marker selection on patterns of haplotype blocks and haplotype frequency estimates.
Nothnagel, M. and Rohde, K.
American Journal of Human Genetics 77 (6): 988-998. 1 December 2005

Mapping of gene loci for nephronophthisis type 4 and Senior-Loken syndrome, to chromosome 1p36.
Schuermann, M.J., Otto, E., Becker, A., Saar, K., Rueschendorf, F., Polak, B.C., Ala-Mello, S., Hoefele, J., Wiedensohler, A., Haller, M., Omran, H., Nuernberg, P. and Hildebrandt, F.
American Journal of Human Genetics 70 (5): 1240-1246. May 2002

A novel form of "central pouchlike" cataract, with sutural opacities, maps to chromosome 15q21-22.
Vanita, A., Singh, J.R., Sarhadi, V.K., Singh, D., Reis, A., Rueschendorf, F., Becker-Follmann, J., Jung, M. and Sperling, K.
American Journal of Human Genetics 68 (2): 509-514. February 2001

Splitting schizophrenia: Periodic catatonia-susceptibility locus on chromosome 15q15.
Stoeber, G., Saar, K., Rueschendorf, F., Meyer, J., Nuernberg, G., Jatzke, S., Franzek, E., Reis, A., Lesch, K.P., Wienker, T.F. and Beckmann, H.
American Journal of Human Genetics 67 : 1201-1207. 1 November 2000

Genomewide scan in German families reveals evidence for a novel psoriasis-susceptibility locus on chromosome 19p13.
Lee, Y.A., Rueschendorf, F., Windemuth, C., Schmitt-Egenolf, M., Stadelmann, A., Nuernberg, G., Staender, M., Wienker, T.F., Reis, A. and Traupe, H.
American Journal of Human Genetics 67 (4): 1020-1024. 1 October 2000

A cholesterol-lowering gene maps to chromosome 13q.
Knoblauch, H., Mueller-Myhsok, B., Busjahn, A., Avi, L.B., Bähring, S., Baron, H., Heath, S.C., Uhlmann, R., Faulhaber, H.D., Shpitzen, S., Aydin, A., Reshef, A., Rosenthal, M., Eliav, O., Muhl, A., Lowe, A., Schurr, D., Harats, D., Jeschke, E., Friedlander, Y., Schuster, H., Luft, F.C. and Leitersdorf, E.
American Journal of Human Genetics 66 (1): 157-166. 1 January 2000

Localization of the gene causing keratolytic winter erythema to chromosome 8p22-p23, and evidence for a founder effect in south african afrikaans-speakers.
Starfield, M., Hennies, H.C., Jung, M., Jenkins, T., Wienker, T.F., Hull, P., Spurdle, A., Kuester, W., Ramsay, M. and Reis, A.
American Journal of Human Genetics 61 (2): 370-378. August 1997

The gene for the ataxia telangiectasia variant, nijmegen breakage syndrome, maps to a 1 cm interval on chromosome 8q21.
Saar, K., Chrzanowska, K.H., Stumm, M., Jung, M., Nuernberg, G., Wienker, T.F., Seemanova, E., Wegner, R.D., Reis, A. and Sperling, K.
American Journal of Human Genetics 60 (3): 605-610. March 1997

Analysis of genetic linkage and somatic loss of heterozygosity in affected pairs of first-degree relatives.
Rohde, K., Teare, M.D. and Koref, M.S.
American Journal of Human Genetics 61 : 418-422. 1 January 1997

Deletion at 12p in a japanese child with brachydactyly overlaps the assigned locus of brachydactyly with hypertension in a turkish family.
Bähring, S., Nagai, T., Toka, H.R., Nitz, I., Toka, O., Aydin, A., Muhl, A., Wienker, T.F., Schuster, H. and Luft, F.C.
American Journal of Human Genetics 60 : 732-735. 1 January 1997

Detection of a major gene for heterocellular hereditary persistence of fetal hemoglobin after accounting for genetic modifiers.
Thein, S.L., Sampietro, M., Rohde, K., Rochette, J., Weatherall, D.J., Lathrop, G.M. and Demenais, F.
American Journal of Human Genetics 54 (2): 214-228. February 1994

Linkage analysis in German breast cancer families with early onset of the disease, using highly polymorphic markers from the chromosome 17q11-q24 region.
Zimmermann, W., Bender, E., Rohde, K., Reis, A., Wiseman, R., Futreal, A., Krause, H., Prokoph, H., Werner, S. and Scherneck, S.
American Journal of Human Genetics 52 (4): 789-791. April 1993

American Journal of Medical Genetics

Assignment of PGL3 to chromosome 1 (q21-q23) in a family with autosomal dominant non-chromaffin paraganglioma.
Niemann, S., Becker-Follmann, J., Nuernberg, G., Rueschendorf, F., Sieweke, N., Huegens-Penzel, M., Traupe, H., Wienker, T.F., Reis, A. and Mueller, U.
American Journal of Medical Genetics 98 (1): 32-36. 1 January 2001

Allelic association of juvenile absence epilepsy with a glur5 kainate receptor gene (grik1) polymorphism.
Sander, T., Hildmann, T., Kretz, R., Fuerst, R., Sailer, U., Bauer, G., Schmitz, B., Beck-Mannagetta, G., Wienker, T.F. and Janz, D.
American Journal of Medical Genetics 74 : 416-421. 1 January 1997

Common subtypes of idiopathic generalized epilepsies: lack of linkage to d20s19 close to candidate loci (ebn1, eegv1) on chromosome 20.
Sander, T., Hildmann, T., Wienker, T.F., Ramel, C., Beckmannagetta, G., Bianchi, A., Sailer, U., Berek, K., Bauer, G., Neitzel, H., Schmitz, B., Durner, M., Johnson, K.J. and Janz, D.
American Journal of Medical Genetics 67 (1): 31-39. 1 January 1996

American Journal of Pharmacogenomics

DNA testing for familial hypercholesterolemia: improving disease recognition and patient care.
Vergopoulos, A., Knoblauch, H. and Schuster, H.
American Journal of Pharmacogenomics 2 (4): 253-262. December 2002

American Journal of Physiology Gastrointestinal and Liver Physiology

Gut microbiota differs between children with inflammatory bowel disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis.
Knoll, R.L., Forslund, K., Kultima, J.R., Meyer, C.U., Kullmer, U., Sunagawa, S., Bork, P. and Gehring, S.
American Journal of Physiology Gastrointestinal and Liver Physiology 312 (4): G327-G339. 1 April 2017

American Journal of Respiratory and Critical Care Medicine

Genomewide linkage analysis identifies novel genetic loci for lung function in mice.
Reinhard, C., Meyer, B., Fuchs, H., Stoeger, T., Eder, G., Rueschendorf, F., Heyder, J., Nuernberg, P., Hrabe de Angelis, M. and Schulz, H.
American Journal of Respiratory and Critical Care Medicine 171 : 880-888. 7 January 2005

Analytical Biochemistry

Homology-based gene prediction using neural nets.
Cai, Y.D. and Bork, P.
Analytical Biochemistry 265 : 269-274. 15 December 1998

Analytical Chemistry

Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching.
Shevchenko, A., Sunyaev, S., Loboda, A., Shevchenko, A., Bork, P., Ens, W. and Standing, K.G.
Analytical Chemistry 73 (9): 1917-1926. 1 May 2001

Annals of Human Genetics

Characterization of polymorphisms in the promoter of the human angiotensin II subtype 1 (AT1) receptor gene.
Erdmann, J., Riedel, K., Rohde, K., Folgmann, I., Wienker, T.F., Fleck, E. and Regitz-Zagrosek, V.
Annals of Human Genetics 63 Part 4 : 369-374. 1 July 1999

Annals of Neurology

The phenotypic spectrum related to the human epilepsy susceptibility gene ejm1.
Sander, T., Hildmann, T., Janz, D., Wienker, T.F., Neitzel, H., Bianchi, A., Bauer, G., Sailer, U., Berek, K., Schmitz, B. and Beckmannagetta, G.
Annals of Neurology 38 (2): 210-217. 1 January 1995

Anticancer Research

Differential gene expression in mammary carcinoma cell lines: identification of DRIM, a new gene down-regulated in metastasis.
Schwirzke, M., Gnirke, A., Bork, P., Tarin, D. and Weidle, U.H.
Anticancer Research 18 : 1409-1421. 1 May 1998

BMC Bioinformatics

DCD - a novel plant specific domain in proteins involved in development and programmed cell death.
Tenhaken, R., Doerks, T. and Bork, P.
BMC Bioinformatics 6 : 169. 11 July 2005

PASBio: predicate-argument structures for event extraction in molecular biology.
Wattarujeekrit, T., Shah, P.K. and Collier, N.
BMC Bioinformatics 5 : 155. 19 October 2004

The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold.
Ciccarelli, F.D., Izaurralde, E. and Bork, P.
BMC Bioinformatics 4 : 64. 19 December 2003

Information extraction from full text scientific articles: Where are the keywords?
Shah, P., Perez-Iratxeta, C., Bork, P. and Andrade, M.A.
BMC Bioinformatics 4 (1): 20. 29 May 2003

BMC Cancer

Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability.
Korff, S., Woerner, S.M., Yuan, Y.P., Bork, P., von Knebel Doeberitz, M. and Gebert, J.
BMC Cancer 8 (1): 329. 10 November 2008

BMC Evolutionary Biology

Consistent mutational paths predict eukaryotic thermostability.
van Noort, V., Bradatsch, B., Arumugam, M., Amlacher, S., Bange, G., Creevey, C., Falk, S., Mende, D.R., Sinning, I., Hurt, E. and Bork, P.
BMC Evolutionary Biology 13 : 7. 10 January 2013

BMC Genetics

Linkage analysis of alcohol dependence using MOD scores.
Strauch, K., Fuerst, R., Rueschendorf, F., Windemuth, C., Dietter, J., Flaquer, A., Baur, M.P. and Wienker, T.F.
BMC Genetics 6 (Suppl 1): S162. 30 December 2005

G2D: A tool for mining genes associated with disease.
Perez-Iratxeta, C., Wjst, M., Bork, P. and Andrade, M.A.
BMC Genetics 6 : 45. 22 August 2005

Similarity by state/descent and genetic vector spaces: analysis of a longitudinal family study.
Stassen, H.H., Hoffman, K. and Scharfetter, C.
BMC Genetics 4 (Suppl 1): S59. 31 December 2003

BMC Genomics

FragIdent - automatic identification and characterisation of cDNA-fragments.
Seelow, D., Goehler, H. and Hoffmann, K.
BMC Genomics 10 : 95. 2 March 2009

Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?
Palleja, A., Harrington, E.D. and Bork, P.
BMC Genomics 9 (1): 335. 15 July 2008

Non-random retention of protein-coding overlapping genes in Metazoa.
Solda', G., Suyama, M., Pelucchi, P., Boi, S., Guffanti, A., Rizzi, E., Bork, P., Tenchini, M.L. and Ciccarelli, F.D.
BMC Genomics 9 (1): 174. 16 April 2008

Verification of predicted alternatively spliced Wnt genes reveals two new splice variants (CTNNB1 and LRP5) and altered Axin-1 expression during tumour progression.
Pospisil, H., Herrmann, A., Butherus, K., Pirson, S., Reich, J.G. and Kemmner, W.
BMC Genomics 7 : 148. 13 June 2006

Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome.
Jensen, L.J., Skovgaard, M., Sicheritz-Ponten, T., Jorgensen, M.K., Lundegaard, C., Pedersen, C.C., Petersen, N. and Ussery, D.
BMC Genomics 4 (1): 12. 2 April 2003

BMC Systems Biology

Systems analysis of iron metabolism: the network of iron pools and fluxes.
Lopes, T.J., Luganskaja, T., Vujic-Spasic, M., Hentze, M.W., Muckenthaler, M.U., Schumann, K. and Reich, J.G.
BMC Systems Biology 4 (1): 112. 13 August 2010

Modelling phagosomal lipid networks that regulate actin assembly.
Kuehnel, M., Mayorga, L.S., Dandekar, T., Thakar, J., Schwarz, R., Anes, E., Griffiths, G. and Reich, J.
BMC Systems Biology 2 (1): 107. 5 December 2008

BMJ Open

Metagenomic analysis of gut microbial communities from a Central Asian population.
Kushugulova, A., Forslund, S.K., Costea, P.I., Kozhakhmetov, S., Khassenbekova, Z., Urazova, M., Nurgozhin, T., Zhumadilov, Z., Benberin, V., Driessen, M., Hercog, R., Voigt, A.Y., Benes, V., Kandels-Lewis, S., Sunagawa, S., Letunic, I. and Bork, P.
BMJ Open 8 (7): e021682. 28 July 2018

Beginnings

In gratitude: Charlie.
Reich, J.
Beginnings 28 (4): 39. 2008

BioEssays

Orthology prediction methods: a quality assessment using curated protein families.
Trachana, K., Larsson, T.A., Powell, S., Chen, W.H., Doerks, T., Muller, J. and Bork, P.
BioEssays 33 (10): 769-780. October 2011

Shared components of protein complexes - versatile building blocks or biochemical artefacts?
Krause, R., von Mering, C., Bork, P. and Dandekar, T.
BioEssays 26 : 1333-1343. 1 December 2004

Alternative splicing and evolution.
Boue, S., Letunic, I. and Bork, P.
BioEssays 25 : 1031-1034. 1 November 2003

O6-alkylguanine-DNA alkyltransferase: role in carcinogenesis and chemotherapy.
Margison, G.P. and Santibanez-Koref, M.F.
BioEssays 24 (3): 255-266. 1 January 2002

BioTec

Differential display reverse transcription PCR.
Bauer, D., Mueller, H., Reich, J., Riedel, H., Ahrenkiel, V., Warthoe, P. and Strauss, M.
BioTec 2 : 32-35. 1 January 1994

Biochemical Genetics

Biochemical genetics of methylglyoxal dehydrogenases in the laboratory rat (Rattus norvegicus).
Bender, K., Seibert, R.T., Wienker, T.F., Kren, V., Pravenec, M. and Bissbort, S.
Biochemical Genetics 32 : 147-154. 1 January 1994

Biochemical Journal

Pathway alignment: application to the comparative analysis of glycolytic enzymes.
Dandekar, T., Schuster, S., Snel, B., Huynen, M. and Bork, P.
Biochemical Journal 343 : 115-124. 1 January 1999

Biochimica et Biophysica Acta

Conformational stability studies of the pleckstrin DEP domain: definition of the domain boundaries.
Kharrat, A., Millevoi, S., Baraldi, E., Ponting, C.P., Bork, P. and Pastore, A.
Biochimica et Biophysica Acta 1385 : 157-164. 1 January 1998

Control analysis of metabolic systems involving quasi- equilibrium reactions.
Kholodenko, B.N., Schuster, S., Garcia, J., Westerhoff, H.V. and Cascante, M.
Biochimica et Biophysica Acta 1379 : 337-352. 1 January 1998

Computational methods for the prediction of protein folds.
Dandekar, T. and Koenig, R.
Biochimica et Biophysica Acta 1343 : 1-15. 14 November 1997

Probing Flp: a new approach to analyze the structure of a DNA recognizing protein by combining the genetic algorithm, mutagenesis and non-canonical DNA target sites.
Saxena, P., Whang, I., Voziyanov, Y., Harkey, C., Argos, P., Jayaram, M. and Dandekar, T.
Biochimica et Biophysica Acta 1340 : 187-204. 1 January 1997

Biochimica et Biophysica Acta - Gene Structure and Expression

Identification and characterization of UEV3, a human cDNA with similarities to inactive E2 ubiquitin-conjugating enzymes.
Kloor, M., Bork, P., Duwe, A., Klaes, R., Doeberitz, M.V. and Ridder, R.
Biochimica et Biophysica Acta - Gene Structure and Expression 1579 : 219-224. 1 January 2002

Bioelectrochemistry and Bioenergetics

Modelling oscillations of calcium and endoplasmic reticulum transmembrane potential role of the signalling and buffering proteins and of the size of the Ca2+ sequestering ER subcompartments.
Marhl, M., Schuster, S., Brumen, M. and Heinrich, R.
Bioelectrochemistry and Bioenergetics 46 : 79-90. 1 January 1998

Modelling the interrelation between the transmembrane potential and pH difference across membranes with electrogenic proton transport upon build-up of the proton-motive force.
Schuster, S., Ouhabi, R., Rigoulet, M. and Mazat, J.P.
Bioelectrochemistry and Bioenergetics 45 : 181-192. 1 January 1998

Biofizika

[An approach to the inverse folding problem based on the multiple alignment].
Sunyaev, S.R., Eisenhaber, F. and Tumanyan, V.G.
Biofizika 44 (4): 620-623. July 1999

Bioinformatics

Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features.
Li, Y., Kuhn, M., Gavin, A.C. and Bork, P.
Bioinformatics 36 (4): 1213-1218. 15 February 2020

