Computational Biology Center Publications

A mammalian microRNA expression atlas based on small RNA library sequencing. (2007)

Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M, Tuschl T

Cell. 2007 Jun 29;129(7):1401-14.

The prediction of human microRNA targets (review) (2006)

John B, Marks DS, Sander C

Humana Press, 101-113

Pathguide: a pathway resource list. (2006)

Bader GD, Cary MP, Sander C

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D504-6.

Signal processing in the TGF-beta superfamily ligand-receptor network (2006)

Vilar J, Jansen R, Sander C

PloS Computational Biology, Jan; 2 (1) :e3

A novel class of small RNAs bind to MILI protein in mouse testes. (2006)

Aravin A, Gaidatzis D, Pfeffer S, Lagos-Quintana M, Landgraf P, Iovino N, Morris P, Brownstein MJ, Kuramochi-Miyagawa S, Nakano T, Chien M, Russo JJ, Ju J, Sheridan R, Sander C, Zavolan M, Tuschl T

Nature. 2006 Jun 4;

The developmental miRNA profiles of zebrafish as determined by small RNA cloning. (2005)

Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T.

Genes Dev. 2005 Jun 1;19(11):1288-93.

Pathway information for systems biology. (2005)

Cary MP, Bader GD, Sander C.

FEBS Lett. 2005 Mar 21;579(8):1815-20.

MicroRNA profiling of the murine hematopoietic system. (2005)

Monticelli S, Ansel KM, Xiao C, Socci ND, Krichevsky AM, Thai TH, Rajewsky N, Marks DS, Sander C, Rajewsky K, Rao A, Kosik KS.

Genome Biol. 2005;6(8):R71.

Identification of microRNAs of the herpesvirus family. (2005)

Pfeffer S, Sewer A, Lagos-Quintana M, Sheridan R, Sander C, Grasser FA, van Dyk LF, Ho CK, Shuman S, Chien M, Russo JJ, Ju J, Randall G, Lindenbach BD, Rice CM, Simon V, Ho DD, Zavolan M, Tuschl T.

Nat Methods. 2005 Apr;2(4):269-76.

Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development. (2005)

Leaman D, Chen PY, Fak J, Yalcin A, Pearce M, Unnerstall U, Marks DS, Sander C, Tuschl T, Gaul U.

Cell. 2005 Jul 1;121(7):1097-108.

Detection of activity centers in cellular pathways using transcriptional profiling (2004)

Pradines J, Rudolph-Owen L, Hunter J, Leroy P, Dancik V, Leroy L, Rowley S, Ruttenberg A, Wieghardt P, Reich C, Sander C

J Biopharm Stat. 2004 Aug;14(3):701-21.

Human microRNA targets (2004)

John B, Enright AJ, Aravin, A, Tuschl T, Sander C, Marks DS

PLoS Biol. 2004 Nov;2(11):e363. Epub 2004 Oct 5

Identification of virus-encoded microRNAs (2004)

Pfeffer S, Zavolan M, Grasser FA, Chien M, Russo JJ, Ju J, John B, Enright AJ, Marks D, Sander C, Tuschl T

Science. 2004 Apr 30;304(5671):734-6.

Global mapping of the yeast genetic interaction network (2004)

Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C , Sander C

Science. 2004 Feb 6;303(5659):808-13.

miR-122, a Mammalian Liver-Specific microRNA, is Processed from hcr mRNA and May Downregulate the High Affinity Cationic Amino Acid Transporter CAT-1 (2004)

JH Chang, E Nicolas, DS Marks, C Sander, A Lerro, MA Buendia, CX Xu, WS Mason, T Moloshok, R Bort, KS Zaret, JM Taylor

RNA Biology 1:2, 106-113; July/August

Evaluation of annotation strategies using an entire genome sequence (2003)

Iliopoulos I, Tsoka S, Andrade MA, Enright AJ, Carroll M, Poullet P, Promponas V, Liakopoulos T, Palaios G, Pasquier C, Hamodrakas S, Tamames J, Yagnik AT, Tramontano A, Devos D, Blaschke C, Valencia A, Brett D, Martin D, Leroy C, Rigoutsos I, Ouzounis CA, Sander C

Bioinformatics. 2003 Apr 12;19(6):717-26

MicroRNA targets in Drosophila (2003)

Enright AJ, John B, Gaul U, Tuschl T, Marks, DS, Sander C

Genome Biol. 2003;5(1):R1. Epub 2003 Dec 12.

