Søren Brunak

144.9k total citations · 25 hit papers
350 papers, 55.8k citations indexed

About

Søren Brunak is a scholar working on Molecular Biology, Genetics and Artificial Intelligence. According to data from OpenAlex, Søren Brunak has authored 350 papers receiving a total of 55.8k indexed citations (citations by other indexed papers that have themselves been cited), including 223 papers in Molecular Biology, 51 papers in Genetics and 31 papers in Artificial Intelligence. Recurrent topics in Søren Brunak's work include Machine Learning in Bioinformatics (56 papers), RNA and protein synthesis mechanisms (52 papers) and Bioinformatics and Genomic Networks (35 papers). Søren Brunak is often cited by papers focused on Machine Learning in Bioinformatics (56 papers), RNA and protein synthesis mechanisms (52 papers) and Bioinformatics and Genomic Networks (35 papers). Søren Brunak collaborates with scholars based in Denmark, United States and Sweden. Søren Brunak's co-authors include Henrik Nielsen, Gunnar von Heijne, Jannick Dyrløv Bendtsen, Nikolaj Blom, Jacob Engelbrecht, Olof Emanuelsson, Steen Gammeltoft, Ramneek Gupta, Lars Juhl Jensen and Pierre Baldi and has published in prestigious journals such as Nature, Science and Cell.

In The Last Decade

Søren Brunak

341 papers receiving 54.7k citations

Hit Papers

5 papers align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

Improved Prediction of Signal Peptides: SignalP 3.0

2004 5.6k citations Søren Brunak et al. profile →
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites

1997 4.9k citations Søren Brunak et al. profile →
Predicting Subcellular Localization of Proteins Based on their N-terminal Amino Acid Sequence

2000 3.6k citations Søren Brunak et al. profile →
SignalP 5.0 improves signal peptide predictions using deep neural networks

2019 3.0k citations Søren Brunak et al. profile →
Locating proteins in the cell using TargetP, SignalP and related tools

2007 2.7k citations Søren Brunak et al. profile →
Sequence and structure-based prediction of eukaryotic protein phosphorylation sites

1999 2.6k citations Søren Brunak et al. profile →
Prediction of post‐translational glycosylation and phosphorylation of proteins from the amino acid sequence

2004 1.6k citations Søren Brunak et al. profile →
Assessing the accuracy of prediction algorithms for classification: an overview

2000 1.6k citations Søren Brunak et al. profile →
SignalP 6.0 predicts all five types of signal peptides using protein language models

2022 1.4k citations Søren Brunak et al. profile →
Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

2010 1.2k citations Jesper V. Olsen, Lars Juhl Jensen et al. profile →
Precision mapping of the human O‐GalNAc glycoproteome through SimpleCell technology

2013 1.1k citations Søren Brunak et al. profile →
Mining electronic health records: towards better research applications and clinical care

2012 1.0k citations Peter Bjødstrup Jensen, Lars Juhl Jensen et al. profile →
Feature-based prediction of non-classical and leaderless protein secretion

2004 981 citations Lars Juhl Jensen, Søren Brunak et al. profile →
Prediction of lipoprotein signal peptides in Gram‐negative bacteria

2003 919 citations Agnieszka Sierakowska Juncker, Søren Brunak et al. profile →
Reliable prediction of T‐cell epitopes using neural networks with novel sequence representations

2003 832 citations Søren Brunak et al. profile →
Prediction of glycosylation across the human proteome and the correlation to protein function

2001 765 citations Søren Brunak et al. PubMed profile →
Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites

2004 742 citations Søren Brunak et al. profile →
A human phenome-interactome network of protein complexes implicated in genetic disorders

2007 659 citations Kasper Lage, E. Olof Karlberg et al. profile →
Analysis and prediction of leucine-rich nuclear export signals

2004 642 citations Søren Brunak et al. profile →
Prediction of human mRNA donor and acceptor sites from the DNA sequence

1991 627 citations Søren Brunak et al. profile →
A Neural Network Method for Identification of Prokaryotic and Eukaryotic Signal Peptides and Prediction of their Cleavage Sites

1997 598 citations Søren Brunak et al. profile →
Bioinformatics the machine learning approach

1998 583 citations Søren Brunak et al. profile →
Non-classical protein secretion in bacteria

2005 577 citations Søren Brunak et al. profile →
Machine learning approaches for the prediction of signal peptides and other protein sorting signals

1999 500 citations Søren Brunak et al. profile →
A scored human protein–protein interaction network to catalyze genomic interpretation

2016 386 citations Søren Brunak, Thomas Jensen et al. profile →

Peers

Countries citing papers authored by Søren Brunak

Since Specialization

Citations

This map shows the geographic impact of Søren Brunak's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Søren Brunak with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Søren Brunak more than expected).