RTK: efficient rarefaction analysis of large datasets.
Saary, P., Forslund, K., Bork, P. and Hildebrand, F.
Bioinformatics 33 (16): 2594-2595. 15 August 2017

CART - a chemical annotation retrieval toolkit.
Deghou, S., Zeller, G., Iskar, M., Driessen, M., Castillo, M., van Noort, V. and Bork, P.
Bioinformatics 32 (18): 2869-2871. 15 September 2016

MOCAT2: a metagenomic assembly, annotation and profiling framework.
Kultima, J.R., Coelho, L.P., Forslund, K., Huerta-Cepas, J., Li, S.S., Driessen, M., Voigt, A.Y., Zeller, G., Sunagawa, S. and Bork, P.
Bioinformatics 32 (16): 2520-2523. 15 August 2016

SmashCell: a software framework for the analysis of single-cell amplified genome sequences.
Harrington, E.D., Arumugam, M., Raes, J., Bork, P. and Relman, D.A.
Bioinformatics 26 (23): 2979-2980. 1 December 2010

SmashCommunity: A metagenomic annotation and analysis tool.
Arumugam, M., Harrington, E.D., Foerstner, K.U., Raes, J. and Bork, P.
Bioinformatics 26 (23): 2977-2978. 1 December 2010

AQUA: Automated quality improvement for multiple sequence alignments.
Muller, J., Creevey, C.J., Thompson, J.D., Arendt, D. and Bork, P.
Bioinformatics 26 (2): 263-265. 15 January 2010

Sircah: a tool for the detection and visualization of alternative transcripts.
Harrington, E.D. and Bork, P.
Bioinformatics 24 (17): 1959-1960. 1 September 2008

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.
Letunic, I. and Bork, P.
Bioinformatics 23 (1): 127-128. 1 January 2007

LSAT: learning about alternative transcripts in MEDLINE.
Shah, P.K. and Bork, P.
Bioinformatics 22 (7): 857-865. 1 April 2006

Extraction of regulatory gene/protein networks from Medline.
Saric, J., Jensen, L.J., Ouzounova, R., Rojas, I. and Bork, P.
Bioinformatics 22 : 645-650. 15 March 2006

Medusa: a simple tool for interaction graph analysis.
Hooper, S.D. and Bork, P.
Bioinformatics 21 (24): 4432-4433. 27 September 2005

Comparison of computational methods for the identification of cell cycle regulated genes.
de Lichtenberg, U., Jensen, L.J., Fausboll, A., Jensen, T.S., Bork, P. and Brunak, S.
Bioinformatics 21 : 1164-1171. 1 January 2005

GandrKB - ontological microarray annotation and visualization.
Schober, D., Leser, U., Zenke, M. and Reich, J.
Bioinformatics 21 (11): 2785-2786. 1 January 2005

The WHy domain mediates the response to desiccation in plants and bacteria.
Ciccarelli, F.D. and Bork, P.
Bioinformatics 21 : 1304-1307. 1 January 2005

BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments.
Suyama, M., Torrents, D. and Bork, P.
Bioinformatics 20 : 1968-1970. 12 August 2004

Gene annotation from scientific literature using mappings between keyword systems.
Perez, A.J., Perez-Iratxeta, C., Bork, P., Thode, G. and Andrade-Navarro, M.A.
Bioinformatics 20 (13): 2084-2091. 1 January 2004

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.
Crass, T., Antes, I., Basekow, R., Bork, P., Buning, C., Christensen, M., Claussen, H., Ebeling, C., Ernst, P., Gailus-Durner, V., Glatting, K.H., Gohla, R., Goessling, F., Grote, K., Heidtke, K., Herrmann, A., O'Keeffe, S., Kiesslich, O., Kolibal, S., Korbel, J.O., Lengauer, T., Liebich, I., van der Linden, M., Luz, H., Meissner, K., von Mering, C., Mevissen, H.T., Mewes, H.W., Michael, H., Mokrejs, M., Mueller, T., Pospisil, H., Rarey, M., Reich, J.G., Schneider, R., Schomburg, D., Schulze-Kremer, S., Schwarzer, K., Sommer, I., Springstubbe, S., Suhai, S., Thoppae, G., Vingron, M., Warfsmann, J., Werner, T., Wetzler, D., Wingender, E. and Zimmer, R.
Bioinformatics 20 (2): 268-270. 1 January 2004

A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens.
Krause, R., von Mering, C. and Bork, P.
Bioinformatics 19 : 1901-1908. 12 October 2003

Evaluation of annotation strategies using an entire genome sequence.
Iliopoulos, I., Tsoka, S., Andrade, M.A., Enright, A.J., Carroll, M., Poullet, P., Promponas, V., Liakopoulos, T., Palaios, G., Pasquier, C., Hamodrakas, S., Tamames, J., Yagnik, A.T., Tramontano, A., Devos, D., Blaschke, C., Valencia, A., Brett, D., Martin, D., Leroy, C., Rigoutsos, I., Sander, C. and Ouzounis, C.A.
Bioinformatics 19 (6): 717-726. 12 April 2003

Prediction of human protein function according to Gene Ontology categories.
Jensen, L.J., Gupta, R., Staerfeldt, H.H. and Brunak, S.
Bioinformatics 19 : 635-642. 22 March 2003

Comparative analysis of protein interaction networks.
Bork, P.
Bioinformatics 18 Suppl 2 : S64. 1 October 2002

Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae.
Schuster, S., Pfeiffer, T., Moldenhauer, F., Koch, I. and Dandekar, T.
Bioinformatics 18 (2): 351-361. 1 January 2002

NAIL - Network Analysis Interface for Linking HMMER results.
Sanchez-Pulido, L., Yuan, Y.P., Andrade, M.A. and Bork, P.
Bioinformatics 16 (7): 656-657. 1 July 2000

Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries.
Eisenhaber, F. and Bork, P.
Bioinformatics 15 : 528-535. 1 July 1999

Automated genome sequence analysis and annotation.
Andrade, M.A., Brown, N.P., Leroy, C., Hoersch, S., de Daruvar, A., Reich, C., Franchini, A., Tamames, J., Valencia, A., Ouzounis, C. and Sander, C.
Bioinformatics 15 (5): 391-412. May 1999

Associative database of protein sequences.
Hanke, J., Lehmann, G., Bork, P. and Reich, J.
Bioinformatics 15 : 741-748. 1 January 1999

METATOOL: for studying metabolic networks.
Pfeiffer, T., Sanchez-Valdenebro, I., Nuno, J.C., Montero, F. and Schuster, S.
Bioinformatics 15 : 251-257. 1 January 1999

Frame: detection of genomic sequencing errors.
Brown, N.P., Sander, C. and Bork, P.
Bioinformatics 14 : 367-371. 1 January 1998

Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches.
Dandekar, T., Beyer, K., Bork, P., Kenealy, M.R., Pantopoulos, K., Hentze, M., Sonntag-Buck, V., Flouriot, G., Gannon, F., Keller, W. and Schreiber, S.
Bioinformatics 14 : 271-278. 1 January 1998

Towards detection of orthologues in sequence databases.
Yuan, Y.P., Eulenstein, O., Vingron, M. and Bork, P.
Bioinformatics 14 : 285-289. 1 January 1998

Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families.
Andrade, M.A. and Valencia, A.
Bioinformatics 14 (7): 600-607. 1998

Biological Cybernetics

Simulation of plasticity in the adult visual cortex.
Andrade-Navarro, M.A., Muro, E.M. and Moran, F.
Biological Cybernetics 84 (6): 445-451. May 2001

Biophysical Chemistry

Treatment of multifunctional enzymes in metabolic pathway analysis.
Schuster, S. and Zevedei-Oancea, I.
Biophysical Chemistry 99 (1): 63-75. 3 September 2002

Mitochondria as an important factor in the maintenance of constant amplitudes of cytosolic calcium oscillations.
Marhl, M., Schuster, S. and Brumen, M.
Biophysical Chemistry 71 : 125-132. 1 January 1998

Bioprocess and Biosystems Engineering

Use of network analysis of metabolic systems in bioengineering.
Schuster, S., Klamt, S., Weckwerth, W., Moldenhauer, F. and Pfeiffer, T.
Bioprocess and Biosystems Engineering 24 (6): 363-372. 1 January 2002

Biospektrum

Ein kurzer Essay zur politischen Lage beim Stammzellgesetz [A short essay on the political situation concerning the stem cell law].
Reich, J.
Biospektrum 13 (3): 227. May 2007

Microarrays, Genexpressionsanalyse und Bioinformatik.
Schober, D.
Biospektrum 8 (3): 307-310. 2002

Bioinformatik.
Bork, P.
Biospektrum 5 (3/1999): 172. 1999

Biosystems

A method for classifying metabolites in topological pathway analyses based on minimization of pathway number.
Dandekar, T., Moldenhauer, F., Bulik, S., Bertram, H. and Schuster, S.
Biosystems 70 (3): 255-270. August 2003

Cellular information transfer regarded from a stoichiometry and control analysis perspective.
Schuster, S., Kholodenko, B.N. and Westerhoff, H.V.
Biosystems 55 (1-3): 73-81. 1 February 2000

Improving genetic algorithms for protein folding simulations by systematic crossover.
Koenig, R. and Dandekar, T.
Biosystems 50 (1): 17-25. April 1999

Modular control analysis of slipping enzymes.
Schuster, S. and Westerhoff, H.V.
Biosystems 49 : 1-15. 1 January 1999

The modelling of metabolic systems. Structure, control and optimality.
Heinrich, R. and Schuster, S.
Biosystems 47 : 61-77. 1 January 1998

Biotechniques

Computing fuzzy associations for the analysis of biological literature.
Perez-Iratxeta, C., Keer, H.S., Bork, P. and Andrade, M.A.
Biotechniques 32 (6): 1380-1385. June 2002

Biotechnology Progress

Metabolic pathway analysis: Basic concepts and scientific applications in the post-genomic era.
Schilling, C.H., Schuster, S., Palsson, B.O. and Heinrich, R.
Biotechnology Progress 15 (3): 296-303. 1 May 1999

Biotechnology and Bioengineering

Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria.
Klamt, S., Schuster, S. and Gilles, E.D.
Biotechnology and Bioengineering 77 (7): 734-751. 1 January 2002

Bone

Association of ANKH gene polymorphisms with radiographic hand bone size and geometry in a Chuvasha population.
Malkin, I., Dahm, S., Suk, A., Kobyliansky, E., Toliat, M.R., Ruf, N., Livshits, G. and Nuernberg, P.
Bone 36 (2): 365-373. 1 January 2005

Brain Research

Dopamine-glutamate abnormalities in the frontal cortex associated with the catechol-O-methyltransferase (COMT) in schizophrenia.
Brisch, R., Bernstein, H.G., Krell, D., Dobrowolny, H., Bielau, H., Steiner, J., Gos, T., Funke, S., Stauch, R., Knueppel, S. and Bogerts, B.
Brain Research 1269 : 166-175. 7 May 2009

Breast Cancer Research

Heat shock protein-90-alpha, a prolactin-STAT5 target gene identified in breast cancer cells, is involved in apoptosis regulation.
Perotti, C., Liu, R., Parusel, C., Boecher, N., Schultz, J., Bork, P., Pfitzner, E., Groner, B. and Shemanko, C.
Breast Cancer Research 10 (6): R94. 13 November 2008

Briefings in Bioinformatics

InterPro: an integrated documentation resource for protein families, domains and functional sites.
Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Biswas, M., Bradley, P., Bork, P., Bucher, P., Copley, R., Courcelle, E., Durbin, R., Falquet, L., Fleischmann, W., Gouzy, J., Griffith-Jones, S., Haft, D., Hermjakob, H., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lopez, R., Letunic, I., Orchard, S., Pagni, M., Peyruc, D., Ponting, C.P., Servant, F. and Sigrist, C.J.
Briefings in Bioinformatics 3 : 225-235. 1 September 2002

British Journal of Cancer

Deletion mapping and linkage analysis provide strong indication for the involvement of the human chromosome region 8p12-p22 in breast carcinogenesis.
Seitz, S., Rohde, K., Bender, E., Nothnagel, A., Pidde, H., Ullrich, O.M., El-Zehairy, A., Haensch, W., Jandrig, B., Koelble, K., Schlag, P.M. and Scherneck, S.
British Journal of Cancer 76 : 983-991. 1 January 1997

British Journal of Dermatology

Interleukin-10 promoter polymorphism IL10.G and familial early onset psoriasis.
Hensen, P., Asadullah, K., Windemuth, C., Rueschendorf, F., Hueffmeier, U., Staender, M., Schmitt-Egenolf, M., Wienker, T.F., Reis, A. and Traupe, H.
British Journal of Dermatology 149 (2): 381-385. August 2003

Bulletin of Mathematical Biology

A distance measure based on binary character data and its application to phylogeny reconstruction.
Schmidt, W. and Mueller, E.C.
Bulletin of Mathematical Biology 58 : 449-469. 1 January 1996

Cancer

Loss of constitutional heterozygosity on chromosome 11p in human ovarian cancer. Positive correlation with grade of differentiation.
Kiechle-Schwarz, M., Bauknecht, T., Wienker, T.F., Walz, L. and Pfleiderer, A.
Cancer 72 : 2423-2432. 1 January 1993

Cancer Cell

Dissecting the intracellular pancreatic tumor microbiome at single-cell level.
Schmidt, T.S.B. and Bork, P.
Cancer Cell 40 (10): 1083-1085. 10 October 2022

Cancer Research

Novel drug candidates for the treatment of metastatic colorectal cancer through global inverse gene-expression profiling.
van Noort, V., Schoelch, S., Iskar, M., Zeller, G., Ostertag, K., Schweitzer, C., Werner, K., Weitz, J., Koch, M. and Bork, P.
Cancer Research 74 (20): 5690-5699. 15 October 2014

Carcinogenesis

Quantitative trait locus analysis reveals two intragenic sites that influence O6-alkylguanine-DNA alkyltransferase activity in peripheral blood mononuclear cells.
Margison, G.P., Heighway, J., Pearson, S., McGown, G., Thorncroft, M.R., Watson, A.J., Harrison, K.L., Lewis, S.J., Rohde, K., Barber, P.V., Povey, A.C., O'Donnell, P. and Santibanez-Koref, M.F.
Carcinogenesis 26 (8): 1473-1480. 1 January 2005

Cell

Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations.
Nishijima, S., Stankevic, E., Aasmets, O., Schmidt, T.S.B., Nagata, N., Keller, M.I., Ferretti, P., Juel, H.B., Fullam, A., Robbani, S.M., Schudoma, C., Hansen, J.K., Holm, L.A., Israelsen, M., Schierwagen, R., Torp, N., Telzerow, A., Hercog, R., Kandels, S., Hazenbrink, D.H.M., Arumugam, M., Bendtsen, F., Brøns, C., Fonvig, C.E., Holm, J.C., Nielsen, T., Pedersen, J.S., Thiele, M.S., Trebicka, J., Org, E., Krag, A., Hansen, T., Kuhn, M. and Bork, P.
Cell 13 November 2024 (In Press)

Emergence of community behaviors in the gut microbiota upon drug treatment.
Garcia-Santamarina, S., Kuhn, M., Devendran, S., Maier, L., Driessen, M., Mateus, A., Mastrorilli, E., Brochado, A.R., Savitski, M.M., Patil, K.R., Zimmermann, M., Bork, P. and Typas, A.
Cell 187 (22): 6346-6357.e20. 31 October 2024

Discovery of antimicrobial peptides in the global microbiome with machine learning.
Santos-Júnior, C.D., Torres, M.D.T., Duan, Y., Rodríguez Del Río, Á., Schmidt, T.S.B., Chong, H., Fullam, A., Kuhn, M., Zhu, C., Houseman, A., Somborski, J., Vines, A., Zhao, X.M., Bork, P., Huerta-Cepas, J., de la Fuente-Nunez, C. and Coelho, L.P.
Cell 187 (14): 3761-3778. 11 July 2024

Gene expression changes and community turnover differentially shape the global ocean metatranscriptome.
Salazar, G., Paoli, L., Alberti, A., Huerta-Cepas, J., Ruscheweyh, H.J., Cuenca, M., Field, C.M., Coelho, L.P., Cruaud, C., Engelen, S., Gregory, A.C., Labadie, K., Marec, C., Pelletier, E., Royo-Llonch, M., Roux, S., Sánchez, P., Uehara, H., Zayed, A.A., Zeller, G., Carmichael, M., Dimier, C., Ferland, J., Kandels, S., Picheral, M., Pisarev, S., Poulain, J., Acinas, S.G., Babin, M., Bork, P., Bowler, C., de Vargas, C., Guidi, L., Hingamp, P., Iudicone, D., Karp-Boss, L., Karsenti, E., Ogata, H., Pesant, S., Speich, S., Sullivan, M.B., Wincker, P. and Sunagawa, S.
Cell 179 (5): 1068-1083. 14 November 2019