A four-helix bundle modelling scaffold: the ROP protein (2001)

S.C. Emery, H. Bloecker, G. Cesareni, A. Kingswell, C. Sander

Protein Engineering 3, 298-299

Locating domains in protein 3D structures (2001)

L. Holm, Sander C

In: International Tables for Crystallography, Volume F. Crystallography of Biological Macromolecules

Dordrecht: Kluwer Academic Publishers, The Netherlands

Bioinformatics - Challenges in 2001 (2001)

Sander C

Bioinformatics 17, 1-2 (editorial)

Completeness in structural genomics (2001)

Vitkup D, Melamud D, Moult J, Sander C

Nature Struc.Biol. 8, 559-566

Genomic medicine and the future of health care (2000)

Sander C

Science 287, 1977-1978

CAST: an iterative algorithm for the complexity analysis of sequence tracts Ouzounis (2000)

V.J. Promponas, A.J. Enright, S.Tsoka, D. Kreil, C. Leroy, S. Hamodrakas, C.A. , C. Sander

Bioinformatics 16, 915-922

The GeneQuiz web server: protein functional analysis on the web (2000)

Hoersch S, Leroy C, Brown NP, Andrade MA, Sander C

Trends Biochem Sci 25, 33-35

Genome sequences and great expectations (2000)

I.Iliopoulos, S.Tsoka, M.Andrade, P.Janssen, B.Audit, A.Tramontano, A.Valencia, C.Leroy, C.A.Ouzounis, C. Sander

Genome Biology 2, 0001.1-0001.3

Functional classes in the three domains of life (1999)

Andrade MA, Ouzounis C, Tamames J, Valencia A, Sander C

J Mol Evol 49, 551-557

Protein folds and families: sequence and structure alignments (1999)

L Holm, Sander C

Nucleic Acids Res 27, 244-247

Automated genome sequence analysis and annotation on the web (1999)

Andrade MA, Brown NP, Leroy C, Hoersch S, de DaruvarA, Reich C, Franchini A, Tamames J, Valencia A, Ouzounis C, Sander C

Bioinformatics 15, 391-412

Frame: detection of genomic sequencing errors (1998)

N.P. Brown, P. Bork C. Sander

Bioinformatics 14, 367-371

The HSSP database of protein structure-sequence alignments and family profiles (1998)

C. Dodge, R. Schneider, C. Sander

Nucleic Acids Research 26, 313-315

Updated catalog of human-disease related proteins in the yeast genome (1998)

M.A. Andrade, A. Valencia, C. Sander

FEBS Letters 426, 7-16

Touring protein fold space with Dali/FSSP (1998)

L. Holm, C. Sander

Nucleic Acids Res. 26, 316-319

Removing near-neighbor redundancy from large protein sequence collections (1998)

L. Holm, C. Sander

Bioinformatics 14, 423-429

Dictionary of recurrent domains in protein structures (1998)

L. Holm, C. Sander

Proteins 33, 88-96

MView: a web compatible database search or multiple alignment viewer (1998)

N.P. Brown, C. Leroy, C. Sander

Bioinformatics 14, 380-381

Are binding residues conserved? (1998)

Ouzounis C, Perez-Irratxeta C, Valencia A, Sander C

Pac Symp Biocomput 1998, 401-412

EUCLID: automatic classification of proteins in functional classes by their database annotations (1998)

J. Tamames, C. Ouzounis, G. Casari, A. Valencia, C. Sander

Bioinformatics 14, 542-543

Bioinformatics: from genome data to biological knowledge (1997)

M.A. Andrade, C. Sander

Current Opinion in Biotechnology 8,675-683

DNA sequencing and analysis of 130 kilobases from yeast chromosome XV (1997)

Voss H., Benes V., M. Andrade, A. Valencia, S. Rechmann, C. Teodoru, C. Schwager, V Paces and W. Ansorge, C. Sander

Yeast 13, 655-672

The HSSP database of protein structure-sequence alignments (1997)

R. Schneider, C. Sander

Nucleic Acids Res 25, 226-230

Protein fold recognition by prediction-based threading. (1997)

B. Rost, R. Schneider, C. Sander

J. Mol. Biol. 270, 471-480

An evolutionary treasure: Unification of a broad set of amidohydrolases related to urease (1997)

L. Holm, C. Sander

Proteins 28, 72-82

Enzyme HIT (1997)

L. Holm, C. Sander

Trends Biochem Sci, 22(4), 116-117

New Structure--novel fold? (1997)

L. Holm, C. Sander

Structure, 5, (2), 165-171

Characterization of new proteins found by analysis of short open reading frames from the full yeast genome (1997)

M.A. Andrade, A. Daruvar, G. Casari, R. Schneider and M. Termier, C. Sander

Yeast, 13, 1363-1374

Classification of protein families and detection of the determinant residues with a self-organising neural network (1997)

M.A. Andrade, G. Casari, A. Valencia, C. Sander

Biological Cybernetics 76, 441-450

Sequence analysis of the Methanococcus janaschii genome and the prediction of protein function (1997)

M.A. Andrade, G. Casari, A. Daruvar, R. Schneider, J. Tamames, A. Valencia, C. Ouzounis, C. Sander