Fields of papers citing papers by Søren Brunak

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Søren Brunak. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Søren Brunak. The network helps show where Søren Brunak may publish in the future.

Co-authorship network of co-authors of Søren Brunak

This figure shows the co-authorship network connecting the top 25 collaborators of Søren Brunak. A scholar is included among the top collaborators of Søren Brunak based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Søren Brunak. Søren Brunak is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

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20 of 20 papers shown

#	Work	Indexed citations
1	Implementing a Nordic-Baltic Federated Health Data Network: A Case Report 2025 ·Studies in health technology and informatics ·Taridzo Chomutare, (unknown), Laura‐Maria Peltonen, (unknown), Peter Lundberg, Arne Jönsson, (unknown), (unknown), (unknown), Raivo Kolde, (unknown), Martin Hansson, (unknown), Miroslav Mužný, (unknown), Søren Brunak, Hercules Dalianis	1
2	Learning the natural history of human disease with generative transformers 2025 ·Nature ·Artem Shmatko, Alexander W. Jung, Kumar Gaurav, Søren Brunak, Laust Hvas Mortensen, Ewan Birney, Tomas Fitzgerald, Moritz Gerstung	4
3	Advancing rare disease therapeutics through digital twins: Opportunities in drug development and precision dosing 2025 ·Computational and Structural Biotechnology Journal ·(unknown), (unknown), (unknown), Dominik Selzer, (unknown), Nicola Luigi Bragazzi, (unknown), Søren Brunak, Ewan R. Pearson, Tobias Zahn, Dimitra Kiritsi, Matthias Schwab, Thorsten Lehr	0
4	Immune changes in pregnancy: associations with pre-existing conditions and obstetrical complications at the 20th gestational week—a prospective cohort study 2024 ·BMC Medicine ·David Westergaard, Agnete Troen Lundgaard, Kilian Vomstein, Line Olsen, (unknown), Pia Egerup, (unknown), (unknown), (unknown), (unknown), Tanja Schlaikjær Hartwig, Finn Stener Jørgensen, Anne Zedeler, Astrid Marie Kolte, Henrik Westh, Henrik L. Jørgensen, Nina la Cour Freiesleben, Karina Banasik, Søren Brunak, Henriette Svarre Nielsen	2
5	Population-Based Characterization of Menstrual Migraine and Proposed Diagnostic Criteria 2023 ·JAMA Network Open ·Mona Ameri Chalmer, Lisette J. A. Kogelman, Henrik Ullum, Erik Sørensen, Maria Didriksen, Susan Mikkelsen, Khoa Manh Dinh, Thorsten Brodersen, (unknown), Mie Topholm Bruun, Karina Banasik, Søren Brunak, Christian Erikstrup, Ole Birger Pedersen, Sisse Rye Ostrowski, Jes Olesen, Thomas Folkmann Hansen	9
6	Precision medicine in complex diseases—Molecular subgrouping for improved prediction and treatment stratification 2023 ·Journal of Internal Medicine ·Åsa Johansson, Ole A. Andreassen, Søren Brunak, Paul W. Franks, Harald Hedman, Ruth J. F. Loos, Benjamin Meder, Erik Melén, Craig E. Wheelock, Bo Jacobsson	35
7	Text mining of electronic health records can validate a register‐based diagnosis of epilepsy and subgroup into focal and generalized epilepsy 2023 ·Epilepsia ·(unknown), (unknown), Isabella Friis Jørgensen, (unknown), (unknown), Gitte M. Knudsen, Søren Brunak, Lars H. Pinborg	3
8	A unidirectional mapping of ICD-8 to ICD-10 codes, for harmonized longitudinal analysis of diseases 2023 ·European Journal of Epidemiology ·(unknown), Robert Eriksson, (unknown), (unknown), Helle Pedersen, (unknown), Christian Simon, (unknown), Michael Larsen, Anna Pors Nielsen, Kirstine Belling, Søren Brunak	8
9	Pancreatic cancer symptom trajectories from Danish registry data and free text in electronic health records 2023 ·eLife ·Jessica Xin Hjaltelin, (unknown), Isabella Friis Jørgensen, (unknown), (unknown), David Westergaard, Julia S. Johansen, Inna M. Chen, Lars Juhl Jensen, Søren Brunak	2