Disentangling genetic and environmental effects on the proteotypes of individuals.
Romanov, N., Kuhn, M., Aebersold, R., Ori, A., Beck, M. and Bork, P.
Cell 177 (5): 1308-1318. 16 May 2019

Pervasive protein thermal stability variation during the cell cycle.
Becher, I., Andrés-Pons, A., Romanov, N., Stein, F., Schramm, M., Baudin, F., Helm, D., Kurzawa, N., Mateus, A., Mackmull, M.T., Typas, A., Müller, C.W., Bork, P., Beck, M. and Savitski, M.M.
Cell 173 (6): 1495-1507. 31 May 2018

Transposase-DNA complex structures reveal mechanisms for conjugative transposition of antibiotic resistance.
Rubio-Cosials, A., Schulz, E.C., Lambertsen, L., Smyshlyaev, G., Rojas-Cordova, C., Forslund, K., Karaca, E., Bebel, A., Bork, P. and Barabas, O.
Cell 173 (1): 208-220. 22 March 2018

The human gut microbiome: from association to modulation.
Schmidt, T.S.B., Raes, J. and Bork, P.
Cell 172 (6): 1198-1215. 8 March 2018

Systematic discovery of in vivo phosphorylation networks.
Linding, R., Jensen, L.J., Ostheimer, G.J., van Vugt, M.A., Jorgensen, C., Miron, I.M., Diella, F., Colwill, K., Taylor, L., Elder, K., Metalnikov, P., Nguyen, V., Pasculescu, A., Jin, J., Park, J.G., Samson, L.D., Woodgett, J.R., Russell, R.B., Bork, P., Yaffe, M.B. and Pawson, T.
Cell 129 (7): 1415-1426. 29 June 2007

Towards cellular systems in 4D.
Bork, P. and Serrano, L.
Cell 121 : 507-509. 1 January 2005

Nibrin, a novel DNA double-strand break repair protein, is mutated in Nijmegen breakage syndrome.
Varon, R., Vissinga, C., Platzer, M., Cerosaletti, K.M., Chrzanowska, K.H., Saar, K., Beckmann, G., Seemanova, E., Cooper, P.R., Nowak, N.J., Stumm, M., Weemaes, C.M.R., Gatti, R.A., Wilson, R.K., Digweed, M., Rosenthal, A., Sperling, K., Concannon, P. and Reis, A.
Cell 93 (3): 467-476. 1 May 1998

Secreted fringe like signaling molecules may be glycosyltransferases.
Yuan, Y.P., Schultz, J., Mlodzik, M. and Bork, P.
Cell 88 : 9-11. 1 January 1997

Polycystic kidney disease: the complete structure of the PKD1 gene and its protein.
Gluecksmann-Kuis, M.A., Tayber, O., Woolf, E.A., Bougueleret, L., Deng, N.H., Alperin, G.D., Iris, F., Hawkins, F., Munro, C., Lakey, N., Duyk, G., Schneider, M.C., Geng, L., Zhang, F., Zhao, Z.H., Torosian, S., Zhou, J., Reeders, S.T., Bork, P., Pohlschmidt, M., Lohning, C., Kraus, B., Nowicka, U., Leung, A.L.S. and Frischauf, A.M.
Cell 81 (2): 289-298. 21 April 1995

A phosphotyrosine interaction domain.
Bork, P. and Margolis, B.
Cell 80 (5): 693-694. 1 January 1995

Cell Cycle

Evolution of cell cycle control: same molecular machines, different regulation.
de Lichtenberg, U., Jensen, T.S., Brunak, S., Bork, P. and Jensen, L.J.
Cell Cycle 6 (15): 1819-1825. 1 August 2007

Cell Genomics

Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean.
Delmont, T.O., Gaia, M., Hinsinger, D.D., Frémont, P., Vanni, C., Fernandez-Guerra, A., Eren, A.M., Kourlaiev, A., d'Agata, L., Clayssen, Q., Villar, E., Labadie, K., Cruaud, C., Poulain, J., Da Silva, C., Wessner, M., Noel, B., Aury, J.M., de Vargas, C., Bowler, C., Karsenti, E., Pelletier, E., Wincker, P. and Jaillon, O.
Cell Genomics 2 (5): 100123. 11 May 2022

Cell Host & Microbe

Dispersal strategies shape persistence and evolution of human gut bacteria.
Hildebrand, F., Gossmann, T.I., Frioux, C., Özkurt, E., Myers, P.N., Ferretti, P., Kuhn, M., Bahram, M., Nielsen, H.B. and Bork, P.
Cell Host & Microbe 29 (7): 1167-1176. 14 June 2021

Cell Reports Methods

Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics.
Pryszlak, A., Wenzel, T., Seitz, K.W., Hildebrand, F., Kartal, E., Cosenza, M.R., Benes, V., Bork, P. and Merten, C.A.
Cell Reports Methods 2 (1): 100137. 24 January 2022

Cell Systems

Integrated transcriptome and proteome analyses reveal organ-specific proteome deterioration in old rats.
Ori, A., Toyama, B.H., Harris, M.S., Bock, T., Iskar, M., Bork, P., Ingolia, N.T., Hetzer, M.W. and Beck, M.
Cell Systems 1 (3): 224-237. 23 September 2015

Cellular Physiology and Biochemistry

A genotype-phenotype correlation with gender-effect for hearing impairment caused by TECTA mutations.
Pfister, M., Thiele, H., Van Camp, G., Fransen, E., Apaydin, F., Aydin, O., Leistenschneider, P., Devoto, M., Zenner, H.P., Blin, N., Nuernberg, P., Ozkarakas, H. and Kupka, S.
Cellular Physiology and Biochemistry 14 (4-6): 369-376. 1 January 2004

Chemtracts

The large-scale organization of metabolic networks.
Dandekar, T. and Schuster, S.
Chemtracts 14 : 137-141. 2001

Crystal structures of the membrane-binding C2 domain of human coagulation factor V structure of the C2 domain of human factor VIII at 1.5 A resolution.
Dandekar, T.
Chemtracts 13 (6): 398-401. June 2000

Stochastic sensing of organic analytes by a pore-forming protein containing a molecular adapter.
Schultzberg, M., Boulin, C. and Dandekar, T.
Chemtracts 13 (3): 198-202. March 2000

A genetic framework for floral patterning.
Koch, G. and Dandekar, T.
Chemtracts 12 (13): 956-959. December 1999

RNA-catalysed nucleotide synthesis.
Koch, G. and Dandekar, T.
Chemtracts 12 (13): 938-943. December 1999

Mutation of the mouse klotho gene leads to a syndrome resembling ageing. Condensation and commentary.
Sharma, K., Kelly, L. and Dandekar, T.
Chemtracts 12 (10): 703-707. September 1999

Exploring the metabolic and genetic control of gene expression on a genomic scale.
Koenig, R. and Dandekar, T.
Chemtracts 12 (3): 148-152. March 1999

Mice lacking bombesin receptor subtype-3 develop metabolic defects and obesity (Condensation and commentary).
Kelly, L., Sharma, K. and Dandekar, T.
Chemtracts 12 : 223-228. March 1999

Determination of the fold of the core protein of Hepatitis B virus by electron cryomicroscopy.
Dandekar, T. and Argos, P.
Chemtracts 11 : 161-165. 1 January 1998

Structural basis for the binding of a globular antifreeze to ice.
Dandekar, T. and Argos, P.
Chemtracts 11 : 229-232. 1 January 1998

Computational Biology

Comparative genome analysis: exploiting the context of genes to infer evolution and predict function.
Bork, P., Snel, B., Lehmann, G., Suyama, M., Dandekar, T., Lathe, W. and Huynen, M.
Computational Biology 1 : 281-294. 2000

Computer Applications in the Biosciences

The sequence alerting server-a new WEB server.
Hegyi, H., Lai, J. and Bork, P.
Computer Applications in the Biosciences 13 : 619-620. 1 January 1997

Kohonen map as visualization tool for the analysis of protein sequences: multiple alignments, domains and segments of secondary structures.
Hanke, J. and Reich, J.
Computer Applications in the Biosciences 12 : 447-454. 1 January 1996

A fast, sensitive pattern-matching approach for protein sequences.
Rohde, K. and Bork, P.
Computer Applications in the Biosciences 9 : 183-189. 1 January 1993

Computers & Chemical Engineering

A theoretical framework for detecting signal transfer routes in signalling networks.
Zevedei-Oancea, I. and Schuster, S.
Computers & Chemical Engineering 29 (3): 597-617. 1 January 2005

Computers and Chemistry

Medical target prediction from genome sequence: combining different sequence analysis algorithms with expert knowledge and input from artificial intelligence approaches.
Dandekar, T., Du, F., Schirmer, R.H. and Schmidt, S.
Computers and Chemistry 26 (1): 15-21. December 2001

Current Biology

Ice-age climate adaptations trap the alpine marmot in a state of low genetic diversity.
Gossmann, T.I., Shanmugasundram, A., Börno, S., Duvaux, L., Lemaire, C., Kuhl, H., Klages, S., Roberts, L.D., Schade, S., Gostner, J.M., Hildebrand, F., Vowinckel, J., Bichet, C., Mülleder, M., Calvani, E., Zelezniak, A., Griffin, J.L., Bork, P., Allaine, D., Cohas, A., Welch, J.J., Timmermann, B. and Ralser, M.
Current Biology 29 (10): 1712-1720. 20 May 2019

The Spir actin organizers are involved in vesicle transport processes.
Kerkhoff, E., Simpson, J.C., Leberfinger, C.B., Otto, I.M., Doerks, T., Bork, P., Rapp, U.R., Raabe, T. and Pepperkok, R.
Current Biology 11 : 1963-1968. 11 December 2001

The p150-Spir protein provides a link between c-Jun N-terminal kinase function and actin reorganization.
Otto, I.M., Raabe, T., Rennefahrt, U.E., Bork, P., Rapp, U.R. and Kerkhoff, E.
Current Biology 10 : 345-348. 23 March 2000

Phospholipases A2 and Wnts are unlikely to share a common ancestor.
Copley, R.R., Ponting, C.P. and Bork, P.
Current Biology 9 : R718-R719. 7 October 1999

A latrophilin/CL-1-like GPS domain in polycystin-1.
Ponting, C.P., Hofmann, K. and Bork, P.
Current Biology 9 (16): R585-R588. 26 August 1999

Metabolism and evolution of Haemophilus influenzae deduced from a whole genome comparison with Escherichia coli.
Tatusov, R.L., Mushegian, A.R., Bork, P., Brown, N.P., Hayes, W.S., Borodovsky, M., Rudd, K.E. and Koonin, E.V.
Current Biology 6 (3): 279-291. 1 January 1996

Current Opinion in Biotechnology

Drug discovery in the age of systems biology: the rise of computational approaches for data integration.
Iskar, M., Zeller, G., Zhao, X.M., van Noort, V. and Bork, P.
Current Opinion in Biotechnology 23 (4): 609-616. August 2012

Current Opinion in Cell Biology

Function prediction and protein networks.
Huynen, M.A., Snel, B., von Mering, C. and Bork, P.
Current Opinion in Cell Biology 15 : 191-198. 1 January 2003

Current Opinion in Chemical Biology

Genome and protein evolution in eukaryotes.
Copley, R.R., Letunic, I. and Bork, P.
Current Opinion in Chemical Biology 6 : 39-45. 1 January 2002

Current Opinion in Microbiology

Get the most out of your metagenome: computational analysis of environmental sequence data.
Raes, J., Foerstner, K.U. and Bork, P.
Current Opinion in Microbiology 10 (5): 490-498. October 2007

Current Opinion in Structural Biology

Protein function space: viewing the limits or limited by our view?
Raes, J., Harrington, E.D., Singh, A.H. and Bork, P.
Current Opinion in Structural Biology 17 (3): 362-369. June 2007

Sequences and topology. Genes and structures in context.
Bork, P. and Orengo, C.A.
Current Opinion in Structural Biology 14 : 261-263. 1 January 2004

Integration of genome data and protein structures: prediction of protein folds, protein interactions and 'molecular phenotypes' of single nucleotide polymorphisms.
Sunyaev, S.R., Lathe, W. and Bork, P.
Current Opinion in Structural Biology 11 (1): 125-130. 1 January 2001

Exploitation of gene context.
Huynen, M.A., Snel, B., Lathe, W. and Bork, P.
Current Opinion in Structural Biology 10 (3): 366-370. 1 June 2000

Sequences and topology. Genome and proteome informatics - Editorial overview.
Bork, P. and Eisenberg, D.
Current Opinion in Structural Biology 10 (3): 341-342. 1 June 2000

Protein families in multicellular organisms.
Copley, R.R., Schultz, J., Ponting, C.P. and Bork, P.
Current Opinion in Structural Biology 9 : 408-415. 1 January 1999

Sequences and topology deriving biological knowledge from genomic sequences.
Bork, P. and Eisenberg, D.
Current Opinion in Structural Biology 8 : 331-332. 1 January 1998

Protein sequence motifs.
Bork, P. and Koonin, E.V.
Current Opinion in Structural Biology 6 : 366-376. 1 January 1996

From genome sequences to protein function.
Bork, P., Ouzounis, C. and Sander, C.
Current Opinion in Structural Biology 4 : 393-403. 1 January 1994

Epidermal growth factor-like modules.
Campbell, I.D. and Bork, P.
Current Opinion in Structural Biology 3 (3): 385-392. 1 January 1993

Mobile modules and motifs.
Bork, P.
Current Opinion in Structural Biology 2 : 413-421. 1 January 1992

Cytometry

A comment on "Can measurement of potential doubling time (TPOT) be compared between laboratories ? A quality control study".
Schmidt, W.
Cytometry 21 : 218-219. 1 January 1995

Developmental Biology

Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome.
Raible, F., Tessmar-Raible, K., Arboleda, E., Kaller, T., Bork, P., Arendt, D. and Arnone, M.I.
Developmental Biology 300 (1): 461-475. 1 December 2006

Developmental Cell

A temporal map of transcription factor activity: Mef2 directly regulates target genes at all stages of muscle development.
Sandmann, T., Jensen, L.J., Jakobsen, J.S., Karzynski, M.M., Eichenlaub, M.P., Bork, P. and Furlong, E.E.
Developmental Cell 10 : 797-807. June 2006

Developments in Industrial Microbiology

Comparative genome analysis: From sequences to functions.
Bork, P.
Developments in Industrial Microbiology 34 : 21-23. 1 January 1997

Diabetologia

A German genome-wide linkage scan for type 2 diabetes supports the existence of a metabolic syndrome locus on chromosome 1p36.13 and a type 2 diabetes locus on chromosome 16p12.2.
Hoffmann, K., Mattheisen, M., Dahm, S., Nuernberg, P., Roe, C., Johnson, J., Cox, N.J., Wichmann, H.E., Wienker, T.F., Schulze, J., Schwarz, P.E. and Lindner, T.H.
Diabetologia 50 (7): 1418-1422. July 2007

Drug Discovery Today: TARGETS

Quality analysis and integration of large-scale molecular data sets.
Jensen, L.J. and Bork, P.
Drug Discovery Today: TARGETS 3 : 51-56. 1 January 2004

Drugs of Today

Exploring Medline abstracts with XplorMed.
Perez-Iratxeta, C., Bork, P. and Andrade, M.A.
Drugs of Today 38 : 381-389. 1 June 2002

EBioMedicine

Gut microbiota linked to sexual preference and HIV infection.
Noguera-Julian, M., Rocafort, M., Guillen, Y., Rivera, J., Casadella, M., Nowak, P., Hildebrand, F., Zeller, G., Parera, M., Bellido, R., Rodriguez, C., Carrillo, J., Mothe, B., Coll, J., Bravo, I., Estany, C., Herrero, C., Saz, J., Sirera, G., Torrela, A., Navarro, J., Crespo, M., Brander, C., Negredo, E., Blanco, J., Guarner, F., Calle, M.L., Bork, P., Soennerborg, A., Clotet, B. and Paredes, R.
EBioMedicine 5 : 135-146. March 2016

EMBO Journal

Splicing factors stimulate polyadenylation via USEs at non-canonical 3' end formation signals.
Danckwardt, S., Kaufmann, I., Gentzel, M., Foerstner, K.U., Gantzert, A.S., Gehring, N.H., Neu-Yilik, G., Bork, P., Keller, W., Wilm, M., Hentze, M.W. and Kulozik, A.E.
EMBO Journal 26 (11): 2658-2669. 6 June 2007

Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways.
Gatfield, D., Unterholzner, L., Ciccarelli, F.D., Bork, P. and Izaurralde, E.
EMBO Journal 22 : 3960-3970. 1 January 2003

Yeast chromosome III: new gene functions.
Koonin, E., Bork, P. and Sander, C.
EMBO Journal 13 : 493-503. 1 January 1994

