I. Makałowska

发表

Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

Kanako O. Koyanagi, Michael A. Thomas, H. Mewes, 2004, PLoS Biology.

SLC24A5, a Putative Cation Exchanger, Affects Pigmentation in Zebrafish and Humans

Keith C. Cheng, Izabela Makalowska, Mark D. Shriver, 2005, Science.

Mammalian overlapping genes: the comparative perspective.

Michal Galdzicki, Vamsi Veeramachaneni, Wojciech Makałowski, 2004, Genome research.

Transcriptional interference by small transcripts in proximal promoter regions

J. Brosius, W. Makałowski, I. Makałowska, 2018, Nucleic acids research.

Natural antisense transcripts in diseases: From modes of action to targeted therapies

M. Szcześniak, I. Makałowska, Elżbieta Wanowska, 2018, Wiley interdisciplinary reviews. RNA.

Primate and Rodent Specific Intron Gains and the Origin of Retrogenes with Splice Variants

I. Rogozin, M. Szcześniak, I. Makałowska, 2010, Molecular biology and evolution.

CANTATAdb: A Collection of Plant Long Non-Coding RNAs

M. Szcześniak, I. Makałowska, Wojciech Rosikiewicz, 2015, Plant & cell physiology.

lncRNA-RNA Interactions across the Human Transcriptome

M. Szcześniak, I. Makałowska, 2016, PloS one.

Identification of apple miRNAs and their potential role in fire blight resistance

M. Axtell, M. Szcześniak, I. Makałowska, 2015, Tree Genetics & Genomes.

Rootstock-regulated gene expression patterns associated with fire blight resistance in apple

Izabela Makalowska, Gennaro Fazio, Noemi O. Halbrendt, 2012, BMC Genomics.

miRNEST 2.0: a database of plant and animal microRNAs

Izabela Makalowska, Michal Wojciech Szczesniak, M. Szcześniak, 2013, Nucleic Acids Res..

ERISdb: a database of plant splice sites and splicing signals.

Adam Gudyś, Izabela Makałowska, M. Szcześniak, 2013, Plant & cell physiology.

The human RGL (RalGDS-like) gene: cloning, expression analysis and genomic organization.

K. Klinger, J. Carpten, D. Stephan, 2000, Biochimica et biophysica acta.

Contribution of Transposable Elements to Human Proteins

Tabea G. Kischka, W. Makałowski, I. Makałowska, 2017 .

Birth and death of gene overlaps in vertebrates

Chiao-Feng Lin, I. Makałowska, Krisitina Hernandez, 2007, BMC Evolutionary Biology.

Correction: Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

Kanako O. Koyanagi, Michael A. Thomas, Gopal R. Gopinath, 2004, PLoS biology.

Germline mutations in the ribonuclease L gene in families showing linkage with HPC1

K. Klinger, P. Meltzer, J. Carpten, 2002, Nature Genetics.

Chromosomes and expression mechanisms

W. Makałowski, I. Makałowska, Tyra Wolfsburg, 2000 .

Inter-population Differences in Retrogene Loss and Expression in Humans

A. Polański, S. Deorowicz, I. Makałowska, 2015, PLoS Genetics.

Brief Communication RetrogeneDB—A Database of Animal Retrogenes

I. Makałowska, Joanna Ciomborowska, Michał Kabza, 2014 .

Functional Retrogenes in Animal Genomes

I. Makałowska, M. Kubiak, Joanna Ciomborowska, 2012 .

Plant pathogen culture collections: it takes a village to preserve these resources vital to the advancement of agricultural security and plant pathology.

M. Gahegan, D. Geiser, N. Veeraraghavan, 2006, Phytopathology.

SyntDB: defining orthologues of human long noncoding RNAs across primates

M. Szcześniak, I. Makałowska, Oleksii Bryzghalov, 2019, Nucleic Acids Res..

Computational Biology: Annotated Glossary of Terms

Graziano Pesole, William R. Taylor, M.J.C. Crabbe, 2004 .

Cloning, genomic organization and expression of a putative human transmembrane protein related to the Caenorhabditis elegans M01F1.4 gene.

C. Robbins, I. Makałowska, M. Leyne, 1999, Gene.

Towards a deeper annotation of human lncRNAs.

U. Ohler, M. Szcześniak, I. Makałowska, 2020, Biochimica et biophysica acta. Gene regulatory mechanisms.

Biological functions of natural antisense transcripts.

I. Makałowska, Wojciech Rosikiewicz, Wojciech Rosikiewicz, 2016, Acta biochimica Polonica.

Physical and transcript map of the hereditary prostate cancer region at xq27.

Tanya M. Teslovich, J. Carpten, E. Gillanders, 2002, Genomics.

A 6-Mb high-resolution physical and transcription map encompassing the hereditary prostate cancer 1 (HPC1) region.

G. Landes, J. Carpten, D. Stephan, 2000, Genomics.

Chromosomes and expression mechanisms

W. Makałowski, I. Makałowska, Tyra Wolfsburg, 1996, Current Opinion in Genetics and Development.

Gene Feature Identification

I. Makałowska, 2007 .

The Histone Database

David Landsman, Izabela Makalowska, Kenneth L. Trout, 2002, Nucleic Acids Res..

Cloning, mapping, and expression of a novel brain-specific transcript in the Familial Dysautonomia candidate region on Chromosome 9q31

J. Gusella, C. Robbins, I. Makałowska, 2000, Mammalian Genome.

Tissue-specific expression of a splicing mutation in the IKBKAP gene causes familial dysautonomia.