10	Targeted serum proteomics of longitudinal samples from newly diagnosed youth with type 1 diabetes distinguishes markers of disease and C-peptide trajectory 2023 ·Diabetologia ·Robert Moulder, Tommi Välikangas, (unknown), Tomi Suomi, Caroline Brorsson, Niina Lietzén, Sylvaine F. A. Bruggraber, Lut Overbergh, David B. Dunger, Mark Peakman, Piotr Jaroslaw Chmura, Søren Brunak, Anke M. Schulte, Chantal Mathieu, Mikael Knip, Laura L. Elo, Riitta Lahesmaa	11
11	Population-wide analysis of hospital laboratory tests to assess seasonal variation and temporal reference interval modification 2023 ·Patterns ·Victorine Muse, Alejandro Aguayo‐Orozco, (unknown), Søren Brunak	5
12	Randomized Phase II Study of Nivolumab With or Without Ipilimumab Combined With Stereotactic Body Radiotherapy for Refractory Metastatic Pancreatic Cancer (CheckPAC) 2022 ·Journal of Clinical Oncology ·Inna M. Chen, Julia S. Johansen, Susann Theile, Jessica Xin Hjaltelin, (unknown), Søren Brunak, Jane Preuss Hasselby, Gro Linno Willemoe, Torben Lorentzen, Kasper Madsen, Benny Vittrup Jensen, (unknown), Poul Geertsen, C.F. Behrens, Christian Nolsøe, (unknown), Inge Marie Svane, Dorte Nielsen	68
13	Detection of Molecular Signatures of Homologous Recombination Deficiency in Bladder Cancer 2021 ·Clinical Cancer Research ·(unknown), Miklós Dióssy, Zsófia Sztupinszki, (unknown), Viktória Tisza, Sándor Spisák, Orsolya Rusz, (unknown), Helle Pappot, István Csabai, Søren Brunak, Kent W. Mouw, Zoltán Szállási	18
14	Phenome‐Wide Analysis of Short‐ and Long‐Run Disease Incidence Following Recurrent Pregnancy Loss Using Data From a 39‐Year Period 2020 ·Journal of the American Heart Association ·David Westergaard, Anna Pors Nielsen, Laust Hvas Mortensen, Henriette Svarre Nielsen, Søren Brunak	17
15	Estimating heritability and genetic correlations from large health datasets in the absence of genetic data 2019 ·Nature Communications ·(unknown), Yu Li, Hanxin Zhang, Ishanu Chattopadhyay, Anders Boeck Jensen, David Blair, Lea K. Davis, Peter N. Robinson, Torsten Dahlén, Søren Brunak, Mikael Benson, Gustaf Edgren, Nancy J. Cox, Xin Gao, Andrey Rzhetsky	20
16	Combinatorial Drug Screening Identifies Ewing Sarcoma–specific Sensitivities 2016 ·Molecular Cancer Therapeutics ·Branka Radic-Sarikas, Kalliopi P. Tsafou, Kristina B. Emdal, Theodore Papamarkou, K. Huber, (unknown), Jeffrey A. Toretsky, Keiryn L. Bennett, Jesper V. Olsen, Søren Brunak, Heinrich Kovar, Giulio Superti‐Furga	16
17	Finding Cervical Cancer Symptoms in Swedish Clinical Text using a Machine Learning Approach and NegEx. 2015 ·PubMed ·Rebecka Weegar, Maria Kvist, Karin Sundström, Søren Brunak, Hercules Dalianis	17
18	Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients 2014 ·Nature Communications ·Anders Boeck Jensen, Pope Moseley, Tudor I. Oprea, Sabrina Gade Ellesøe, Robert Eriksson, Henriette Schmock, Peter Bjødstrup Jensen, Lars Juhl Jensen, Søren Brunak	257
19	Analysis of Gene Expression Profiles of Microdissected Cell Populations Indicates that Testicular Carcinoma In situ Is an Arrested Gonocyte 2009 ·Cancer Research ·Si Brask Sonne, Kristian Almstrup, Marlene Dalgaard, Agnieszka Sierakowska Juncker, Daniel Edsgärd, Ludmila Ruban, Neil J. Harrison, Christian Schwager, Amir Abdollahi, Peter E. Huber, Søren Brunak, Lise Mette Rahbek Gjerdrum, H. D. M. Moore, Peter W. Andrews, Niels E. Skakkebæk, Ewa Rajpert-De Meyts, Henrik Leffers	141
20	A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes 2008 ·Proceedings of the National Academy of Sciences ·Kasper Lage, Niclas Tue Hansen, E. Olof Karlberg, Aron C. Eklund, Francisco S. Roque, Patricia K. Donahoe, Zoltán Szállási, Thomas Jensen, Søren Brunak	225

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