EMBO Reports

Evolution and regulation of cellular periodic processes: a role for paralogues.
Trachana, K., Jensen, L.J. and Bork, P.
EMBO Reports 11 (3): 233-238. March 2010

Environments shape the nucleotide composition of genomes.
Foerstner, K.U., von Mering, C., Hooper, S.D. and Bork, P.
EMBO Reports 6 (12): 1208-1213. 30 September 2005

The way we write - Country-specific variations of the English language in the biomedical literature.
Netzel, R., Perez-Iratxeta, C., Bork, P. and Andrade, M.A.
EMBO Reports 4 : 446-451. 1 January 2003

The rhodanese/Cdc25 phosphatase superfamily. Sequence-structure-function relations.
Bordo, D. and Bork, P.
EMBO Reports 3 : 741-746. 1 August 2002

A complex prediction: three-dimensional model of the yeast exosome.
Aloy, P., Ciccarelli, F.D., Leutwein, C., Gavin, A.C., Superti-Furga, G., Bork, P., Boettcher, B. and Russell, R.B.
EMBO Reports 3 : 628-635. 1 January 2002

Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins.
Suyama, M., Doerks, T., Braun, I.C., Sattler, M., Izaurralde, E. and Bork, P.
EMBO Reports 1 (1): 53-58. 1 July 2000

Ecology and Evolution

Gut microbiota composition is associated with environmental landscape in honey bees.
Jones, J.C., Fruciano, C., Hildebrand, F., Al Toufalilia, H., Balfour, N.J., Bork, P., Engel, P., Ratnieks, F.L.W. and Hughes, W.O.H.
Ecology and Evolution 8 (1): 441-451. January 2018

Endocrinology

The 3'-untranslated region of the human estrogen receptor alpha gene mediates rapid messenger ribonucleic acid turnover.
Kenealy, M.R., Flouriot, G., Sonntag-Buck, V., Dandekar, T., Brand, H. and Gannon, F.
Endocrinology 141 (8): 2805-2813. August 2000

Environmental Microbiology

Metagenomic assessment of the global diversity and distribution of bacteria and fungi.
Bahram, M., Netherway, T., Frioux, C., Ferretti, P., Coelho, L.P., Geisen, S., Bork, P. and Hildebrand, F.
Environmental Microbiology 23 (1): 316-326. January 2021

Environmental Microbiology Reports

Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment.
Bahram, M., Anslan, S., Hildebrand, F., Bork, P. and Tedersoo, L.
Environmental Microbiology Reports 11 (4): 487-494. August 2018

Epilepsy Research

Association of the 867Asp variant of the human anion exchanger 3 gene with common subtypes of idiopathic generalized epilepsy.
Sander, T., Toliat, M.R., Heils, A., Leschik, G., Becker, C., Rueschendorf, F., Rohde, K., Mundlos, S. and Nuernberg, P.
Epilepsy Research 51 (3): 249-255. 1 October 2002

Exclusion of linkage between idiopathic generalized epilepsies and the GABAA receptor alpha1 and gamma2 subunit gene cluster on chromosome 5.
Sander, T., Hildmann, T., Janz, D., Wienker, T.F., Bianchi, A., Bauer, G., Sailer, U., Scaramelli, A., Neitzel, H., Schmitz, B., Bailey, M.E.S., Beckmannagetta, G., Johnson, K.J. and Darlison, M.G.
Epilepsy Research 23 (3): 235-244. 1 January 1996

European Archives of Psychiatry and Clinical Neuroscience

Towards the genetic basis of periodic catatonia: pedigree sample for genome scan I and II.
Stoeber, G., Pfuhlmann, B., Nuernberg, G., Schmidtke, A., Reis, A., Franzek, E. and Wienker, T.F.
European Archives of Psychiatry and Clinical Neuroscience 251 (Suppl 1): I25-I30. May 2001

European Journal of Biochemistry

Modelling of simple and complex calcium oscillations - From single-cell responses to intercellular signalling.
Schuster, S., Marhl, M. and Hoefer, T.
European Journal of Biochemistry 269 (5): 1333-1355. 1 January 2002

Pore-forming peptides of Entamoeba dispar : similarity and divergence to amoebapores in structure, expression and activity.
Nickel, R., Ott, C., Dandekar, T. and Leippe, M.
European Journal of Biochemistry 265 (3): 1002-1007. 1 November 1999

European Journal of Human Genetics

In NF1, CFTR, PER3, CARS and SYT7, alternatively included exons show higher conservation of surrounding intron sequences than constitutive exons.
Kaufmann, D., Kenner, O., Nuernberg, P., Vogel, W. and Bartelt, B.
European Journal of Human Genetics 12 (2): 139-149. 1 January 2004

Discovery, scoring and utilization of human single nucleotide polymorphisms: a multidisciplinary problem.
Isaksson, A., Landegren, U., Syvanen, A.C., Bork, P., Stein, C., Ortigao, F. and Brookes, A.J.
European Journal of Human Genetics 8 : 154-156. 1 February 2000

European Journal of Neuroscience

Gene expression profiling of the rat superior olivary complex using serial analysis of gene expression.
Koehl, A., Schmidt, N., Rieger, A., Pilgram, S.M., Letunic, I., Bork, P., Soto, F., Friauf, E. and Nothwang, H.G.
European Journal of Neuroscience 20 : 3244-3258. 1 December 2004

Experimental Dermatology

Association scan of the novel psoriasis susceptibility region on chromosome 19: evidence for both susceptible and protective loci.
Hensen, P., Windemuth, C., Hueffmeier, U., Rueschendorf, F., Stadelmann, A., Hoppe, V., Fenneker, D., Staender, M., Schmitt-Egenolf, M., Wienker, T.F., Traupe, H. and Reis, A.
Experimental Dermatology 12 (4): 490-496. August 2003

Experimental Eye Research

Characterization of a mutation in the lens-specific MP70 encoding gene of the mouse leading to a dominant cataract.
Graw, J., Loster, J., Soewarto, D., Fuchs, H., Meyer, B., Reis, A., Wolf, E., Balling, R. and de Angelis, M.H.
Experimental Eye Research 73 (6): 867-876. 1 January 2001

FASEB Journal

A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins.
Bork, P., Hofmann, K., Bucher, P., Neuwald, A., Altschul, S.F. and Koonin, E.V.
FASEB Journal 11 (1): 68-76. 1 January 1997

FEBS Letters

Large-scale prediction of drug-target relationships.
Kuhn, M., Campillos, M., Gonzalez, P., Jensen, L.J. and Bork, P.
FEBS Letters 582 (8): 1283-1290. 9 April 2008

Predicting biological networks from genomic data.
Harrington, E.D., Jensen, L.J. and Bork, P.
FEBS Letters 582 (8): 1251-1258. 9 April 2008

Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii.
Suyama, M., Lathe, W.C. and Bork, P.
FEBS Letters 579 (24): 5281-5286. 21 September 2005

Consistency of genome-based methods in measuring Metazoan evolution.
Zdobnov, E.M., von Mering, C., Letunic, I. and Bork, P.
FEBS Letters 579 : 3355-3361. 1 January 2005

Protein domain analysis in the era of complete genomes.
Copley, R.R., Doerks, T., Letunic, I. and Bork, P.
FEBS Letters 513 (1): 129-134. 1 January 2002

Evolution of tuf genes: ancient duplication, differential loss and gene conversion.
Lathe, W.C. and Bork, P.
FEBS Letters 502 (3): 113-116. 1 January 2001

Automated extraction of information in molecular biology.
Andrade, M.A. and Bork, P.
FEBS Letters 476 (1-2): 12-17. 30 June 2000

EST comparison indicates 38% of human mRNAs contain possible alternative splice forms.
Brett, D., Hanke, J., Lehmann, G., Haase, S., Delbrueck, S., Krueger, S., Reich, J. and Bork, P.
FEBS Letters 474 (1): 83-86. 1 January 2000

Microinjected glutathione reductase crystals as indicators of the redox status in living cells.
Keese, M.A., Saffrich, R., Dandekar, T., Becker, K. and Schirmer, R.H.
FEBS Letters 447 (2-3): 135-138. 26 March 1999

Evolution of new protein function: recombinational enhancer Fis originated by horizontal gene transfer from the transcriptional regulator NtrC.
Morett, E. and Bork, P.
FEBS Letters 433 : 108-112. 14 August 1998

Differential genome analysis applied to the species-specific features of Helicobacter pylori.
Huynen, M., Dandekar, T. and Bork, P.
FEBS Letters 426 : 1-5. 1 January 1998

Characterization of a novel protein-binding module - the WW domain.
Sudol, M., Chen, H.I., Bourgeret, C., Einbond, A. and Bork, P.
FEBS Letters 369 (1): 67-71. 1 January 1995

The modular architecture of a new family of growth regulators related to connective tissue growth factor.
Bork, P.
FEBS Letters 327 (2): 125-130. 26 July 1993

A hybrid protein kinase - RNase in an interferon-induced pathway.
Bork, P. and Sander, C.
FEBS Letters 334 : 149-152. 1 January 1993

A large domain common to sperm receptors (Zp2 and Zp3) and TGF-beta type III receptor.
Bork, P. and Sander, C.
FEBS Letters 300 : 237-240. 1 January 1992

The modular architecture of vertebrate collagens.
Bork, P.
FEBS Letters 307 : 49-54. 1 January 1992

Folding & Design

Molecular modeling of amoebapore and nk lysin: a four-alpha-helix bundle motif of cytolytic peptides from distantly related organisms.
Dandekar, T. and Leippe, M.
Folding & Design 2 : 47-52. 1 January 1997

Forschung & Lehre

Humanisierte Maeuse und chimaerische Menschen.
Reich, J.
Forschung & Lehre 12 : 304. 1 January 2005

Frauenarzt

Klonierung des Brustkrebsgens BRCA1. Stellungnahme erarbeitet durch eine adhoc-Gruppe im Rahmen des "Gesamtprogramms zur Krebsbekaempfung".
Chang-Claude, J., Hundsdoerfer, G., Jonat, W., Scherneck, S. and Wienker, T.F.
Frauenarzt 36 (5): 572-574. 1 January 1995

Frontiers in Ecology and Evolution

Pole-to-Pole connections: similarities between arctic and antarctic microbiomes and their vulnerability to environmental change.
Kleinteich, J., Hildebrand, F., Bahram, M., Voigt, A.Y., Wood, S.A., Jungblut, A.D., Kuepper, F.C., Quesada, A., Camacho, A., Pearce, D.A., Convey, P., Vincent, W.F., Zarfl, C., Bork, P. and Dietrich, D.R.
Frontiers in Ecology and Evolution 5 : 137. 10 November 2017

Gastroenterology

Recurrent frameshift neoantigen vaccine elicits protective immunity with reduced tumor burden and improved overall survival in a Lynch syndrome mouse model.
Gebert, J., Gelincik, O., Oezcan-Wahlbrink, M., Marshall, J.D., Hernandez-Sanchez, A., Urban, K., Long, M., Cortes, E., Tosti, E., Katzenmaier, E.M., Song, Y., Elsaadi, A., Deng, N., Vilar, E., Fuchs, V., Nelius, N., Yuan, Y.P., Ahadova, A., Sei, S., Shoemaker, R.H., Umar, A., Wei, L., Liu, S., Bork, P., Edelmann, W., von Knebel Doeberitz, M., Lipkin, S.M. and Kloor, M.
Gastroenterology 161 (4): 288-1302.e13. October 2021

T-cell receptor variable genes and genetic susceptibility to celiac disease: an association and linkage study.
Roschmann, E., Wienker, T.F., Gerok, W. and Volk, B.A.
Gastroenterology 105 : 1790-1796. 1 January 1993

Gene

Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families.
Shah, P.K., Tripathi, L.P., Jensen, L.J., Gahnim, M., Mason, C., Furlong, E.E., Rodrigues, V., White, K.P., Bork, P. and Sowdhamini, R.
Gene 407 (1-2): 199-215. 15 January 2008

Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism.
Pachkov, M., Dandekar, T., Korbel, J., Bork, P. and Schuster, S.
Gene 396 (2): 215-225. 15 July 2007

The black-pearl gene of Drosophila defines a novel conserved protein family and is required for larval growth and survival.
Becker, S., Gehrsitz, A., Bork, P., Buchner, S. and Buchner, E.
Gene 262 : 15-22. 10 January 2001

Cloning of a gene from Bacillus cereus with homology to the mreb gene of Echerichia coli.
Nahara, A., Naterstad, K., Kristensen, T., Lopez, R., Bork, P. and Kolsto, A.B.
Gene 122 : 181-185. 1 January 1992

Gene Expression Patterns

Very-KIND is a novel nervous system specific guanine nucleotide exchange factor for Ras GTPases.
Mees, A., Rock, R., Ciccarelli, F.D., Leberfinger, C.B., Borawski, J.M., Bork, P., Wiese, S., Gessler, M. and Kerkhoff, E.
Gene Expression Patterns 6 : 79-85. 11 August 2005

Genes & Development

Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing.
Eulalio, A., Rehwinkel, J., Stricker, M., Huntzinger, E., Yang, S.F., Doerks, T., Dorner, S., Bork, P., Boutros, M. and Izaurralde, E.
Genes & Development 21 (20): 2558-2570. 15 October 2007

mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes.
Behm-Ansmant, I., Rehwinkel, J., Doerks, T., Stark, A., Bork, P. and Izaurralde, E.
Genes & Development 20 : 1885-1898. 15 July 2006

Genes and Immunity

Murine susceptibility to Chagas' disease maps to chromosomes 5 and 17.
Graefe, S.E., Meyer, B.S., Mueller-Myhsok, B., Rueschendorf, F., Drosten, C., Laue, T., Steeg, C., Nuernberg, P. and Fleischer, B.
Genes and Immunity 4 (5): 321-325. July 2003

GenomXpress

Proteinkomplexe und Netzwerke: Neue Herausforderungen fuer die Proteomik.
von Mering, C. and Bork, P.
GenomXpress 2002 (2): 2-4. June 2002

Genome Biology

GUNC: detection of chimerism and contamination in prokaryotic genomes.
Orakov, A., Fullam, A., Coelho, L.P., Khedkar, S., Szklarczyk, D., Mende, D.R., Schmidt, T.S.B. and Bork, P.
Genome Biology 22 (1): 178. 13 June 2021

Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.
Wirbel, J., Zych, K., Essex, M., Karcher, N., Kartal, E., Salazar, G., Bork, P., Sunagawa, S. and Zeller, G.
Genome Biology 22 (1): 93. 30 March 2021

Spatiotemporal variation of mammalian protein complex stoichiometries.
Ori, A., Iskar, M., Buczak, K., Kastritis, P., Parca, L., Andres-Pons, A., Singer, S., Bork, P. and Beck, M.
Genome Biology 17 (1): 47. 14 March 2016

Temporal and technical variability of human gut metagenomes.
Voigt, A.Y., Costea, P.I., Kultima, J.R., Li, S.S., Zeller, G., Sunagawa, S. and Bork, P.
Genome Biology 16 (1): 73. 8 April 2015

High-resolution transcription atlas of the mitotic cell cycle in budding yeast.
Granovskaia, M.V., Jensen, L.J., Ritchie, M.E., Toedling, J., Ning, Y., Bork, P., Huber, W. and Steinmetz, L.M.
Genome Biology 11 (3): R24. 1 March 2010

Sequence-based feature prediction and annotation of proteins.
Juncker, A.S., Jensen, L.J., Pierleoni, A., Bernsel, A., Tress, M.L., Bork, P., von Heijne, G., Valencia, A., Ouzounis, C.A., Casadio, R. and Brunak, S.
Genome Biology 10 (2): 206. 2 February 2009

Selective maintenance of Drosophila tandemly-arranged duplicated genes during evolution.
Quijano, C., Tomancak, P., Lopez-Marti, J., Suyama, M., Bork, P., Milan, M., Torrents, D. and Manzanares, M.
Genome Biology 9 (12): R176. 16 December 2008

Circular reasoning rather than cyclic expression.
Jensen, L.J., de Lichtenberg, U., Jensen, T.S., Brunak, S. and Bork, P.
Genome Biology 9 (6): 403. 23 June 2008

Prediction of effective genome size in metagenomic samples.
Raes, J., Korbel, J.O., Lercher, M.J., von Mering, C. and Bork, P.
Genome Biology 8 (1): R10. 15 January 2007

NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria.
Andrade, M.A., Ciccarelli, F.D., Perez-Iratxeta, C. and Bork, P.
Genome Biology 3 (9): research0047. 15 August 2002

Identification of attenuation and antitermination regulation in prokaryotes.
Lathe, W.C., Suyama, M. and Bork, P.
Genome Biology 3 : preprint0003.1. 30 April 2002

Genome sequences and great expectations.
Iliopoulos, I., Tsoka, S., Andrade, M.A., Janssen, P., Audit, B., Tramontano, A., Valencia, A., Leroy, C., Sander, C. and Ouzounis, C.A.
Genome Biology 2 (1): Interactions0001.1-Interactions0001.3. 1 January 2001

Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences.
Iyer, L.M., Aravind, L., Bork, P., Hofmann, K., Mushegian, A.R., Zhulin, I.B. and Koonin, E.V.
Genome Biology 2 (12): RESEARCH0051. 2001

Genome Biology and Evolution

Quest for Orthologs entails quest for Tree of Life: in search of the gene stream.
Boeckmann, B., Marcet-Houben, M., Rees, J.A., Forslund, K., Huerta-Cepas, J., Muffato, M., Yilmaz, P., Xenarios, I., Bork, P., Lewis, S.E. and Gabaldon, T.
Genome Biology and Evolution 7 (7): 1988-1999. 1 July 2015

Genome Medicine

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naive Parkinson's disease patients.
Bedarf, J.R., Hildebrand, F., Coelho, L.P., Sunagawa, S., Bahram, M., Goeser, F., Bork, P. and Wuellner, U.
Genome Medicine 9 (1): 39. 28 April 2017

Genome Research

Selective maternal seeding and environment shape the human gut microbiome.
Korpela, K., Costea, P., Coelho, L.P., Kandels-Lewis, S., Willemsen, G., Boomsma, D.I., Segata, N. and Bork, P.
Genome Research 28 (4): 561-568. April 2018

Identification and analysis of evolutionarily cohesive functional modules in protein networks.
Campillos, M., von Mering, C., Jensen, L.J. and Bork, P.
Genome Research 16 : 374-382. 31 January 2006

Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages.
Bourque, G., Zdobnov, E.M., Bork, P., Pevzner, P.A. and Tesler, G.
Genome Research 15 : 98-110. 1 January 2005

Complex genomic rearrangements lead to novel primate gene function.
Ciccarelli, F.D., von Mering, C., Suyama, M., Harrington, E.D., Izaurralde, E. and Bork, P.
Genome Research 15 (3): 343-351. 1 January 2005

A genome-wide survey of human pseudogenes.
Torrents, D., Suyama, M., Zdobnov, E. and Bork, P.
Genome Research 13 : 2559-2567. 1 December 2003

Functionality of system components: conservation of protein function in protein feature space.
Jensen, L.J., Ussery, D.W. and Brunak, S.
Genome Research 13 : 2444-2449. November 2003

Predicting protein cellular localization using a domain projection method.
Mott, R., Schultz, J., Bork, P. and Ponting, C.P.
Genome Research 12 (8): 1168-1174. August 2002

Genomes in flux: The evolution of archaeal and proteobacterial gene content.
Snel, B., Bork, P. and Huynen, M.A.
Genome Research 12 (1): 17-25. 1 January 2002

Systematic identification of novel protein domain families associated with nuclear functions.
Doerks, T., Copley, R.R., Schultz, J., Ponting, C.P. and Bork, P.
Genome Research 12 (1): 47-56. 1 January 2002

Novel protein domains and repeats in Drosophila melanogaster: insights into structure, function, and evolution.
Ponting, C.P., Mott, R., Bork, P. and Copley, R.R.
Genome Research 11 : 1996-2008. 1 December 2001

Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences.
Huynen, M., Snel, B., Lathe, W. and Bork, P.
Genome Research 10 (8): 1204-1210. 1 August 2000

Powers and pitfalls in sequence analysis: The 70% hurdle.
Bork, P.
Genome Research 10 (4): 398-400. 1 April 2000

Genomics

ASTD: The Alternative Splicing and Transcript Diversity database.
Koscielny, G., Texier, V.L., Gopalakrishnan, C., Kumanduri, V., Riethoven, J.J., Nardone, F., Stanley, E., Fallsehr, C., Hofmann, O., Kull, M., Harrington, E., Boue, S., Eyras, E., Plass, M., Lopez, F., Ritchie, W., Moucadel, V., Ara, T., Pospisil, H., Herrmann, A., Reich, J.G., Guigo, R., Bork, P., Doeberitz, M.V., Vilo, J., Hide, W., Apweiler, R., Thanaraj, T.A. and Gautheret, D.
Genomics 93 (3): 213-220. March 2009

The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegia.
Ciccarelli, F.D., Proukakis, C., Patel, H., Cross, H., Azam, S., Patton, M.A., Bork, P. and Crosby, A.H.
Genomics 81 (4): 437-441. April 2003

Molecular characterization of a cDNA encoding functional human CLK4 kinase and localization to chromosome 5q35 [correction of 4q35].
Schultz, J., Jones, T., Bork, P., Sheer, D., Blencke, S., Steyrer, S., Wellbrock, U., Bevec, D., Ullrich, A. and Wallasch, C.
Genomics 71 : 368-370. 1 February 2001

Refinement of the gene locus for autosomal dominant medullary cystic kidney disease type 1 (MCKD1) and construction of a physical and partial transcriptional map of the region.
Fuchshuber, A., Kroiss, S., Karle, S., Berthold, S., Huck, K., Burton, C., Rahman, N., Koptides, M., Deltas, C., Otto, E., Rueschendorf, F., Feest, T. and Hildebrandt, F.
Genomics 72 (3): 278-284. 1 January 2001

Genomic organization of a 225-kb region in Xq28 containing the gene for X-linked myotubular myopathy (MTM1) and a related gene (MTMR1).
Kioschis, P., Wiemann, S., Heiss, N.S., Francis, F., Goetz, C., Poustka, A., Taudien, S., Platzer, M., Wiehe, T., Beckmann, G., Weber, J., Nordsiek, G. and Rosenthal, A.
Genomics 54 : 256-266. 1 December 1998

Genomics and Proteomics: Functional and Computational Aspects

An essay on individual sequence variation in Expressed Sequence Tags(ESTs).
Reich, J., Brett, D. and Hanke, J.
In: Genomics and Proteomics: Functional and Computational Aspects. Springer, 83-94. ISBN 978-0-306-46312-9 2002

Global Biogeochemical Cycles

Community-level responses to iron availability in open ocean plankton ecosystems.
Caputi, L., Carradec, Q., Eveillard, D., Kirilovsky, A., Pelletier, E., Pierella Karlusich, J.J., Rocha Jimenez Vieira, F., Villar, E., Chaffron, S., Malviya, S., Scalco, E., Acinas, S.G., Alberti, A., Aury, J.M., Benoiston, A.S., Bertrand, A., Biard, T., Bittner, L., Boccara, M., Brum, J.R., Brunet, C., Busseni, G., Carratalà, A., Claustre, H., Coelho, L.P., Colin, S., D'Aniello, S., Da Silva, C., Del Core, M., Doré, H., Gasparini, S., Kokoszka, F., Jamet, J.L., Lejeusne, C., Lepoivre, C., Lescot, M., Lima‐Mendez, G., Lombard, F., Lukeš, J., Maillet, N., Madoui, M.A., Martinez, E., Mazzocchi, M.G., Néou, M.B., Paz‐Yepes, J., Poulain, J., Ramondenc, S., Romagnan, J.B., Roux, S., Salvagio Manta, D., Sanges, R., Speich, S., Sprovieri, M., Sunagawa, S., Taillandier, V., Tanaka, A., Tirichine, L., Trottier, C., Uitz, J., Veluchamy, A., Veselá, J., Vincent, F., Yau, S., Kandels‐Lewis, S., Searson, S., Dimier, C., Picheral, M., Bork, P., Boss, E., Vargas, C., Follows, M.J., Grimsley, N., Guidi, L., Hingamp, P., Karsenti, E., Sordino, P., Stemmann, L., Sullivan, M.B., Tagliabue, A., Zingone, A., Garczarek, L., d'Ortenzio, F., Testor, P., Not, F., Ribera d'Alcalà, M., Wincker, P., Bowler, C. and Iudicone, D.
Global Biogeochemical Cycles 33 (3): 391-419. March 2019

Gut

A faecal microbiota signature with high specificity for pancreatic cancer.
Kartal, E., Schmidt, T.S.B., Molina-Montes, E., Rodríguez-Perales, S., Wirbel, J., Maistrenko, O.M., Akanni, W.A., Alashkar Alhamwe, B., Alves, R.J., Carrato, A., Erasmus, H.P., Estudillo, L., Finkelmeier, F., Fullam, A., Glazek, A.M., Gómez-Rubio, P., Hercog, R., Jung, F., Kandels, S., Kersting, S., Langheinrich, M., Márquez, M., Molero, X., Orakov, A., Van Rossum, T., Torres-Ruiz, R., Telzerow, A., Zych, K., Benes, V., Zeller, G., Trebicka, J., Real, F.X., Malats, N. and Bork, P.
Gut 71 (7): 1359-1372. 7 June 2022

Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota.
Tito, R.Y., Chaffron, S., Caenepeel, C., Lima-Mendez, G., Wang, J., Vieira-Silva, S., Falony, G., Hildebrand, F., Darzi, Y., Rymenans, L., Verspecht, C., Bork, P., Vermeire, S., Joossens, M. and Raes, J.
Gut 68 (7): 1180-1189. 7 June 2019

HNO

Phaenotypische Charakterisierung einer DFNA6-Familie mit Tieftonschwerhoerigkeit [Phenotypic characterization of a DFNA6 family with low-frequency hearing loss].
Toth, T., Kupka, S., Nuernberg, P., Thiele, H., Zenner, H.R., Sziklai, I. and Pfister, M.
HNO 52 (2): 132-136. February 2004

Haematologica

The diversity of the microbiome impacts chronic lymphocytic leukemia development in mice and humans.
Faitova, T., Coelho, M., Da Cunha-Bang, C., Ozturk, S., Kartal, E., Bork, P., Seiffert, M. and Niemann, C.U.
Haematologica 109 (10): 3237-3250. October 2024

Human Genetics

Periodic catatonia: confirmation of linkage to chromosome 15 and further evidence for genetic heterogeneity.
Stoeber, G., Seelow, D., Rueschendorf, F., Ekici, A., Beckmann, H. and Reis, A.
Human Genetics 111 (4-5): 323-330. October 2002

Localisation of a gene for Papillon-Lefevre syndrome to chromosome 11q14-q21 by homozygosity mapping.
Laass, M.W., Hennies, H.C., Preis, S., Stevens, H.P., Jung, M., Leigh, I.M., Wienker, T.F. and Reis, A.
Human Genetics 101 : 376-382. 1 January 1997

Localization of the gene for Wieacker Wolff syndrome in the pericentromeric region of the X chromosome.
Kloos, D.U., Jakubiczka, S., Wienker, T.F., Wolff, G. and Wieacker, P.
Human Genetics 100 : 426-430. 1 January 1997

DNA polymorphisms in adhesion molecule genes: a new risk factor for early atherosclerosis.
Wenzel, K., Ernst, M., Rohde, K., Baumann, G. and Speer, A.
Human Genetics 97 (1): 15-20. 1 January 1996

Human Heredity

Concordant association of lipid gene variation with a combined HDL/LDL-cholesterol phenotype in two European populations.
Bauerfeind, A., Knoblauch, H., Costanza, M.C., Luganskaja, T., Toliat, M.R., Nuernberg, P., Luft, F.C., Reich, J.G. and Morabia, A.
Human Heredity 61 (3): 123-131. August 2006

Entropy as a Measure for Linkage Disequilibrium over Multilocus Haplotype Blocks.
Nothnagel, M., Fuerst, R. and Rohde, K.
Human Heredity 54 (4): 186-198. May 2003

Single nucleotide polymorphism haplotypes in the cholesteryl-ester transfer protein (CETP) gene and lipid phenotypes.
Bauerfeind, A., Knoblauch, H., Schuster, H., Luft, F.C. and Reich, J.G.
Human Heredity 54 (4): 166-173. May 2003

Association of genetic traits to estimated haplotypes from SNP genotypes using EM algorithm and Markov chain Monte Carlo techniques.
Rohde, K. and Fuerst, R.
Human Heredity 56 (1-3): 41-47. 1 January 2003

Power and sample size calculations for case-control genetic association tests when errors are present: Application to single nucleotide polymorphisms.
Gordon, D., Finch, S.J., Nothnagel, M. and Ott, J.
Human Heredity 54 (1): 22-33. November 2002

A complete enumeration and classification of two-locus disease models.
Li, W.T. and Reich, J.
Human Heredity 50 (6): 334-349. 1 November 2000

Multi-locus nonparametric linkage analysis of complex trait loci with neural networks.
Lucek, P., Hanke, J., Reich, J., Solla, S.A. and Ott, J.
Human Heredity 48 : 275-284. 1 September 1998

A program using loss-of-constitutional- heterozygosity data to ascertain the location of predisposing genes in cancer families.
Rohde, K., Teare, M.D., Scherneck, S. and Santibanez-Koref, M.F.
Human Heredity 45 : 337-345. 1 January 1995

Human Immunology

Multiple sclerosis associated amino acids of polymorphic regions relevant for the HLA antigen binding are confined to HLA-DR2.
Zipp, F., Windemuth, C., Pankow, H., Dichgans, J., Wienker, T.F., Martin, R. and Mueller, C.
Human Immunology 61 (10): 1021-1030. 1 October 2000

Human Molecular Genetics

Haplotypes and SNPs in 13 lipid-relevant genes explain most of the genetic variance in high-density lipoprotein and low-density lipoprotein cholesterol.
Knoblauch, H., Bauerfeind, A., Toliat, M.R., Becker, C., Luganskaja, T., Guenther, U.P., Rohde, K., Schuster, H., Junghans, C., Luft, F.C., Nuernberg, P. and Reich, J.G.
Human Molecular Genetics 13 (10): 993-1004. 15 May 2004

Genome-wide linkage reveals a locus for human essential (primary) hypertension on chromosome 12p.
Gong, M., Zhang, H.Y., Schulz, H., Lee, Y.A., Sun, K., Bähring, S., Luft, F.C., Nürnberg, P., Reis, A., Rohde, K., Ganten, D., Hui, R.T. and Hübner, N.
Human Molecular Genetics 12 (11): 1273-1277. 1 June 2003

Impact of selection, mutation rate and genetic drift on human genetic variation.
Sunyaev, S., Kondrashov, F.A., Bork, P. and Ramensky, V.
Human Molecular Genetics 12 (24): 3325-3330. 1 January 2003

Common exon duplication in animals and its role in alternative splicing.
Letunic, I., Copley, R.R. and Bork, P.
Human Molecular Genetics 11 : 1561-1567. 15 June 2002

Common haplotypes in five genes influence genetic variance of LDL and HDL cholesterol in the general population.
Knoblauch, H., Bauerfeind, A., Kraehenbuehl, C., Daury, A., Rohde, K., Bejanin, S., Essioux, L., Schuster, H., Luft, F.C. and Reich, J.
Human Molecular Genetics 11 (12): 1477-1485. 1 June 2002

STAT6 as an asthma candidate gene: polymorphism-screening, association and haplotype analysis in a Caucasian sib-pair study.
Duetsch, G., Illig, T., Loesgen, S., Rohde, K., Klopp, N., Herbon, N., Gohlke, H., Altmueller, J. and Wjst, M.
Human Molecular Genetics 11 (6): 613-621. 1 January 2002

Prediction of deleterious human alleles.
Sunyaev, S.R., Ramensky, V., Koch, I., Lathe, W., Kondrashov, A.S. and Bork, P.
Human Molecular Genetics 10 (6): 591-597. 1 January 2001

The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly.
Huynen, M.A., Snel, B., Bork, P. and Gibson, T.J.
Human Molecular Genetics 10 (21): 2463-2468. 1 January 2001

A genome wide search for susceptibility loci in three european malignant hyperthermia pedigrees.
Robinson, R.I., Monnier, N., Wolz, W., Jung, M., Reis, A., Nuernberg, G., Curran, J.L., Monsieurs, K., Stieglitz, P., Heytens, L., Fricker, R., Vanbroeckhoven, C., Deufel, T., Hopkins, P.M., Lunardi, J. and Mueller, C.R.
Human Molecular Genetics 6 (6): 953-961. June 1997

Linkage of the gene for the triple a syndrome to chromosome 12q13 near the type II keratin gene cluster.
Weber, A., Wienker, T.F., Jung, M., Easton, D., Dean, H.J., Heinrichs, C., Reis, A. and Clark, A.J.L.
Human Molecular Genetics 5 (12): 2061-2066. 1 December 1996

E-selectin polymorphism and atherosclerosis: an association study.
Wenzel, K., Felix, S., Kleber, F.X., Brachold, R., Menke, T., Schattke, S., Schulte, K.L., Glaser, C., Rohde, K. and Baumann, G.
Human Molecular Genetics 3 (11): 1935-1937. 1 November 1994

Human Mutation

Fine mapping and single nucleotide polymorphism association results of candidate genes for asthma and related phenotypes.
Immervoll, T., Loesgen, S., Duetsch, G., Gohlke, H., Herbon, N., Klugbauer, S., Dempfle, A., Bickeboeller, H., Becker-Follmann, J., Rueschendorf, F., Saar, K., Reis, A., Wichmann, H.E. and Wjst, M.
Human Mutation 18 : 327-336. 1 January 2001