Comp. Appl. Biosc. 13,481-483

Dali/FSSP classification of three-dimensional protein folds (1997)

L. Holm, C. Sander

Nucleic Acids Research 25, 231-234

Predicting Protein Structure Using Hidden Markov Models (1997)

K. Karplus, K.Sjoelander, C.Barrett, M.Cline, D.Haussler, R.Hughey, L.Holm, C. Sander

Proteins, Suppl. 1, 134-139

Genomes with distinct function composition (1996)

J. Tamames, C. Ouzounis, A. Valencia, C. Sander

FEBS Letters 389: 96-101

GeneCrunch: Experiences on the SGI POWER CHALLENGE array with Bioinformatic applications (1996)

R. Schneider, G. Casari, A. de Daruvar, P. Bremer, M. Schlenkrich, R. Mercille, H. Vollhardt, C. Sander

In: Proceedings Supercomputing 96

K.G. Sauer Verlag

Sequence-function correlation in G protein-coupled receptors (1996)

W. Kuipers, L. Oliveira, A.C.M. Paiva, F. Rippmann, G. Vriend, A.P. IJzerman, C. Sander

In: Membrane Protein Models

BIOS Scientific Publishers: Oxford

A comparison of structural and dynamic properties of different simulation methods applied to SH3 (1996)

D.M van Aalten, A. Amadei, R. Bywater, J. B. Findlay, H. J. Berendsen and P.F. Stouten, C. Sander

Biophys J 70: 684-692

The prediction of protein contacts from multiple sequence alignments (1996)

D. J. Thomas, G. Casari, C. Sander

Protein Engineering 9, 941-948

Genomes with distinct functional composition (1996)

J. Tamames, C. Ouzounis, A. Valencia, C. Sander

FEBS Lett. 389, 96-101

The HSSP database of protein structure-sequence alignments (1996)

R. Schneider, C. Sander

Nucleic Acids Res. 24, 201-205

Computational comparisons of model genomes (1996)

C. Ouzounis, G. Casari, J. Tamames, A. Valencia, C. Sander

Trends in Biotech. 14, 280-285

Bridging the protein sequence-structure gap by structure predictions (1996)

B. Rost, C. Sander

Ann. Rev. of Biophys. and Biomol. Structure, 25, 113-136

Anomalies in protein structures (1996)

R.W.W. Hooft, G. Vriend, E.E. Abola, C. Sander

Nature 381, 272-272

Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures (1996)

R.W.W. Hooft, G. Vriend, C. Sander

Proteins 26, 363-376

Verification of Protein Structures: Side-Chain Planarity (1996)

R.W.W. Hooft, G. Vriend, C. Sander

J. App. Cryst. 29, 714-716

The PDBFinder database: a summary of PDB,DSSP and HSSP information with added value (1996)

R.W.W. Hooft, M. Scharf, G. Vriend, C. Sander

Cabios 12, 525-529

Alignment of three-dimensional protein structures (1996)

L. Holm, C. Sander

Meth. Enz. 266, 653-662

The FSSP database: fold classification based on structure-structure alignment of proteins (1996)

L. Holm, C. Sander

Nucl. Acids Res. 24, 206-210

Mapping the protein universe (1996)

L. Holm, C. Sander

Science 273, 595-602

Macromolecular structure information and databases. The EU BRIDGE Database Project Consortium (1996)

P.M. Gray, G.J. Kemp, C.J. Rawlings, N.P. Brown, J.M.Thornton, C.M. Orengo, S.J. Wodak, J. Richelle, C. Sander

Trends Biochem Sci 21: 251-256

Sequencing and analysis of a 35.4 kb region on the left arm of chromosome IV from Saccharomyces cerevisiae reveal 23 open reading frames (1996)

L.G. Eide, H. Prydz, C. Sander

Yeast 12, 1085-1090

GeneQuiz II: automatic function assignment for genome sequence analysis (1996)

G. Casari, C. Ouzounis, A. Valencia, C. Sander

In: Proceedings of the First Annual Pacific Symposium on Biocomputing

Bioinformatics and the discovery of gene function (1996)

G. Casari, A. de Daruvar, R. Schneider, C. Sander

Trends in Genetics 12, 244-245

Novelties from the complete genome of Mycoplasma genitalium (1996)

C. Ouzounis, G. Casari, A. Valencia, C. Sander

Mol. Microbiol. 20, 897-899

Comparative structure analysis (1995)

L. Holm, C. Sander

In: Making the Most of Your Model. Proceedings of the CCP4 Study Weekend held at Chester, January 1995

Daresbury Report Series

Sequence-function correlation in G protein-coupled receptors (1995)

W. Kuipers, L. Oliveira, A.C.M. Paiva, F. Rippmann, G. Vriend, C.G. Kruese, I.van Wijngaarden, A.P. IJzerman, C. Sander

In: Membrane protein models

BIOS Sci. Pub. Ltd

A method to predict functional residues in proteins (1995)

