Bernardo P. de Almeida

1.6k total citations · 1 hit paper
23 papers, 643 citations indexed

About

Bernardo P. de Almeida is a scholar working on Molecular Biology, Oncology and Cell Biology. According to data from OpenAlex, Bernardo P. de Almeida has authored 23 papers receiving a total of 643 indexed citations (citations by other indexed papers that have themselves been cited), including 18 papers in Molecular Biology, 3 papers in Oncology and 3 papers in Cell Biology. Recurrent topics in Bernardo P. de Almeida's work include Genomics and Chromatin Dynamics (8 papers), RNA and protein synthesis mechanisms (4 papers) and RNA Research and Splicing (4 papers). Bernardo P. de Almeida is often cited by papers focused on Genomics and Chromatin Dynamics (8 papers), RNA and protein synthesis mechanisms (4 papers) and RNA Research and Splicing (4 papers). Bernardo P. de Almeida collaborates with scholars based in Portugal, Austria and Germany. Bernardo P. de Almeida's co-authors include Alexander Stark, Michaela Pagani, Franziska Reiter, Alexandra Binnie, Pedro Castelo‐Branco, Joana Apolónio, Nuno L. Barbosa‐Morais, André Filipe Vieira, Joana Paredes and Mónica Bettencourt‐Dias and has published in prestigious journals such as Nature, Nature Communications and Nature Genetics.

In The Last Decade

Bernardo P. de Almeida

21 papers receiving 638 citations

Hit 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.

Nucleotide Transformer: building and evaluating robust foundation models for human genomics

2024 95 citations Hugo Dalla-Torre, Javier Mendoza‐Revilla et al. Nature Methods profile →

Peers — A (Enhanced Table)

Peers by citation overlap · career bar shows stage (early→late) cites · hero ref

Name	h						Papers	Cites
Bernardo P. de Almeida Portugal	10	506	106	75	75	57	23	643
R. Brachmann United States	9	513 1.0×	72 0.7×	50 0.7×	41 0.5×	154 2.7×	18	610
Nancy George United Kingdom	7	483 1.0×	113 1.1×	47 0.6×	91 1.2×	64 1.1×	9	670
Frances Tong United States	7	396 0.8×	77 0.7×	74 1.0×	38 0.5×	68 1.2×	8	530
Charles Tilford United States	7	294 0.6×	69 0.7×	181 2.4×	34 0.5×	32 0.6×	7	492
Sofie V. Nielsen Denmark	13	628 1.2×	168 1.6×	97 1.3×	101 1.3×	90 1.6×	17	704
Jin Ok Yang South Korea	11	439 0.9×	58 0.5×	84 1.1×	187 2.5×	79 1.4×	32	633
Herman H. H. B. M. van Haagen Netherlands	7	253 0.5×	35 0.3×	68 0.9×	58 0.8×	40 0.7×	7	361
Sandeep Ayyar United States	6	379 0.7×	53 0.5×	71 0.9×	59 0.8×	46 0.8×	7	436
Ken Chen China	8	545 1.1×	59 0.6×	73 1.0×	51 0.7×	95 1.7×	18	615
Marta Dziechciarková Czechia	9	287 0.6×	71 0.7×	49 0.7×	121 1.6×	166 2.9×	17	527

Countries citing papers authored by Bernardo P. de Almeida

Since Specialization

Citations

This map shows the geographic impact of Bernardo P. de Almeida'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 Bernardo P. de Almeida with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Bernardo P. de Almeida more than expected).

Fields of papers citing papers by Bernardo P. de Almeida

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Bernardo P. de Almeida. 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 Bernardo P. de Almeida. The network helps show where Bernardo P. de Almeida may publish in the future.

Co-authorship network of co-authors of Bernardo P. de Almeida

This figure shows the co-authorship network connecting the top 25 collaborators of Bernardo P. de Almeida. A scholar is included among the top collaborators of Bernardo P. de Almeida 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 Bernardo P. de Almeida. Bernardo P. de Almeida 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

Almeida, Bernardo P. de, Hugo Dalla-Torre, Guillaume Richard, et al.. (2025). Annotating the genome at single-nucleotide resolution with DNA foundation models. Nature Methods. 22(11). 2301–2315.