Haplotyping and estimation of haplotype frequencies for closely linked biallelic multilocus genetic phenotypes including nuclear family information.
Rohde, K. and Fuerst, R.
Human Mutation 17 (4): 289-295. 1 January 2001

Hypertension

Autosomal dominant hypertension and brachydactyly in a turkish kindred resembles essential hypertension.
Schuster, H., Wienker, T.F., Toka, H.R., Bähring, S., Jeschke, E., Toka, O., Busjahn, A., Hempel, A., Tahlhammer, C., Oelkers, W., Kunze, J., Bilginturan, N., Haller, H. and Luft, F.C.
Hypertension 28 : 1085-1092. 1 January 1996

ISME Journal

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity.
Maistrenko, O.M., Mende, D.R., Luetge, M., Hildebrand, F., Schmidt, T.S.B., Li, S.S., Rodrigues, J.F.M., von Mering, C., Pedro Coelho, L., Huerta-Cepas, J., Sunagawa, S. and Bork, P.
ISME Journal 14 (5): 1247-1259. May 2020

In Silico Biology

A database on alternative splice forms on the integrated genetic map service (IGMS).
Pospisil, H., Herrmann, A., Pankow, H. and Reich, J.
In Silico Biology 3 (1-2): 229-234. 16 December 2003

Topological analysis of metabolic networks based on Petri net theory.
Zevedei-Oancea, I. and Schuster, S.
In Silico Biology 3 (3): 323-345. 7 June 2003

Informationstechnik und technische Informatik

Von Genomsequenzen zu Proteinfunktionen.
Bork, P.
Informationstechnik und technische Informatik 5 : 20-26. 1 January 1996

Insectes Sociaux

The gut microbiome is associated with behavioural task in honey bees.
Jones, J.C., Fruciano, C., Marchant, J., Hildebrand, F., Forslund, S., Bork, P., Engel, P. and Hughes, W.O.H.
Insectes Sociaux 65 (3): 419-429. August 2018

International Journal of Cancer

Distinct methylation profiles of glioma subtypes.
Uhlmann, K., Rohde, K., Zeller, C., Szymas, J., Vogel, S., Marczinek, K., Thiel, G., Nuernberg, P. and Laird, P.W.
International Journal of Cancer 106 (1): 52-59. 10 August 2003

Frameshift peptide-derived T-cell epitopes: a source of novel tumor-specific antigens.
Linnebacher, M., Gebert, J., Rudy, W., Woerner, S., Yuan, Y.P. and von Knebel-Doeberitz, M.
International Journal of Cancer 93 (1): 6-11. 1 January 2001

Systematic identification of genes with coding microsatellites mutated in DNA mismatch repair-deficient cancer cells.
Woerner, S.M., Gebert, J., Yuan, Y.P., Sutter, C., Ridder, R., Bork, P. and von Knebel-Doeberitz, M.
International Journal of Cancer 93 (1): 12-19. 1 January 2001

A tumor suppressor locus in familial and sporadic chordoma maps to 1p36.
Miozzo, M., Dalpra, L., Riva, P., Volonte, M., Macciardi, F., Pericotti, S., Tibiletti, M.G., Cerati, M., Rohde, K., Larizza, L. and Conti, A.M.F.
International Journal of Cancer 87 (1): 68-72. 1 July 2000

BRCA1 mutations in German breast-cancer families.
Jandrig, B., Grade, K., Seitz, S., Waindzoch, B., Mueller, M., Bender, E., Nothnagel, A., Rohde, K., Schlag, P.M., Kath, R., Hoeffken, K. and Scherneck, S.
International Journal of Cancer 68 : 188-192. 1 January 1996

International Journal of Molecular Sciences

(Phospho)proteomic profiling of microsatellite unstable CRC cells reveals alterations in nuclear signaling and cholesterol metabolism caused by frameshift mutation of NMD regulator UPF3A.
Michalak, M., Katzenmaier, E.M., Roeckel, N., Woerner, S.M., Fuchs, V., Warnken, U., Yuan, Y.P., Bork, P., Neu-Yilik, G., Kulozik, A., von Knebel Doeberitz, M., Kloor, M., Kopitz, J. and Gebert, J.
International Journal of Molecular Sciences 21 (15): 5234. 23 July 2020

International Journal of Oncology

The tumour-Clostridium phenomenon: 50 years of developmental research.
Schmidt, W., Fabricius, E.M. and Schneeweiss, U.
International Journal of Oncology 29 (6): 1479-1492. 1 December 2006

International Psychogeriatrics

Quality-of-life assessment in the old using the WHOQOL 100: differences between patients with senile dementia and patients with cancer.
Struttmann, T., Fabro, M., Romieu, G., de Roquefeuil, G., Touchon, J., Dandekar, T. and Ritchie, K.
International Psychogeriatrics 11 : 273-279. 1 September 1999

Journal fuer Reproduktionsmedizin und Endokrinologie

Neue Wege der Stammzellforschung: Reprogrammierung von differenzierten Koerperzellen [New methods in stem cell research: reprogramming of differentiated body cells].
Beier, H.M., Fehse, B., Friedrich, B., Goetz, M., Hansmann, I., Hucho, F., Koechy, K., Mueller-Roeber, B., Rheinberger, H.J., Reich, J., Ropers, H.H., Schoeler, H.R., Schoene-Seifert, B., Sperling, K., Tanner, K., Taupitz, J. and Wobus, A.M.
Journal fuer Reproduktionsmedizin und Endokrinologie 7 (2): 68-77. 2010

Journal of Allergy and Clinical Immunology

Lack of association of the G protein-coupled receptor for asthma susceptibility gene with atopic dermatitis.
Soederhaell, C., Marenholz, I., Nickel, R., Grueber, C., Kehrt, R., Rohde, K., Griffioen, R.W., Meglio, P., Tarani, L., Gustafsson, D., Hoffmann, U., Gerstner, B., Mueller, S., Wahn, U. and Lee, Y.A.
Journal of Allergy and Clinical Immunology 116 (1): 220-221. 1 January 2005

Journal of Applied Crystallography

Probabilistic evaluation of similarity between pairs of three-dimensional protein structures utilizing temperature factors.
Carugo, O. and Eisenhaber, F.
Journal of Applied Crystallography 30 (5/1): 547-549. 1 October 1997

Journal of Bacteriology

Discovering functional novelty in metagenomes: examples from light-mediated processes.
Singh, A.H., Doerks, T., Letunic, I., Raes, J. and Bork, P.
Journal of Bacteriology 191 (1): 32-41. January 2009

Journal of Biological Chemistry

The phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus is a unique glycolytic enzyme that belongs to the cupin superfamily.
Verhees, C.H., Huynen, M.A., Ward, D.E., Schiltz, E., de Vos, W.M. and van der Oost, J.
Journal of Biological Chemistry 276 (44): 40926-40932. 2 November 2001

DNA recognition, strand selectivity, and cleavage mode during integrase family site-specific recombination.
Tribble, G., Ahn, Y.T., Lee, J., Dandekar, T. and Jayaram, M.
Journal of Biological Chemistry 275 (29): 22255-22267. 21 July 2000

RNA ligands selected by cleavage stimulation factor (CstF) contain distinct sequence motifs that function as downstream elements in 3' end processing of pre-mRNA.
Beyer, K., Dandekar, T. and Keller, W.
Journal of Biological Chemistry 272 : 26769-26779. 1 January 1997

Identification of residues within the shc phosphotyrosine binding phosphotyrosine interaction domain crucial for phosphopeptide interaction.
Yajnik, V., Blaikie, P., Bork, P. and Margolis, B.
Journal of Biological Chemistry 271 (4): 1813-1816. 1 January 1996

Characterization of the mammalian YAP (Yes-associated protein) gene and its role in defining a novel module - the WW domain.
Sudol, M., Bork, P., Einbond, A., Kastury, K., Druck, T., Negrini, M., Huebner, K. and Lehman, D.
Journal of Biological Chemistry 270 : 14733-14741. 1 January 1995

Journal of Biological Systems

Bifurcation analysis of calcium oscillations: time-scale separation, canards, and frequency lowering.
Schuster, S. and Marhl, M.
Journal of Biological Systems 9 (4): 291-314. 1 January 2001

Journal of Biotechnology

Sequence-based factors influencing the expression of heterologous genes in the yeast Pichia pastoris: A comparative view on 79 human genes.
Boettner, M., Steffens, C., von Mering, C., Bork, P., Stahl, U. and Lang, C.
Journal of Biotechnology 130 (1): 1-10. 31 May 2007

Journal of Cancer Research and Clinical Oncology

BRCA1 mutations and phenotype.
Grade, K., Hoeffken, K., Kath, R., Nothnagel, A., Bender, E. and Scherneck, S.
Journal of Cancer Research and Clinical Oncology 123 : 69-70. 1 January 1997

Journal of Cell Biology

The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR.
Scharaw, S., Iskar, M., Ori, A., Boncompain, G., Laketa, V., Poser, I., Lundberg, E., Perez, F., Beck, M., Bork, P. and Pepperkok, R.
Journal of Cell Biology 215 (4): 543-558. 21 November 2016

Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system.
Taxis, C., Keller, P., Kavagiou, Z., Jensen, L.J., Colombelli, J., Bork, P., Stelzer, E.H. and Knop, M.
Journal of Cell Biology 171 (4): 627-640. 21 November 2005

A novel class of RanGTP binding proteins.
Goerlich, D., Dabrowski, M., Bischoff, F.R., Kutay, U., Bork, P., Hartmann, E., Prehn, S. and Izaurralde, E.
Journal of Cell Biology 138 (1): 65-80. 14 July 1997

Journal of Cellular Biochemistry

Characterization of naturally occurring myosin heavy chain antisense mRNA in rat heart.
Luther, H.P., Haase, H., Hohaus, A., Beckmann, G., Reich, J. and Morano, I.
Journal of Cellular Biochemistry 70 : 110-120. 1 January 1998

Mammalian protein homologous to VAT-1 of torpedo californica: isolation from Ehrlich Ascites Tumor cells, biochemical characterization and organization of its gene.
Hayess, K., Kraft, R., Sachsinger, J., Janke, J., Jandrig, B., Beckmann, G., Rohde, K. and Benndorf, R.
Journal of Cellular Biochemistry 69 : 304-315. 1 January 1998

Journal of Chemical Information and Computer Sciences

A versatile structural domain analysis server using profile weight matrices.
Schmidt, S., Bork, P. and Dandekar, T.
Journal of Chemical Information and Computer Sciences 42 (2): 405-407. March 2002

Journal of Clinical Endocrinology and Metabolism

Isolated familial somatotropinomas: Establishment of linkage to chromosome 11q13.1-11q13.3 and evidence for a potential second locus at chromosome 2p16-12.
Gadelha, M.R., Une, K.N., Rohde, K., Vaisman, M., Kineman, R.D. and Frohman, L.A.
Journal of Clinical Endocrinology and Metabolism 85 (2): 707-714. 1 February 2000

Journal of Hepatology

Review: Opportunities and barriers for omics-based biomarker discovery in steatotic liver diseases.
Thiele, M., Villesen, I.., Niu, L., Johansen, S., Sulek, K., Nishijima, S., Van Espen, L., Keller, M., Israelsen, M., Suvitaival, T., de Zawadzki, A., Juel, H.B., Brol, M.J., Stinson, S.E., Huang, Y., Alvarez Silva, M.C., Kuhn, M., Anastasiadou, E., Leeming, D.J., Karsdal, M., Matthijnssens, J., Arumugam, M., Dalgaard, L.T., Legido-Quigley, C., Mann, M., Trebicka, J., Bork, P., Jensen, L.J., Hansen, T. and Krag, A.
Journal of Hepatology 81 (2): 345-359. August 2024

Journal of Hypertension

Treasure your exceptions: what we can learn from autosomal-dominant inherited forms of hypertension.
Luft, F.C., Schuster, H., Bilginturan, N. and Wienker, T.F.
Journal of Hypertension 13 (12): 1535-1538. 1 January 1995

Journal of Immunological Methods

Use of a modified binding model for the investigation of affinity dependence on antibody concentration in immunoassay systems.
Strohner, P., Sarrach, D. and Reich, J.
Journal of Immunological Methods 203 : 113-122. 1 January 1997

Journal of Immunology

Comparison of CD45 extracellular domain sequences from divergent vertebate species suggests the conservation of three fibronectin type III domains.
Okumura, M., Matthew, R.J., Robb, B., Litmann, G.W., Bork, P. and Thomas, M.L.
Journal of Immunology 157 : 1569-1575. 1 January 1996

Journal of Liposome Research

Glycoprotein mediated cell binding of lectin coated liposomes.
Schaefer, H., Stahn, R., Schreiber, J. and Schmidt, W.
Journal of Liposome Research 6 : 479-496. 1 January 1996

Journal of Mathematical Biology

Reaction routes in biochemical reaction systems: Algebraic properties, validated calculation procedure and example from nucleotide metabolism.
Schuster, S., Hilgetag, C., Woods, J.H. and Fell, D.A.
Journal of Mathematical Biology 45 (2): 153-181. August 2002

Journal of Medical Genetics

Acropectorovertebral dysgenesis (F syndrome) maps to chromosome 2q36.
Thiele, H., McCann, C., vant Padje, S., Schwabe, G.C., Hennies, H.C., Camera, G., Opitz, J., Laxova, R., Mundlos, S. and Nuernberg, P.
Journal of Medical Genetics 41 (3): 213-218. March 2004

Localisation of a gene for an autosomal recessive syndrome of macrocephaly, multiple epiphyseal dysplasia, and distinctive facies to chromosome 15q26.
Bayoumi, R., Saar, K., Lee, Y.A., Nuernberg, G., Reis, A., Nur-E-Kamal, M. and Al Gazali, L.I.
Journal of Medical Genetics 38 (6): 369-373. 1 January 2001

The use of loss of constitutional heterozygosity data to ascertain the location of predisposing genes in cancer families.
Teare, M.D., Rohde, K. and Santibanez-Koref, M.F.
Journal of Medical Genetics 31 : 448-452. 1 January 1994

On the genetics of mandibular prognathism: analysis of large European noble families.
Wolff, G., Wienker, T.F. and Sander, H.
Journal of Medical Genetics 30 : 112-116. 1 January 1993

Journal of Molecular Biology

Protein feature based identification of cell cycle regulated proteins in yeast.
de Lichtenberg, U., Jensen, T.S., Jensen, L.J. and Brunak, S.
Journal of Molecular Biology 329 : 663-674. 13 June 2003

Comparison of ARM and HEAT protein repeats.
Andrade, M.A., Petosa, C., O'Donoghue, S.I., Mueller, C.W. and Bork, P.
Journal of Molecular Biology 309 (1): 1-18. 1 January 2001

Homology among (betaalpha)8barrels: implications for the evolution of metabolic pathways.
Copley, R.R. and Bork, P.
Journal of Molecular Biology 303 : 627-641. 3 November 2000

Homology-based method for identification of protein repeats using statistical significance estimates.
Andrade, M.A., Ponting, C.P., Gibson, T.J. and Bork, P.
Journal of Molecular Biology 298 (3): 521-537. 5 May 2000

Prediction of potential GPI-modification sites in proprotein sequences.
Eisenhaber, B., Bork, P. and Eisenhaber, F.
Journal of Molecular Biology 292 : 741-758. 24 September 1999

Domain organization of Mac-2 binding protein and its oligomerization to linear and ring-like structures.
Mueller, S.A., Sasaki, T., Bork, P., Wolpensinger, B., Schulthess, T., Timpl, R., Engel, A. and Engel, J.
Journal of Molecular Biology 291 : 801-813. 27 August 1999

Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer.
Ponting, C.P., Aravind, L., Schultz, J., Bork, P. and Koonin, E.V.
Journal of Molecular Biology 289 : 729-745. 18 June 1999

Predicting function: From genes to genomes and back.
Bork, P., Dandekar, T., Diaz-Lazcoz, Y., Eisenhaber, F., Huynen, M. and Yuan, Y.P.
Journal of Molecular Biology 283 : 707-725. 6 November 1998

Homology-based fold predictions for Mycoplasma genitalium proteins.
Huynen, M., Doerks, T., Eisenhaber, F., Orengo, C., Sunyaev, S.R., Yuan, Y.P. and Bork, P.
Journal of Molecular Biology 280 : 323-326. 1 January 1998

Merging extracellular domains: Fold prediction for laminin G- like and amino-terminal thrombospondin-like modules based on homology to pentraxins.
Beckmann, G., Hanke, J., Bork, P. and Reich, J.
Journal of Molecular Biology 275 : 725-730. 1 January 1998