G. Casari, A. Valencia, C. Sander

Nature Struc Biol 2, 171-178

A sequence property approach to searching protein sequence databases (1995)

U. Hobohm, C. Sander

J. Mol. Biol. 251, 390-399

Nucleotide sequence and analysis of the centromeric region of yeast chromosome IX (1995)

H. Voss, J. Tamames, C. Teodoru, A. Valencia, C. Sensen, , C. Sander, C. Schwager, J. Zimmermann, W. Ansorge

Yeast 11, 61-78

The ras superfamily (1995)

A. Valencia, C. Sander

In: Guidebook to the Small GTPases

Sambrook and Tooze publication at Oxford University Press

Transmembrane helices predicted at 95% accuracy (1995)

B. Rost, R. Casadio, P. Fariselli, C. Sander

Protein Science 4, 521-533

Progress of 1D structure prediction at last (1995)

B. Rost, C. Sander

Proteins 23, 295-300

The functional composition of living machines (as a design principle for artificial organisms) (1995)

C. Ouzounis, A. Valencia, J. Tamames, P. Bork, C. Sander

In: Advances in Artificial Life, Third European Conference on Artificial Life, Granada, Spain, June 1995, Proceedings

Springer Verlag, Heidelberg

Novel protein families in archaean genomes (1995)

C. Ouzounis, N. Kyprides, C. Sander

Nucl. Acids Res. 23, 565-570

New protein functions in yeast chromosome VIII (1995)

C. Ouzounis, P. Bork, G. Casari, C. Sander

Protein Science 4, 2424-2428

A drosophila hsp70 gene contains long, antiparallel, coupled open reading frames (LAC ORFs) conserved in homologous loci (1995)

I. Konstantopoulou, C.A. Ouzounis, E. Drosopooulou, M. Yiangou, P. Sideras, Z.G. Scouras, C. Sander

J. Mol. Evol. 41, 414-420

Fast protein structure database searches at 90% reliability (1995)

L. Holm, C. Sander

In: Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology

AAAI Press, Menlo Park, California

Evolutionary link between glycogen phosphorylase and a DNA modifying enzyme (1995)

L. Holm, C. Sander

EMBO J.14, 1287-1293

DNA polymerase belongs to an ancient nucleotidyltransferase superfamily (1995)

L. Holm, C. Sander

TIBS 20, 345-347

Investigating the structural determinants of the ras p21-like triphosphate and Mg2+ binding site (1995)

P. Cronet, L. Bellsolell, M. Coll, L. Serrano, C. Sander

J. Mol. Biol. 249, 654-664

The use of position-specific rotamers in model building by homology (1995)

G. Chinea, G. Padron, R. W. W. Hooft, G. Vriend, C. Sander

Proteins 23, 415-421

Sequence Space Analysis: Identification of Functionally and Structurally Important Residues in Protein Sequence Families (1995)

G. Casari, A. Valencia, C. Sander

In: PROTEIN FOLDS: A Distance-Based Approach

CRC Press Inc.

Challenging times for bioinformatics: Automated protein sequence analysis of the Haemophilus Influenzae genome (1995)

G. Casari, M.A. Andrade, P. Bork, J. Boyle, A. Daruvar, C. Ouzounis, R. Schneider, J. Tamames, A. Valencia, C. Sander

Nature 376, 647-648

The cytidyltransferase superfamily: identification of nucleotide binding site and fold prediction (1995)

P. Bork, L. Holm, E. Koonin, C. Sander

Proteins 22, 259-266

Exploring the mycoplasma capricolum genome: a minimal cell reveals its physiology (1995)

P. Bork, C. Ouzounis, G. Casari, R. Schneider, M. Dolan, C. Sander,W. Gilbert, P.M. Gillevet

Molecular Microbiology 16, 955-967

Molecular modelling using WHATIF on personal computers (1994)

M. Scheeren, E. Scheeren-Groot, R.W.W. Hooft, G. Vriend, C. Sander

Chemical Design Automation News, May 1994, 11-13.

PHD- an automatic mail server for protein secondary structure prediction (1994)

B. Rost, R. Schneider, C. Sander

CABIOS 10, 53-60

Combining evolutionary information and neural networks to predict protein secondary structure (1994)

B. Rost, C. Sander

Proteins19, 55-72

Structure prediction of proteins - where are we now? (1994)

B. Rost, C. Sander

Curr. Opin. Biotech. 5, 372-380

Redefining the goals of secondary structure prediction (1994)

B. Rost, C. Sander

J. Mol. Biol. 235, 13-26

Conservation and prediction of solvent accessibility in protein families (1994)

B Rost, C. Sander

Proteins, 20, 216-226

GeneQuiz: a workbench for sequence analysis (1994)

