Taipale, Jussi

The Human Transcription Factors

Lambert, S. A., Jolma, A., Campitelli, L. F., Das, P. K., Yin, Y., Albu, M., Chen, X., Taipale, J., Hughes, T. R., & Weirauch, M. T. (2018) · Cell

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 3,399

CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response

Haapaniemi, E., Botla, S., Persson, J., Schmierer, B., & Taipale, J. (2018) · Nature Medicine

CRISPR and Genetic EngineeringDNA Repair Mechanisms

Cited by 1,264

Impact of cytosine methylation on DNA binding specificities of human transcription factors

Yin, Y., Morgunova, E., Jolma, A., Kaasinen, E., Sahu, B., Khund-Sayeed, S., Das, P. K., Kivioja, T., Dave, K., Zhong, F., et al. (2017) · Science

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 1,257

Hedgehog: functions and mechanisms

Varjosalo, M., & Taipale, J. (2008) · Genes & Development

Hedgehog Signaling Pathway StudiesHippo pathway signaling and YAP/TAZ

Cited by 1,217

Counting absolute numbers of molecules using unique molecular identifiers

Kivioja, T., Vähärautio, A., Karlsson, K., Bonke, M., Enge, M., Linnarsson, S., & Taipale, J. (2012) · Nature Methods

Genomics and Phylogenetic StudiesSingle-cell and spatial transcriptomics

Cited by 1,010

Patched acts catalytically to suppress the activity of Smoothened

Taipale, J., Cooper, M. K., Maiti, T., & Beachy, P. A. (2002) · Nature

Hedgehog Signaling Pathway StudiesWnt/β-catenin signaling in development and cancer

Cited by 794

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

Wei, G., Badis, G., Berger, M. F., Kivioja, T., Palin, K., Enge, M., Bonke, M., Jolma, A., Varjosalo, M., Gehrke, A. R., et al. (2010) · The EMBO Journal

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 568

The Human Transcription Factors

Lambert, S. A., Jolma, A., Campitelli, L. F., Das, P. K., Yin, Y., Albu, M., Chen, X., Taipale, J., Hughes, T. R., & Weirauch, M. T. (2018) · Cell

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 550

CTCF/cohesin-binding sites are frequently mutated in cancer

Katainen, R., Dave, K., Pitkänen, E., Palin, K., Kivioja, T., Välimäki, N., Gylfe, A. E., Ristolainen, H., Hänninen, U. A., Cajuso, T., et al. (2015) · Nature Genetics

Genetic factors in colorectal cancerCancer Genomics and Diagnostics

Cited by 447

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

Jolma, A., Kivioja, T., Toivonen, J., Cheng, L., Wei, G., Enge, M., Taipale, M., Vaquerizas, J. M., Yan, J., Sillanpää, M. J., et al. (2010) · Genome Research

Genomics and Chromatin DynamicsAdvanced biosensing and bioanalysis techniques

Cited by 441

A defective response to Hedgehog signaling in disorders of cholesterol biosynthesis

Cooper, M. K., Wassif, C. A., Krakowiak, P. A., Taipale, J., Gong, R., Kelley, R. I., Porter, F. D., & Beachy, P. A. (2003) · Nature Genetics

Hedgehog Signaling Pathway StudiesCholesterol and Lipid Metabolism

Cited by 390

A comparative genomics multitool for scientific discovery and conservation

Zoonomia Consortium, Genereux, D. P., Serres, A., Armstrong, J., Johnson, J., Marinescu, V. D., Murén, E., Juan, D., Bejerano, G., Casewell, N. R., et al. (2020) · Nature

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 373

Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function

Dodonova, S. O., Zhu, F., Dienemann, C., Taipale, J., & Cramer, P. (2020) · Nature

Genomics and Chromatin DynamicsProtein Structure and Dynamics

Cited by 265

Genetic and epigenetic characteristics of inflammatory bowel disease-associated colorectal cancer

Rajamäki, K., Taira, A., Katainen, R., Välimäki, N., Kuosmanen, A., Plaketti, R.-M., Seppälä, T. T., Ahtiainen, M., Wirta, E.-V., Vartiainen, E., et al. (2021) · Gastroenterology

Genetic factors in colorectal cancerInflammatory Bowel Disease

Cited by 230

Myt1l safeguards neuronal identity by actively repressing many non-neuronal fates

Mall, M., Kareta, M. S., Chanda, S., Ahlenius, H., Perotti, N., Zhou, B., Grieder, S. D., Ge, X., Drake, S., Euong Ang, C., et al. (2017) · Nature

Pluripotent Stem Cells ResearchNeurogenesis and neuroplasticity mechanisms

Cited by 225

Sequence determinants of human gene regulatory elements

Sahu, B., Hartonen, T., Pihlajamaa, P., Wei, B., Dave, K., Zhu, F., Kaasinen, E., Lidschreiber, K., Lidschreiber, M., Daub, C. O., et al. (2022) · Nature Genetics

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 198

Multiparameter functional diversity of human C2H2 zinc finger proteins

Schmitges, F. W., Radovani, E., Najafabadi, H. S., Barazandeh, M., Campitelli, L. F., Yin, Y., Jolma, A., Zhong, G., Guo, H., Kanagalingam, T., et al. (2016) · Genome Research

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 193

Transcription factor family-specific DNA shape readout revealed by quantitative specificity models

Yang, L., Orenstein, Y., Jolma, A., Yin, Y., Taipale, J., Shamir, R., & Rohs, R. (2017) · Molecular Systems Biology

Genomics and Chromatin DynamicsDNA and Nucleic Acid Chemistry

Cited by 126

Hold out the genome: a roadmap to solving the cis-regulatory code

de Boer, C. G., & Taipale, J. (2024) · Nature

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 107

Impact of constitutional TET2 haploinsufficiency on molecular and clinical phenotype in humans

Kaasinen, E., Kuismin, O., Rajamäki, K., Ristolainen, H., Aavikko, M., Kondelin, J., Saarinen, S., Berta, D. G., Katainen, R., Hirvonen, E. A. M., et al. (2019) · Nature Communications

Acute Myeloid Leukemia ResearchEpigenetics and DNA Methylation

Cited by 92

Interfacial water confers transcription factors with dinucleotide specificity

Morgunova, E., Yin, Y., Zhu, F., Xiao, T., Sokolov, I., Popov, A., Laughton, C., & Taipale, J. (2023) · Nature Structural & Molecular Biology

DNA and Nucleic Acid ChemistryProtein Structure and Dynamics

Cited by 11

Patterns and Processes of Genomic Evolution Inferred From the Ten Smallest Vertebrate Genomes

Liu, K., Wang, Q., Wang, N., Meng, L., Li, S., Wang, H., Liu, Y., Liu, Q., Zhang, Y., Doretto, L. B., et al. (2025) · Advanced Science

Chromosomal and Genetic VariationsGenomics and Phylogenetic Studies

Cited by 3