Assessing the reliability of RNA folding using statistical mechanics.
Huynen, M.A., Guttel, R. and Konings, D.A.M.
Journal of Molecular Biology 267 : 1104-1112. 1 January 1997

Drosophila kelch motif is derived from a common enzyme fold.
Bork, P. and Doolittle, R.F.
Journal of Molecular Biology 236 : 1277-1282. 1 January 1994

The immunoglobulin fold - Structural classification, sequence patterns and common core.
Bork, P., Holm, L. and Sander, C.
Journal of Molecular Biology 242 : 309-320. 1 January 1994

Prokaryotic members of a new family of putative helicases with similarity to transcripton activator SNF2.
Kolsto, A.B., Bork, P., Kvaloy, K., Lindback, T., Gronstadt, A., Kristensen, T. and Sander, C.
Journal of Molecular Biology 230 : 684-688. 1 January 1993

Rotamers - to be or not to be? - An analysis of amino acid side-chains conformations in globular proteins.
Schrauber, H., Eisenhaber, F. and Argos, P.
Journal of Molecular Biology 230 : 592-612. 1 January 1993

The CUB domain: A widespread module in developmentally regulated proteins.
Bork, P. and Beckmann, G.
Journal of Molecular Biology 231 : 539-545. 1 January 1993

Journal of Molecular Evolution

Functional classes in the three domains of life.
Andrade, M.A., Ouzounis, C., Sander, C., Tamames, J. and Valencia, A.
Journal of Molecular Evolution 49 (5): 551-557. November 1999

Phylogeny reconstruction for protein sequences based on amino acid properties.
Schmidt, W.
Journal of Molecular Evolution 41 (4): 522-530. 1 January 1995

Tracing the spread of fibronectin type III domains in bacterial glycohydrolases.
Little, E., Bork, P. and Doolittle, R.F.
Journal of Molecular Evolution 39 : 631-643. 1 January 1994

Journal of Molecular Medicine

Association of the HLA region with multiple sclerosis as confirmed by a genome screen using >10,000 SNPs on DNA chips.
Goedde, R., Rohde, K., Becker, C., Toliat, M., Entz, P., Suk, A., Mueller, N., Sindern, E., Haupts, M., Schimrigk, S., Nuernberg, P. and Epplen, J.
Journal of Molecular Medicine 83 (6): 486-494. 1 January 2005

A pathway model of lipid metabolism to predict the effect of genetic variability on lipid levels.
Knoblauch, H., Schuster, H., Luft, J.C. and Reich, J.
Journal of Molecular Medicine 78 : 507-515. 1 January 2000

Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes.
Sunyaev, S.R., Hanke, J., Aydin, A., Wirkner, U., Zastrow, I., Reich, J. and Bork, P.
Journal of Molecular Medicine 77 (11): 754-760. November 1999

Characterization of targeting domains by sequence analysis: glycogen-binding domains in protein phosphatases.
Bork, P., Dandekar, T., Eisenhaber, F. and Huynen, M.
Journal of Molecular Medicine 76 : 77-79. 1 February 1998

Bioinformatics and molecular medicine: introduction and call for papers.
Bork, P.
Journal of Molecular Medicine 75 : 3-4. 1 January 1997

Relationship of polymorphisms in the renin angiotensin system and in e selectin of patients with early severe coronary heart disease.
Wenzel, K., Blackburn, A., Ernst, M., Affeldt, M., Hanke, R., Baumann, G., Felix, S.B., Kleber, F.X., Rohde, K., Glaser, C. and Speer, A.
Journal of Molecular Medicine 75 : 57-61. 1 January 1997

The breast cancer gene product TSG101: a regulator of ubiquitination?
Ponting, C.P., Cai, Y.D. and Bork, P.
Journal of Molecular Medicine 75 : 467-469. 1 January 1997

Role of T cell receptor delta gene in susceptibility to celiac disease.
Roschmann, E., Wienker, T.F. and Volk, B.A.
Journal of Molecular Medicine 74 (2): 93-98. 1 January 1996

Journal of Molecular Modeling

Refined genetic algorithm simulations to model proteins.
Koenig, R. and Dandekar, T.
Journal of Molecular Modeling 5 (12): 317-324. December 1999

Analyzing the interplay between secondary and tertiary structure predictions in folding simulations with a genetic algorithm.
Dandekar, T. and Du, F.
Journal of Molecular Modeling 5 (4): 78-89. 1 April 1999

Improving protein structure prediction by new strategies: experimental insights and the genetic algorithm.
Dandekar, T.
Journal of Molecular Modeling 3 : 312-314. 1 January 1997

Journal of Molecular Recognition

Fine mapping of the antigen-antibody interaction of scFv215, a recombinant antibody inhibiting RNA polymerase II from Drosophila melanogaster.
Liu, Z., Song, D., Kramer, A., Martin, A.C., Dandekar, T., Schneider-Mergener, J., Bautz, E.K. and Duebel, S.
Journal of Molecular Recognition 12 (2): 103-111. 24 March 1999

Journal of Protein Chemistry

Artificial neural network method for predicting the specificity of GalNAc-transferase.
Cai, Y.D., Yu, H. and Chou, K.C.
Journal of Protein Chemistry 16 : 689-700. 1 January 1997

On the classification and evolution of protein modules.
Hegyi, H. and Bork, P.
Journal of Protein Chemistry 16 : 545-551. 1 January 1997

Journal of Steroid Biochemistry and Molecular Biology

3-aminobenzamide protects the mouse thymocytes in vitro from dexamethasone-mediated apoptotic cell death and cytolysis without changing DNA strand breakage.
Hoshino, J., Beckmann, G. and Kroeger, H.
Journal of Steroid Biochemistry and Molecular Biology 44 : 113-119. 1 January 1993

Journal of Structural Biology

Protein repeats: Structures, functions, and evolution.
Andrade, M.A., Perez-Iratxeta, C. and Ponting, C.P.
Journal of Structural Biology 134 (2-3): 117-131. 1 January 2001

Journal of Theoretical Biology

Under what conditions signal transduction pathways are highly flexible in response to external forcing? A case study on calcium oscillations.
Marhl, M. and Schuster, S.
Journal of Theoretical Biology 224 (4): 491-500. 21 October 2003

Journal of Trace Elements in Medicine and Biology

Iron absorption and distribution in TNF(DeltaARE/+) mice, a model of chronic inflammation.
Schuemann, K., Herbach, N., Kerling, C., Seifert, M., Fillebeen, C., Prysch, I., Reich, J., Weiss, G. and Pantopoulos, K.
Journal of Trace Elements in Medicine and Biology 24 (1): 58-66. January 2010

Journal of the National Cancer Institute

A molecular genetic and statistical approach for the diagnosis of dual-site cancers.
Brinkmann, D., Ryan, A., Ayhan, A., McCluggage, W.G., Feakins, R., Santibanez-Koref, M.F., Mein, C.A., Gayther, S.A. and Jacobs, I.J.
Journal of the National Cancer Institute 96 (19): 1441-1446. 1 January 2004

Mathematical Biosciences

Phylogenetic analysis of nucleotide sequences: an algebraic approach.
Schmidt, W.
Mathematical Biosciences 154 : 39-55. 1 December 1998

Matrix Biology

Exon shuffling and other ways of module exchange: comment.
Bork, P.
Matrix Biology 15 : 311-312. 1 January 1996

Metabolic Engineering

Metabolic anchor reactions for robust biorefining.
Jouhten, P., Huerta-Cepas, J., Bork, P. and Patil, K.R.
Metabolic Engineering 40 : 1-4. March 2017

Use and limitations of modular metabolic control analysis in medicine and biotechnology.
Schuster, S.
Metabolic Engineering 1 : 232-242. 1 January 1999

Methods in Enzymology

Applying motif and profile searches.
Bork, P. and Gibson, T.
Methods in Enzymology 266 : 162-184. 1 January 1996

Methods in Molecular Biology

Bioinformatics analysis of functional associations of PTMs.
Minguez, P. and Bork, P.
Methods in Molecular Biology 1558 (1558): 303-320. 2 February 2017

Nanoelectrospray tandem mass spectrometry and sequence similarity searching for identification of proteins from organisms with unknown genomes.
Shevchenko, A., Sunyaev, S., Liska, A., Bork, P. and Shevchenko, A.
Methods in Molecular Biology 211 : 221-234. 1 January 2003

Microbial Cell Factories

Structural genomics of human proteins - target selection and generation of a public catalog of expression clones.
Buessow, K., Scheich, C., Sievert, V., Harttig, U., Schultz, J., Simon, B., Bork, P., Lehrach, H. and Heinemann, U.
Microbial Cell Factories 4 : 21. 5 July 2005

Microbiome

Enterotypes of the human gut mycobiome.
Lai, S., Yan, Y., Pu, Y., Lin, S., Qiu, J.G., Jiang, B.H., Keller, M.I., Wang, M., Bork, P., Chen, W.H., Zheng, Y. and Zhao, X.M.
Microbiome 11 (1): 179. 11 August 2023

Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses.
Kunath, B.J., Hickl, O., Queirós, P., Martin-Gallausiaux, C., Lebrun, L.A., Halder, R., Laczny, C.C., Schmidt, T.S.B., Hayward, M.R., Becher, D., Heintz-Buschart, A., de Beaufort, C., Bork, P., May, P. and Wilmes, P.
Microbiome 10 (1): 243. 28 December 2022

Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments.
Ruscheweyh, H.J., Milanese, A., Paoli, L., Karcher, N., Clayssen, Q., Keller, M.I., Wirbel, J., Bork, P., Mende, D.R., Zeller, G. and Sunagawa, S.
Microbiome 10 (1): 212. 5 December 2022

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language.
Coelho, L.P., Alves, R., Monteiro, P., Huerta-Cepas, J., Freitas, A.T. and Bork, P.
Microbiome 7 (1): 84. 3 June 2019

Similarity of the dog and human gut microbiomes in gene content and response to diet.
Coelho, L.P., Kultima, J.R., Costea, P.I., Fournier, C., Pan, Y., Czarnecki-Maulden, G., Hayward, M.R., Forslund, S.K., Schmidt, T.S.B., Descombes, P., Jackson, J.R., Li, Q. and Bork, P.
Microbiome 6 (1): 72. 19 April 2018

LotuS: an efficient and user-friendly OTU processing pipeline.
Hildebrand, F., Tito, R.Y., Voigt, A.Y., Bork, P. and Raes, J.
Microbiome 2 (1): 30. 30 September 2014

Microorganisms

Sample preservation and storage significantly impact taxonomic and functional profiles in metaproteomics studies of the human gut microbiome.
Hickl, O., Heintz-Buschart, A., Trautwein-Schult, A., Hercog, R., Bork, P., Wilmes, P. and Becher, D.
Microorganisms 7 (9): 367. 19 September 2019

Modern Genome Annotation: The Biosapiens Network

Modern genome annotation: The BioSapiens network.
Yeats, C., Orengo, C., Veuthey, A.L., Boeckmann, B., Jensen, L.J., Valencia, A., Rausell, A. and Bork, P.
In: Modern Genome Annotation. Springer, 213-238. ISBN 978-3-211-75122-0 2008

Protein-protein interactions: Analysis and prediction.
Frishman, D., Albrecht, M., Blankenburg, H., Bork, P., Harrington, E.D., Hermjakob, H., Jensen, L.J., Juan, D.A., Lengauer, T., Pagel, P., Schachter, V. and Valencia, A.
In: Modern Genome Annotation. Springer, 353-410. ISBN 978-3-211-75122-0 2008

Molecular Biology Reports

Structure of transfection-active histone H1/DNA complexes.
Lucius, H., Haberland, A., Zaitsev, S., Dalluege, R., Schneider, M. and Boettger, M.
Molecular Biology Reports 28 (3): 157-165. September 2002

Calculating as many fluxes as possible in underdetermined metabolic networks.
Klamt, S. and Schuster, S.
Molecular Biology Reports 29 (1-2): 243-248. 1 January 2002

Molecular Biology and Evolution

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
Huerta-Cepas, J., Forslund, K., Coelho, L.P., Szklarczyk, D., Jensen, L.J., von Mering, C. and Bork, P.
Molecular Biology and Evolution 34 (8): 2115-2122. 1 August 2017

ETE 3: reconstruction, analysis and visualization of phylogenomic data.
Huerta-Cepas, J., Serra, F. and Bork, P.
Molecular Biology and Evolution 33 (6): 1635-1638. June 2016

A mitochondrial ancestry of the hydrogenosomes of Nyctotherus ovalis.
van Hoek, A.H.A.M., Akhmanova, A.S., Huynen, M.A. and Hackstein, J.H.P.
Molecular Biology and Evolution 17 (1): 202-206. 1 January 2000

The frequency distribution of gene family sizes in complete genomes.
Huynen, M.A. and van Nimwegen, E.
Molecular Biology and Evolution 15 (5): 583-589. 1 May 1998

Molecular Carcinogenesis

Identical variant TSG101 transcripts in soft tissue sarcomas and various non-neoplastic tissues.
Willeke, F., Ridder, R., Bork, P., Klaes, R., Mechtersheimer, G., Schwarzbach, M., Zimmer, D., Kloor, M., Lehnert, T., Herfarth, C. and Knebel-Doeberitz, M.
Molecular Carcinogenesis 23 : 195-200. 1 December 1998

Molecular Microbiology

Isolation and molecular characterization of a surface-bound proteinase of Entamoeba histolytica.
Jacobs, T., Bruchhaus, I., Dandekar, T., Tannich, E. and Leippe, M.
Molecular Microbiology 27 (2): 269-276. January 1998

Exploring the Mycoplasma capricolum genome: a small bacterium reveals its physiology.
Bork, P., Ouzounis, C., Casari, G., Schneider, R., Sander, C., Dolan, M., Gilbert, W. and Gillevet, P.M.
Molecular Microbiology 16 : 955-967. 1 January 1995

Molecular Psychiatry

A second large family with catatonic schizophrenia supports the region distally of CHRNA7 on chromosome 15q14-15.
Meyer, J., Rueschendorf, F. and Lesch, K.P.
Molecular Psychiatry 8 : 259-260. 1 March 2003

Exclusion of the neuronal nicotinic acetylcholine receptor alpha 7 subunit gene as a candidate for catatonic schizophrenia in a large family supporting the chromosome 15q13-22 locus.
Meyer, J., Ortega, G., Schraut, K., Nuernberg, G., Rueschendorf, F., Saar, K., Moessner, R., Wienker, T.F., Reis, A., Stoeber, G. and Lesch, K.P.
Molecular Psychiatry 7 : 220-223. 1 January 2002

Molecular Systems Biology

Consistency across multi-omics layers in a drug-perturbed gut microbial community.
Wuyts, S., Alves, R., Zimmermann-Kogadeeva, M., Nishijima, S., Blasche, S., Driessen, M., Geyer, P.E, Hercog, R., Kartal, E., Maier, L., Müller, J.B., Garcia Santamarina, S., Schmidt, T.S.B., Sevin, D.C., Telzerow, A., Treit, P.V., Wenzel, T., Typas, A., Patil, K.R, Mann, M., Kuhn, M. and Bork, P.
Molecular Systems Biology 19 (9): e11525. 12 September 2023

Quantifying compartment-associated variations of protein abundance in proteomics data.
Parca, L., Beck, M., Bork, P. and Ori, A.
Molecular Systems Biology 14 (7): e8131. 2 July 2018

Subspecies in the global human gut microbiome.
Costea, P.I., Coelho, L.P., Sunagawa, S., Munch, R., Huerta-Cepas, J., Forslund, K., Hildebrand, F., Kushugulova, A., Zeller, G. and Bork, P.
Molecular Systems Biology 13 (12): 960. 14 December 2017

Computational eco-systems biology in Tara Oceans: translating data into knowledge.
Sunagawa, S., Karsenti, E., Bowler, C. and Bork, P.
Molecular Systems Biology 11 (5): 809. 21 May 2015

Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium.
Lluch-Senar, M., Delgado, J., Chen, W.-H., Llorens-Rico, V., O'Reilly, F.J., Wodke, J.A.H., Unal, E.B., Yus, E., Martinez, S., Nichols, R.J., Ferrar, T., Vivancos, A., Schmeisky, A., Stuelke, J., van Noort, V., Gavin, A.-C., Bork, P. and Serrano, L.
Molecular Systems Biology 11 (1): 780. 21 January 2015

Potential of fecal microbiota for early-stage detection of colorectal cancer.
Zeller, G., Tap, J., Voigt, A.Y., Sunagawa, S., Kultima, J.R., Costea, P.I., Amiot, A., Boehm, J., Brunetti, F., Habermann, N., Hercog, R., Koch, M., Luciani, A., Mende, D.R., Schneider, M.A., Schrotz-King, P., Tournigand, C., Tran Van Nhieu, J., Yamada, T., Zimmermann, J., Benes, V., Kloor, M., Ulrich, C.M., von Knebel Doeberitz, M., Sobhani, I. and Bork, P.
Molecular Systems Biology 10 (11): 766. 28 November 2014