M. Scharf, R. Schneider, G. Casari, P. Bork, A. Valencia, C. Ouzounis, C. Sander

In: Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology

AAAI Press, Menlo Park, CA

The immunoglobulin fold: structural classification, sequence patterns, and common core (1994)

P. Bork, L. Holm, C. Sander

J. Mol. Biol. 242, 309-320

The intracellular localization of bacterial division protein FtsA, a member of the actin family, correlates with its phosphorylation state and its ATP-binding capacity (1994)

M. Sanchez, A. Valencia, M-J Ferrandiz, M. Vicente, C. Sander

EMBO J. 13, 4919-4925

A novel search method for protein sequence-structure relationships using property profiles (1994)

G. Vriend, P.F. Stouten, C. Sander

Protein Engineering 7, no. 1

Design of protein structures: helical bundles and beyond (1994)

C. Sander

Trends in Biotechnology 12, 163-167

The FSSP database of structurally aligned protein fold families (1994)

L. Holm, C. Sander

Nucleic Acids Research 21, 3105-3109

A hybrid protein kinase - RNAase in an interferon-induced pathway (1994)

P. Bork, C. Sander

FEBS Letters 334, 149-152

The HSSP database of protein sequence-structure alignments (1994)

R. Schneider, C. Sander

Nucleic Acids Research 22, 3597-3599

Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? (1994)

I.N. Shindyalov, N.A. Kolchanov, C. Sander

Protein Engineering 7, 349-358

Evolution and neural networks - Protein secondary structure prediction above 71% accuracy (1994)

B. Rost, R. Schneider, C. Sander

In: 27th Hawaii International Conference on System Sciences, Wailea, Hawaii, vol. 5

IEEE Society Press

1D secondary structure prediction through evolutionary profiles (1994)

B. Rost, C. Sander

In: Protein Structure by Distance Analysis

Amsterdam: IOS Press

The modular structure of NifU proteins (1994)

C. Ouzounis, P. Bork, C. Sander

Trends Biochem. Sci. 19, 199-200

A common step for signal transduction in G protein coupled receptors (1994)

L. Oliveira, A.C.M. Paiva, G. Vriend, C. Sander

TIPS 15, 170-172

Yeast chromosome III: new gene functions (1994)

E.V. Koonin, P. Bork, C. Sander

EMBO J. 13, 493-503

A novel RNA_binding motif in omnipotent suppressors of translation termination, ribosomal proteins and a ribosome modification enzyme (1994)

E.V. Koonin, P. Bork, C. Sander

Nucl. Ac. Res. 22: 2166-2167

Reconstruction of symmetry related molecules from Protein Data Bank (PDB) files (1994)

R.W.W. Hooft, G. Vriend, C. Sander

J. Appl. Cryst. 27, 1006-1009

LexA repressor and iron uptake regulator from Escherichia coli: new members of the CAP-like DNA binding domain superfamily (1994)

L. Holm, H. R?terjans, M. Schnarr, R. Fogh, R. Boelens, R. Kaptein, C. Sander

Protein Engineering 7,1449-1453

Data based modelling of proteins (1994)

L. Holm, B. Rost, R. Schneider, G. Vriend, C. Sander

In: Statistical Mechanics, Protein Structure and Protein Substrate Interactions

Plenum Press, New York

Three sisters, different names: 3a,20b-hydroxysteroid dehydrogenase, dihydropteridine reductase, UDP-galactose 4-epimerase (1994)

L. Holm, A. Murzin, C. Sander

Nature Structural Biology 1, 146-147

Structural similarity of plant chitinase and lysozymes from animals and phage: an evolutionary connection (1994)

L. Holm, C. Sander

Febs Letters 340, 129-132

Searching protein structure databases has come of age (1994)

L. Holm, C. Sander

Proteins 19, 165-173

Parser for protein folding units (1994)

L. Holm, C. Sander

Proteins 19, 256-268

Amino acid analysis and protein database compositional search as a rapid and inexpensive method to identify proteins (1994)

U. Hobohm, T. Houthaeve, C. Sander

Anal. Biochem. 222, 202-209

Enlarged representative set of protein structures (1994)

U. Hobohm, C. Sander

Protein Science 3, 522-524

Predicting local structural changes that result from point mutations (1994)

V. De Filippis, G. Vriend, C. Sander

Protein Engineering 7, 1203-1208

A human cDNA coding for the Leydig insulin-like peptide Ley I-L (1994)

E. Burkhardt, J.M. Adham, U. Hobohm, D. Murphy, W.Engel, C. Sander

Human Genetics 94, 91-94

Correlated mutations and residue contacts in proteins (1994)

U. Goebel, R. Schneider, A. Valencia, C. Sander

Proteins 18, 309-317

The chaperone function of DnaK requires the coupling of ATPase activity with substrate binding through residue E171 (1994)