Almeida, Bernardo P. de, Guillaume Richard, Hugo Dalla-Torre, et al.. (2025). A multimodal conversational agent for DNA, RNA and protein tasks. Nature Machine Intelligence. 7(6). 928–941. 7 indexed citations

Trop, Evan, et al.. (2024). Are genomic language models all you need? Exploring genomic language models on protein downstream tasks. Bioinformatics. 40(9). 2 indexed citations

Loubière, Vincent, Bernardo P. de Almeida, Michaela Pagani, & Alexander Stark. (2024). Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila. Nature Communications. 15(1). 8584–8584. 8 indexed citations

Dalla-Torre, Hugo, Javier Mendoza‐Revilla, Nicolás López Carranza, et al.. (2024). Nucleotide Transformer: building and evaluating robust foundation models for human genomics. Nature Methods. 22(2). 287–297. 95 indexed citations breakdown →

Mendoza‐Revilla, Javier, Evan Trop, Maša Roller, et al.. (2024). A foundational large language model for edible plant genomes. Communications Biology. 7(1). 835–835. 34 indexed citations

Xavier, Joana M., Roslin Russell, Bernardo P. de Almeida, et al.. (2024). Identification of candidate causal variants and target genes at 41 breast cancer risk loci through differential allelic expression analysis. Scientific Reports. 14(1). 22526–22526. 2 indexed citations

Almeida, Bernardo P. de, Christoph Schaub, Michaela Pagani, et al.. (2023). Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo. Nature. 626(7997). 207–211. 41 indexed citations

Reiter, Franziska, Bernardo P. de Almeida, & Alexander Stark. (2023). Enhancers display constrained sequence flexibility and context-specific modulation of motif function. Genome Research. 33(3). 346–358. 13 indexed citations

10.

Almeida, Bernardo P. de, Franziska Reiter, Michaela Pagani, & Alexander Stark. (2022). DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers. Nature Genetics. 54(5). 613–624. 133 indexed citations

11.

Xavier, Joana M., Bernardo P. de Almeida, Isabel Duarte, et al.. (2022). Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant. npj Breast Cancer. 8(1). 71–71. 2 indexed citations

12.

Almeida, Bernardo P. de, et al.. (2022). Systematic identification and characterization of repressive domains in Drosophila transcription factors. The EMBO Journal. 42(3). e112100–e112100. 9 indexed citations

13.

Almeida, Bernardo P. de, André Mansinho, Pedro M. Félix, et al.. (2020). Expression of receptor activator of NFkB (RANK) drives stemness and resistance to therapy in ER+HER2- breast cancer. Oncotarget. 11(19). 1714–1728. 14 indexed citations

14.

Rodrigues, Tiago M., Ruth A. Pumroy, João Conde, et al.. (2019). Allosteric Antagonist Modulation of TRPV2 by Piperlongumine Impairs Glioblastoma Progression. SSRN Electronic Journal. 2 indexed citations

15.

Almeida, Bernardo P. de, André Filipe Vieira, Joana Paredes, Mónica Bettencourt‐Dias, & Nuno L. Barbosa‐Morais. (2019). Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome. PLoS Computational Biology. 15(3). e1006832–e1006832. 34 indexed citations

16.

Rodrigues, Tiago, et al.. (2019). Natural product–drug conjugates for modulation of TRPV1-expressing tumors. Bioorganic & Medicinal Chemistry. 27(12). 2531–2536. 8 indexed citations

17.

Almeida, Bernardo P. de, Joana Apolónio, Alexandra Binnie, & Pedro Castelo‐Branco. (2019). Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers. BMC Cancer. 19(1). 219–219. 94 indexed citations

18.

Marteil, Gaëlle, Adán Guerrero, André Filipe Vieira, et al.. (2018). Over-elongation of centrioles in cancer promotes centriole amplification and chromosome missegregation. Nature Communications. 9(1). 1258–1258. 91 indexed citations

19.

Braun, Simon M. G., Monica Enculescu, Mariela Cortés-López, et al.. (2018). Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis. Nature Communications. 9(1). 3315–3315. 43 indexed citations

20.

Almeida, Bernardo P. de, Gaëlle Marteil, Mónica Bettencourt‐Dias, & Nuno L. Barbosa‐Morais. (2017). Discovery of novel mechanisms of centrosome amplification and their therapeutic value in cancer. Porto Biomedical Journal. 2(5). 182–182.

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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