Evolution and functional cross-talk of protein post-translational modifications.
Beltrao, P., Bork, P., Krogan, N.J. and van Noort, V.
Molecular Systems Biology 9 : 714. 22 December 2013

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding.
Iskar, M., Zeller, G., Blattmann, P., Campillos, M., Kuhn, M., Kaminska, K.H., Runz, H., Gavin, A.C., Pepperkok, R., van Noort, V. and Bork, P.
Molecular Systems Biology 9 : 662. 2013

Systematic identification of proteins that elicit drug side effects.
Kuhn, M., Al Banchaabouchi, M., Campillos, M., Jensen, L.J., Gross, C., Gavin, A.C. and Bork, P.
Molecular Systems Biology 9 : 663. 2013

Deciphering a global network of functionally associated post-translational modifications.
Minguez, P., Parca, L., Diella, F., Mende, D.R., Kumar, R., Helmer-Citterich, M., Gavin, A.C., van Noort, V. and Bork, P.
Molecular Systems Biology 8 : 599. 17 July 2012

Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours.
Yamada, T., Waller, A.S., Raes, J., Zelezniak, A., Perchat, N., Perret, A., Salanoubat, M., Patil, K.R., Weissenbach, J. and Bork, P.
Molecular Systems Biology 8 : 581. 8 May 2012

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data.
Raes, J., Letunic, I., Yamada, T., Jensen, L.J. and Bork, P.
Molecular Systems Biology 7 : 473. 15 March 2011

A side effect resource to capture phenotypic effects of drugs.
Kuhn, M., Campillos, M., Letunic, I., Jensen, L.J. and Bork, P.
Molecular Systems Biology 6 : 343. 2010

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat.
Kunin, V., Raes, J., Harris, J.K., Spear, J.R., Walker, J.J., Ivanova, N., von Mering, C., Bebout, B.M., Pace, N.R., Bork, P. and Hugenholtz, P.
Molecular Systems Biology 4 : 198. 2008

Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis.
Hooper, S.D., Boue, S., Krause, R., Jensen, L.J., Mason, C.E., Ghanim, M., White, K.P., Furlong, E.E. and Bork, P.
Molecular Systems Biology 3 : 72. January 2007

Is there biological research beyond Systems Biology? A comparative analysis of terms.
Bork, P.
Molecular Systems Biology 1 : 2005.0012 (Article Number). 1 January 2005

Molecular and Cellular Biology

RanBP2/Nup358 provides a major binding site for NXF1-p15 dimers at the nuclear pore complex and functions in nuclear mRNA export.
Forler, D., Rabut, G., Ciccarelli, F.D., Herold, A., Koecher, T., Niggeweg, R., Bork, P., Ellenberg, J. and Izaurralde, E.
Molecular and Cellular Biology 24 : 1155-1167. 1 February 2004

TAP (NXF1) belongs to a multigene family of putative RNA export factors with a conserved modular architecture.
Herold, A., Suyama, M., Rodrigues, J.P., Braun, I.C., Kutay, U., Carmo-Fonseca, M., Bork, P. and Izaurralde, E.
Molecular and Cellular Biology 20 : 8996-9008. 1 December 2000

Processing of the precursors to small nucleolar RNAs and rRNAs requires common components.
Petfalski, E., Dandekar, T., Henry, Y. and Tollervey, D.
Molecular and Cellular Biology 18 (3): 1181-1189. March 1998

Monatshefte fuer Veterinaermedizin

Vergleichende Untersuchungen des Klostridien-Tumor-Testes an Hunden und Pferden.
Fabricius, E.M., Dietz, O., Schneeweiss, U., Schmidt, W., Wildner, G.P., Baumann, G., Benedix, A. and Weisbrich, C.
Monatshefte fuer Veterinaermedizin 49 : 151-157. 1 January 1994

Mutagenesis

Mechanisms of carcinogenicity/chemotherapy by O(6)-methylguanine.
Margison, G.P., Santibanez-Koref, M.F. and Povey, A.C.
Mutagenesis 17 (6): 483-487. November 2002

Nature

Functional and evolutionary significance of unknown genes from uncultivated taxa.
Rodríguez Del Río, Á., Giner-Lamia, J., Cantalapiedra, C.P., Botas, J., Deng, Z., Hernández-Plaza, A., Munar-Palmer, M., Santamaría-Hernando, S., Rodríguez-Herva, J.J., Ruscheweyh, H.J., Paoli, L., Schmidt, T.S.B., Sunagawa, S., Bork, P., López-Solanilla, E., Coelho, L.P. and Huerta-Cepas, J.
Nature 626 (7998): 377-384. 8 February 2024

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies.
Kennedy, K.M., de Goffau, M.C., Perez-Muñoz, M.E., Arrieta, M.C., Bäckhed, F., Bork, P., Braun, T., Bushman, F.D., Dore, J., de Vos, W.M., Earl, A.M., Eisen, J.A., Elovitz, M.A., Ganal-Vonarburg, S.C., Gänzle, M.G., Garrett, W.S., Hall, L.J., Hornef, M.W., Huttenhower, C., Konnikova, L., Lebeer, S., Macpherson, A.J., Massey, R.C., McHardy, A.C., Koren, O., Lawley, T.D., Ley, R.E., O'Mahony, L., O'Toole, P.W., Pamer, E.G., Parkhill, J., Raes, J., Rattei, T., Salonen, A., Segal, E., Segata, N., Shanahan, F., Sloboda, D.M., Smith, G.C.S., Sokol, H., Spector, T.D., Surette, M.G., Tannock, G.W., Walker, A.W., Yassour, M. and Walter, J.
Nature 613 (7945): 639-649. 26 January 2023

Biosynthetic potential of the global ocean microbiome.
Paoli, L., Ruscheweyh, H.J., Forneris, C.C., Hubrich, F., Kautsar, S., Bhushan, A., Lotti, A., Clayssen, Q., Salazar, G., Milanese, A., Carlström, C.I., Papadopoulou, C., Gehrig, D., Karasikov, M., Mustafa, H., Larralde, M., Carroll, L.M., Sánchez, P., Zayed, A.A., Cronin, D.R., Acinas, S.G., Bork, P., Bowler, C., Delmont, T.O., Gasol, J.M., Gossert, A.D., Kahles, A., Sullivan, M.B., Wincker, P., Zeller, G., Robinson, S.L., Piel, J. and Sunagawa, S.
Nature 607 (7917): 111-118. 7 July 2022

Towards the biogeography of prokaryotic genes.
Coelho, L.P., Alves, R., Del Río, Á.R., Myers, P.N., Cantalapiedra, C.P., Giner-Lamia, J., Schmidt, T.S., Mende, D.R., Orakov, A., Letunic, I., Hildebrand, F., Van Rossum, T., Forslund, S.K., Khedkar, S., Maistrenko, O.M., Pan, S., Jia, L., Ferretti, P., Sunagawa, S., Zhao, X.M., Nielsen, H.B., Huerta-Cepas, J. and Bork, P.
Nature 601 (7892): 252-256. 13 January 2022

Unravelling the collateral damage of antibiotics on gut bacteria.
Maier, L., Goemans, C.V., Wirbel, J., Kuhn, M., Eberl, C., Pruteanu, M., Müller, P., Garcia-Santamarina, S., Cacace, E., Zhang, B., Gekeler, C., Banerjee, T., Anderson, E.E., Milanese, A., Löber, U., Forslund, S.K., Patil, K.R., Zimmermann, M., Stecher, B., Zeller, G., Bork, P. and Typas, A.
Nature 599 : 120-124. 4 November 2021

Bioaccumulation of therapeutic drugs by human gut bacteria.
Klünemann, M., Andrejev, S., Blasche, S., Mateus, A., Phapale, P., Devendran, S., Vappiani, J., Simon, B., Scott, T.A., Kafkia, E., Konstantinidis, D., Zirngibl, K., Mastrorilli, E., Banzhaf, M., Mackmull, M.T., Hövelmann, F., Nesme, L., Brochado, A.R., Maier, L., Bock, T., Periwal, V., Kumar, M., Kim, Y., Tramontano, M., Schultz, C., Beck, M., Hennig, J., Zimmermann, M., Sévin, D.C., Cabreiro, F., Savitski, M.M., Bork, P., Typas, A. and Patil, K.R.
Nature 597 : 533-538. 23 September 2021

Structure and function of the global topsoil microbiome.
Bahram, M., Hildebrand, F., Forslund, S.K., Anderson, J.L., Soudzilovskaia, N.A., Bodegom, P.M., Bengtsson-Palme, J., Anslan, S., Coelho, L.P., Harend, H., Huerta-Cepas, J., Medema, M.H., Maltz, M.R., Mundra, S., Olsson, P.A., Pent, M., Põlme, S., Sunagawa, S., Ryberg, M., Tedersoo, L. and Bork, P.
Nature 560 (7717): 233-237. 9 August 2018

Species-specific activity of antibacterial drug combinations.
Brochado, A.R., Telzerow, A., Bobonis, J., Banzhaf, M., Mateus, A., Selkrig, J., Huth, E., Bassler, S., Zamarreño Beas, J., Zietek, M., Ng, N., Foerster, S., Ezraty, B., Py, B., Barras, F., Savitski, M.M., Bork, P., Göttig, S. and Typas, A.
Nature 559 (7713): 259-263. July 2018

Extensive impact of non-antibiotic drugs on human gut bacteria.
Maier, L., Pruteanu, M., Kuhn, M., Zeller, G., Telzerow, A., Anderson, E.E., Brochado, A.R., Fernandez, K.C., Dose, H., Mori, H., Patil, K.R., Bork, P. and Typas, A.
Nature 555 (7698): 623-628. 29 March 2018

Salt-responsive gut commensal modulates T(H)17 axis and disease.
Wilck, N., Matus, M.G., Kearney, S.M., Olesen, S.W., Forslund, K., Bartolomaeus, H., Haase, S., Mähler, A., Balogh, A., Markó, L., Vvedenskaya, O., Kleiner, F.H., Tsvetkov, D., Klug, L., Costea, P.I., Sunagawa, S., Maier, L., Rakova, N., Schatz, V., Neubert, P., Frätzer, C., Krannich, A., Gollasch, M., Grohme, D.A., Côrte-Real, B.F., Gerlach, R.G., Basic, M., Typas, A., Wu, C., Titze, J.M., Jantsch, J., Boschmann, M., Dechend, R., Kleinewietfeld, M., Kempa, S., Bork, P., Linker, R.A., Alm, E.J. and Müller, D.N.
Nature 551 (7682): 585-589. 30 November 2017

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses.
Roux, S., Brum, J.R., Dutilh, B.E., Sunagawa, S., Duhaime, M.B., Loy, A., Poulos, B.T., Solonenko, N., Lara, E., Poulain, J., Pesant, S., Kandels-Lewis, S., Dimier, C., Picheral, M., Searson, S., Cruaud, C., Alberti, A., Duarte, C.M., Gasol, J.M., Vaque, D., Bork, P., Acinas, S.G., Wincker, P. and Sullivan, M.B.
Nature 537 (7622): 689-693. 29 September 2016

Human gut microbes impact host serum metabolome and insulin sensitivity.
Pedersen, H.K., Gudmundsdottir, V., Nielsen, H.B., Hyotylainen, T., Nielsen, T., Jensen, B.A.H., Forslund, K., Hildebrand, F., Prifti, E., Falony, G., Le Chatelier, E., Levenez, F., Doré, J., Mattila, I., Plichta, D.R., Pöhö, P., Hellgren, L.I., Arumugam, M., Sunagawa, S., Vieira-Silva, S., Jørgensen, T., Holm, J.B., Trošt, K., Kristiansen, K., Brix, S., Raes, J., Wang, J., Hansen, T., Bork, P., Brunak, S., Oresic, M., Ehrlich, S.D. and Pedersen, O.
Nature 535 (7612): 376-381. 21 July 2016

Plankton networks driving carbon export in the oligotrophic ocean.
Guidi, L., Chaffron, S., Bittner, L., Eveillard, D., Larhlimi, A., Roux, S., Darzi, Y., Audic, S., Berline, L., Brum, J., Coelho, L.P., Espinoza, J.C.I., Malviya, S., Sunagawa, S., Dimier, C., Kandels-Lewis, S., Picheral, M., Poulain, J., Searson, S., Stemmann, L., Not, F., Hingamp, P., Speich, S., Follows, M., Karp-Boss, L., Boss, E., Ogata, H., Pesant, S., Weissenbach, J., Wincker, P., Acinas, S.G., Bork, P., de Vargas, C., Iudicone, D., Sullivan, M.B., Raes, J., Karsenti, E., Bowler, C. and Gorsky, G.
Nature 532 (7600): 465-470. 28 April 2016

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.
Forslund, K., Hildebrandt, F., Nielsen, T., Falony, G., Le Chatelier, E., Sunagawa, S., Prifti, E., Vieira-Silva, S., Gudmundsdottir, V., Pedersen, H.K., Arumugam, M., Kristiansen, K., Voigt, A.Y., Vestergaard, H., Hercog, R., Costea, P.I., Kultima, J.R., Li, J., Jørgensen, T., Levenez, F., Dore, J., Nielsen, H.B., Brunak, S., Raes, J., Hansen, T., Wang, J., Ehrlich, S.D., Bork, P. and Pedersen, O.
Nature 528 (7581): 262-266. 10 December 2015

Genomic variation landscape of the human gut microbiome.
Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D.R., Kultima, J.R., Martin, J., Kota, K., Sunyaev, S.R., Weinstock, G.M. and Bork, P.
Nature 493 (7430): 45-50. 3 January 2013

Enterotypes of the human gut microbiome.
Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D.R., Fernandes, G.R., Tap, J., Bruls, T., Batto, J.M., Bertalan, M., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, T., Hattori, M., Hayashi, T., Kleerebezem, M., Kurokawa, K., Leclerc, M., Levenez, F., Manichanh, C., Nielsen, H.B., Nielsen, T., Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E., Zoetendal, E.G., Wang, J., Guarner, F., Pedersen, O., de Vos, W.M., Brunak, S., Dore, J., Weissenbach, J., Ehrlich, S.D. and Bork, P.
Nature 473 (7346): 174-180. 12 May 2011

Ancient animal microRNAs and the evolution of tissue identity.
Christodoulou, F., Raible, F., Tomer, R., Simakov, O., Trachana, K., Klaus, S., Snyman, H., Hannon, G.J., Bork, P. and Arendt, D.
Nature 463 (7284): 1084-1088. 25 February 2010

The genome of the model beetle and pest tribolium castaneum.

Nature 452 (7190): 949-955. 24 April 2008

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans.
King, N., Westbrook, M.J., Young, S.L., Kuo, A., Abedin, M., Chapman, J., Fairclough, S., Hellsten, U., Isogai, Y., Letunic, I., Marr, M., Pincus, D., Putnam, N., Rokas, A., Wright, K.J., Zuzow, R., Dirks, W., Good, M., Goodstein, D., Lemons, D., Li, W., Lyons, J.B., Morris, A., Nichols, S., Richter, D.J., Salamov, A., Sequencing, J.G.I., Bork, P., Lim, W.A., Manning, G., Miller, W.T., McGinnis, W., Shapiro, H., Tjian, R., Grigoriev, I.V. and Rokhsar, D.
Nature 451 (7180): 783-788. 14 February 2008

Insights into social insects from the genome of the honeybee Apis mellifera.

Nature 443 (7114): 931-949. 26 October 2006

Co-evolution of transcriptional and post-translational cell-cycle regulation.
Jensen, L.J., Jensen, T.S., de Lichtenberg, U., Brunak, S. and Bork, P.
Nature 443 (7111): 594-597. 4 October 2006

Proteome survey reveals modularity of the yeast cell machinery.
Gavin, A.C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L.J., Bastuck, S., Duempelfeld, B., Edelmann, A., Heurtier, M.A., Hoffman, V., Hoefert, C., Klein, K., Hudak, M., Michon, A.M., Schelder, M., Schirle, M., Remor, M., Rudi, T., Hooper, S., Bauer, A., Bouwmeester, T., Casari, G., Drewes, G., Neubauer, G., Rick, J.M., Kuster, B., Bork, P., Russell, R.B. and Superti-Furga, G.
Nature 440 (7084): 631-636. 30 March 2006

Initial sequence of the chimpanzee genome and comparison with the human genome.
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Nature 437 (7055): 69-87. 1 September 2005

Generation and annotation of the DNA sequences of human chromosomes 2 and 4.
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Nature 434 : 724-731. 1 January 2005

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
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Nature 432 (7018): 695-716. 9 December 2004

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
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Nature 428 (6982): 493-521. 1 April 2004

The DNA sequence of human chromosome 7.
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Nature 424 : 157-164. 1 January 2003

Initial sequencing and comparative analysis of the mouse genome.
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Nature 420 (6915): 520-562. 5 December 2002