A. Buchberger, A. Valencia, R. McMacken, B. Buckau, C. Sander

EMBO J 13, 1687-1695

Sequenzvergleiche in der Genomanalyse . In: Tagungsband, Bioinformatik:Computereinsatz in den Biowissenschaften (1994)

Peer Bork, Christos Ouzounis, Georg Casari, Pat M. Gillevet, Chris Sander

Jena, 59-60

From genome sequences to protein function (1994)

P. Bork, C. Ouzounis C. Sander

Curr. Opin. Struct. Biol. 4, 393-403

Design of protein strutures: helical bundles and beyond (1994)

C. Sander

Trends in Biotechnology 12, 163-167

Structural Design of Proteins (1994)

C. Sander

In: Concept of Protein Engineering and Design

Walter DeGruyter, Berlin

Quality Control of Protein Models: Directional Atomic Contact Analysis (1993)

G. Vriend, C. Sander

J. Appl. Cryst. 26, 47-60

How does the switch II region of G domains work (1993)

P.F.W. Stouten, A. Wittinghofer, A. Valencia, C. Sander

FEBS Letters 320, 1-6

An efficient solvation term for use in protein simulations based on atomic occupancies (1993)

P. Stouten, C. Froemmel, H. Nakamura, C. Sander

Molecular Simulation 10, 97-120

From Sequence Similarity to Structural Homology of Proteins in: Computation of Biomolecular Structures (1993)

R. Schneider ,C. Sander

In: Achievements, Problems and Perspectives

Springer Verlag

Progress in protein structure prediction? (1993)

B. Rost, R. Schneider C. Sander

Trends in Biochem. Sci 18, 120-123

Secondary structure prediction of all-helical proteins in two states (1993)

B. Rost, C. Sander

Protein Engineering 8, 831-836

Prediction of protein secondary structure at better than 70% accuracy (1993)

B. Rost, C. Sander

J.Mol.Biol. 232, 584-599

Improved prediction of protein secondary structure by use of sequence profiles and neural networks (1993)

B. Rost, C. Sander

P.N.A.S. USA 90, 7558-7562

Prokaryotic polyphosphate phosphatases belong to the actin/hsp70/sugar kinase superfamily (1993)

J. Reizer,A. Reizer,P. Bork, M.H. Saier Jr., C. Sander

TIBS 18, 247-248

Homology of the NifS family of proteins to a new class of pyridoxal phosphate-dependent enzymes (1993)

C. Ouzounis, C. Sander

FEBS Letters 322, 159-164

Norrie disease protein (NDP) is a cysteine knot growth factor (1993)

T. Meitinger, A. Meindl, P .Bork, B. Rost, M. Haasemann, J. Murken, C. Sander

Nature Genetics 5, 376-380

Prokaryotic members of a new family of putative helicases with similarity to the transcription activator SNF2 (1993)

A.B. Kolst¿, P. Bork, K. Kval¿y, T. Lindback, A. Gr¿nstadt, T. Kristensen, C. Sander

J. Mol. Biol. 230, 684-688

A new ATP binding fold. A common structure for actin, hexokinase and the Nt domain of Hsc70 (1993)

K.C. Holmes, A. Valencia, C. Sander

Trends in Cell Biology 3, 53-59

Globin fold in a bacterial toxin (1993)

L. Holm, C. Sander

Nature 361, 309-309

Structural alignment of globins, phycocyanins and colicin A (1993)

L. Holm, C. Sander

Febs Letters 315, 301-306

Protein structure comparison by alignment of distance matrices (1993)

L. Holm, C. Sander

J. Mol. Biol. 233, 123-138

Modeling of transmembrane seven helix bundles (1993)

P. Cronet, G. Vriend, C. Sander

Protein Engineering 6, 59-64

Convergent evolution of similar enzymatic function on different protein folds: the hexokinase, ribokinase and galactokinase families of sugar kinases (1993)

P. Bork, A. Valencia, C. Sander

Protein Science 2, 31-40

The HSSP data base of protein sequence-structure alignments (1993)

R. Schneider, C. Sander

Nucleic Acids Research 21, 3105-3109

Prediction of protein structure by evaluation of sequence-structure fitness: aligning sequences to contact profiles derived from 3D structures (1993)

C. Ouzounis, M. Scharf, R. Schneider, C. Sander

J. Mol. Biol. 232, 805-825

Protein Design on Computers. Five new proteins: Shpilka, Grendel, Fingerclasp, Leather and Aida (1992)

G. Vriend , C. Sander and others

Proteins 12, 105-110

A new triple-helical model for the shaft of the adenovirus fibre (1992)

P.F.W. Stouten, R.W.H. Ruigrok, S. Cusack, C. Sander

J. Mol. Biol. 226, 1073-1084

Exercising Multi-layered Networks on Protein Secondary Structure.International (1992)

B. Rost, C. Sander

Journal of Neural Systems 3 (Supp. 1992), 209-220

Design of Protein Structures (1992)

M. Scharf, R. Schneider, C. Sander

In Protein Engineering, a Practical Approach, A.R.Rees, M.J.E. Sternberg and R. Wetzel eds., Oxford University Press, 1992, p 89- 115 (not refereed)

Jury on Structure Prediction (1992)

B. Rost, C. Sander

Nature 360, 540

Molecular Cloning and Structural Analysis of Genes from Zea mays (L.) coding for members of the ras-related YPT gene family (1992)

K. Palme, T. Diefenthal, M. Vingron, J. Schell, C. Sander

P.N.A.S. USA 89, 787-791

TFIIB, an evolutionary link between the transcription machineries of archaebacteria and eukaryotes (1992)

C. Ouzounis, C. Sander

Cell 71, 189-190

A database of protein structure families with common folding motifs (1992)

L. Holm, C. Ouzounis, G. Tuparev, G. Vriend, C. Sander

Protein Science 1, 1691-1698

Evaluation of protein models by atomic solvation preference (1992)

L Holm, C. Sander

J. Mol. Biol. 225, 93-105

Fast and simple Monte Carlo algorithm for sidechain optimization in proteins. Application to model building by homology (1992)

L Holm, C. Sander

Proteins 14, 213-223

Selection of representative protein data sets (1992)

U. Hobohm, M. Scharf, R. Schneider, C. Sander

Protein Science 1, 409-417

An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins (1992)

P. Bork, A. Valencia, C. Sander

PNAS USA 89, 7290-7294

The internalization signal in the cytoplasmic tail of lysosomal acid phosphatase consists of the hexapeptide PGYRHV (1992)

W. Eberle, K. von Figura, C. Peters, C. Sander

EMBO J. 11, 4391-4399

A module of the DnaJ heat shock proteins found in malaria parasites (1992)

P. Bork, A. Valencia, B. Bukau, C. Sander

TIBS 17, 129-129

Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III (1992)

P. Bork, C. Ouzounis, M. Scharf, R. Schneider, E. Sonnhammer, C. Sander

Protein Science 1, 1677-1690

What's in a genome? (1992)

P. Bork, C. Ouzounis, M. Scharf, R. Schneider, E. Sonnhammer, C. Sander

Nature 338, 287

A large domain common to sperm receptors (Zp2 and Zp3) and TGF-b type III receptor (1992)

P. Bork, C. Sander

FEBS Letters 300, 237-240

The human genome and high performance computing in molecular biology (1992)

R. Schneider, P. Stouten, C. Sander

In: Supercomputer 1992

Springer-Verlag, Berlin

A new triple-helical model for the shaft of the adenovirus fibre (1992)

G. Tuparev, G. Vriend, C. Sander

J. Mol. Graphics 10, 12-16

The Structure of ColE1 Rop in Solution (1991)

W. Eberle, A. Pastore, P.Roesch, C. Sander

J. Biomol. NMR 1, 71-82

Protein Design on Computers (1991)

C. Sander edited with G. Vriend

Biocomputing Technical Document 6

Detection of common three-dimensional substructures in proteins (1991)

G. Vriend, C. Sander

Proteins 11, 52-58

G-domains of ras p21 oncogene protein and elongation factor Tu: analysis of three-dimensional structures, sequence families and functional sites (1991)

A. Valencia, M. Kjeldgaard, E.F. Pai, C. Sander

PNAS 88, 5443-5447

The ras Protein Family: Evolutionary Tree and Role of Conserved Amino Acids (Perspectives in Biochemistry) (1991)

A. Valencia, P. Chardin, F. Wittinghofer, C. Sander

Biochemistry 30, 4637-4648

Database of homology-derived protein structures and the structural meaning of sequence alignment (1991)

R. Schneider, C. Sander

Proteins 9, 56-68

(HX)n repeats: a pH-controlled protein-protein interaction motif of eukaryotic transcription factors? (1991)

R. Janknecht, O. Pongs, C. Sander

FEBS Letters 295, 1-2

A structure-derived sequence pattern for the type I copper binding domain in distantly related proteins (1991)

C. Ouzounis, C. Sander

FEBS Letters 279, 73-78

The functional mechanism of heat shock and chaperone proteins in protein folding. A hypothesis (1991)

T.J.P. Hubbard, C. Sander

Protein Engineering 4, 711-717

Database algorithm for generating protein backbone and side chain coordinates from a C(alpha) trace. Application to model building and detection of coordinate errors (1991)

L. Holm, C. Sander

J. Mol. Biol. 218, 183-194

Identification by computer sequence analysis of transcriptional regulator proteins in dictyostelium discoideum and serratia marcescens (1991)

R. Grandori, C. Sander

Nucl. Acids Res. 19, 2359-2362

The essential tyrosine of the internalization signal of lysosomal acid phosphatase is part of a beta-turn (1991)

W. Eberle, W. Klaus, B. Schmidt, K. von Figura, C. Peters, C. Sander

Cell 67, 1203-1209

De novo design of proteins (1991)

C. Sander

Current Opinion in Structural Biology 1, 630-638

Proton NMR assignments and secondary structure determination of the ColE1 rop (rom) protein (1990)

W. Eberle, W. Klaus, G. Cesareni, P.Roesch, C. Sander

Biochemistry 29, 7402-7407

Excluded Volume Approximation to Protein-Solvent Interaction: the Solvent Contact Model (1990)

F. Colonna-Cesari, C. Sander

Biophysical Journal 57, 1103-1107

Molecular cloning of YPT1/SEC4-related cDNAs from an epithelial line (1990)

P. Chavrier, M. Vingron, K. Simons, M. Zerial, C. Sander

Mol. Cell. Biol. 10, 6578-6585

Inverting the protein folding problem (1990)

C. Sander

Biochem. Soc. Symp. 57, 25-33

Residue contact conservation in a family of Ca-binding proteins (1989)

A. Godzik, C. Sander

Protein Engineering 2 (1989) 589-596

Thermitase, a Thermostable Subtilisin: Comparison of Predicted and Experimental Structures and the Molecular Cause of Thermostability (1989)

C. Froemmel, C. Sander

Proteins 5, 22-37

Polarity as a criterion in protein design (1989)

G. Baumann, C. Froemmel, C. Sander

Protein Engineering 2 (1989) 329-334

How to determine protein secondary structure in solution by Raman spectroscopy: Practical guide and test case DNAse I (1989)

B. Bussian, C. Sander

Biochemistry 28, 4271-4277

Identification of guanine-nucleotide binding proteins in plants: structural and evolutionary analysis of the ras-related YPT gene family from Zea Mays (1989)

K. Palme, T. Diefenthal, Martin Vingron, Jeff Schell, C. Sander

In: The guanine-nucleotide Binding Proteins Common Structural and Functional Properties

Plenum, New York

Exercises in Protein Design on Computers (1988)

C. Sander

Protein Engineering 2, 227-228

Cassette mutagenesis to produce designed ROP protein variants (1988)

S.C. Emery, H. Bloecker, G. Cesareni, A. Kingswell, C. Sander

In: Advances in Protein Design, GBF Workshop, Braunschweig

Protein Design Exercises (1987)

C. Sander

Biocomputing Technical Document 1

Immunization with synthetic peptides of plasmodium falciparum surface antigen induces antimerozoite antibodies (1986)

A. Cheung, J. Leban, A.R. Shaw, B. Merkli, J. Stocker, C. Sander, C. Chizzolini, L.H. Perrin

Proc. Natl. Acad. Sci. (USA) 83, 8328-8332

Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme (1985)

M. Levitt, P. Stern, C. Sander

J. Mol. Biol. 181, 423-447

JAWS. A Film of Enzyme Dynamics (Meeting Abstract) (1985)

M. Levitt, P. Stern

Fresenius Z. Anal

Identical pentapeptides with different backbones (letter) (1985)

W. Kabsch, C. Sander

Nature 317, 207

The primary structure of transcription factor TFIIIA has twelve consecutive repeats (1985)

P. Argos, R.S. Brown, C. Sander

FEBS Letters 186, 271-273

On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations (1984)

W. Kabsch, C. Sander

Proc. Natl. Acad. Sci. (USA) 81, 1075-1078

The normal modes of a protein: native bovine pancreatic trypsin inhibitor (1983)

M. Levitt, P. Stern, C. Sander

Internatl. J. Quant. Chem., Quantum Biology Symposium 10, 181-199

Collective Protein Dynamics: a Film of the Low Frequency Normal Modes of Trypsin Inhibitor (1983)

M. Levitt, P. Stern, C. Sander

Hoppe-Seyler's Zeitschrift f?r Physiol. Chemie 364, 1262

Dictionary of protein secondary structure. Pattern recognition of hydrogen bonded and geometrical features (1983)

W. Kabsch, C. Sander

Biopolymers 22, 2577-2637

How good are predictions of protein secondary structure? (1983)

W. Kabsch, C. Sander

FEBS Letters 155, 179-182

Toward peptide vaccines: prediction of antigenic peptides from protein sequences of influenza virus and foot and mouth disease virus. (Meeting Abstract, material not published elsewhere) (1983)

W. Kabsch, C. Sander

Hoppe-Seyler's Zeitschrift fuer Physiol. Chemie 364, 1152

A yeast gene encoding a protein homologous to the human c-Ha-ras proto-oncogene product (1983)

C. Donath, D. Gallwitz, C. Sander

Nature 306, 704-707 (paper) and 306, 642-642 (news and views)

The ten helical twist angles of B-DNA (1982)

W. Kabsch, Sander C, E. Trifonov

Nucleic Acids Research 10, 1097-1104