C Maayan, J. Gusella, C. Robbins, 2001, American journal of human genetics.

FUS controls the processing of snoRNAs into smaller RNA fragments that can regulate gene expression

M. Szcześniak, I. Makałowska, M. Ruepp, 2018, bioRxiv.

“Orphan” Retrogenes in the Human Genome

Damian Szklarczyk, Wojciech Rosikiewicz, Wojciech Makałowski, 2012, Molecular biology and evolution.

Identification of apple miRNAs and their potential role in fire blight resistance

M. Axtell, M. Szcześniak, I. Makałowska, 2015, Tree Genetics & Genomes.

CACP, encoding a secreted proteoglycan, is mutated in camptodactyly-arthropathy-coxa vara-pericarditis syndrome

S. Schwartz, J. Carpten, J. Trent, 1999, Nature Genetics.

GeneMachine: gene prediction and sequence annotation

Andreas D. Baxevanis, Izabela Makalowska, Joseph F. Ryan, 2001, Bioinform..

FUSARIUM-ID v. 1.0: A DNA Sequence Database for Identifying Fusarium

Izabela Makalowska, Ning Zhang, Todd J. Ward, 2004, European Journal of Plant Pathology.

Oncogenes and cell proliferation

T. Wolfsberg, W. Makałowski, I. Makałowska, 1992, Current Opinion in Genetics & Development.

Melanoma mouse model implicates metabotropic glutamate signaling in melanocytic neoplasia

P. Meltzer, P. Pollock, J. Trent, 2003, Nature Genetics.

Long-Term Waterlogging as Factor Contributing to Hypoxia Stress Tolerance Enhancement in Cucumber: Comparative Transcriptome Analysis of Waterlogging Sensitive and Tolerant Accessions

M. Szcześniak, I. Makałowska, Kinga Kęska, 2021, Genes.

Mutant deoxynucleotide carrier is associated with congenital microcephaly

Alejandro A. Schäffer, Richa Agarwala, Izabela Makalowska, 2002, Nature Genetics.

Transposable Elements: Classification, Identification, and Their Use As a Tool For Comparative Genomics.

Valer Gotea, Wojciech Makałowski, Amit Pande, 2019, Methods in molecular biology.

Transposable elements and their identification.

Valer Gotea, Wojciech Makałowski, Amit Pande, 2012, Methods in molecular biology.

Cancer, Retrogenes, and Evolution

I. Makałowska, Klaudia Staszak, 2021, Life.

Complex Analysis of Retroposed Genes’ Contribution to Human Genome, Proteome and Transcriptome

Izabela Makałowska, M. Szcześniak, I. Makałowska, 2020, Genes.

Protein-Coding Genes’ Retrocopies and Their Functions

Izabela Makałowska, I. Makałowska, M. Kubiak, 2017, Viruses.

miRNEST database: an integrative approach in microRNA search and annotation

Sebastian Deorowicz, Izabela Makalowska, Michal Wojciech Szczesniak, 2011, Nucleic Acids Res..

A chromatin-associated splicing isoform of OIP5-AS1 acts in cis to regulate the OIP5 oncogene

M. Szcześniak, I. Makałowska, Elżbieta Wanowska, 2021, RNA biology.

Sequence-non-specific effects generated by various types of RNA interference triggers.

M. Szcześniak, I. Makałowska, W. Krzyzosiak, 2016, Biochimica et biophysica acta.

Comparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This Species

I. Makałowska, K. Smalla, M. Galardini, 2018, Front. Microbiol..

Computational Aspects of Comparative Genomics

W. Makałowski, I. Makałowska, 2004 .

Comparative genomics in the search for conserved long noncoding RNAs

M. Szcześniak, I. Makałowska, Elżbieta Wanowska, 2021, Essays in biochemistry.

lncEvo: automated identification and conservation study of long noncoding RNAs

Izabela Makalowska, Oleksii Bryzghalov, Michal Wojciech Szczesniak, 2021, BMC Bioinformatics.

Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii

Kanako O. Koyanagi, W. Makałowski, Hidemi Watanabe, 2016, Biology Direct.

RetrogeneDB—A Database of Animal Retrogenes

Izabela Makałowska, I. Makałowska, Joanna Ciomborowska, 2014, Molecular biology and evolution.

siRNA release from pri-miRNA scaffolds is controlled by the sequence and structure of RNA.

Izabela Makalowska, Julia Starega-Roslan, Marta Olejniczak, 2016, Biochimica et biophysica acta.

Cloning, mapping, and expression of two novel actin genes, actin-like-7A (ACTL7A) and actin-like-7B (ACTL7B), from the familial dysautonomia candidate region on 9q31.

J. Gusella, C. Robbins, I. Makałowska, 1999, Genomics.

Identification of human tRNA:m5C methyltransferase catalysing intron-dependent m5C formation in the first position of the anticodon of the pre-tRNA(CAA)Leu

Izabela Makałowska, I. Makałowska, Marcin Schmidt, 2006, Nucleic acids research.

GALA, a database for genomic sequence alignments and annotations.

Webb Miller, Izabela Makalowska, Cathy Riemer, 2003, Genome research.

Not So Dead Genes—Retrocopies as Regulators of Their Disease-Related Progenitors and Hosts

I. Makałowska, M. Kubiak, Klaudia Staszak, 2021, Cells.

The Mediating Role of the Gut Microbiota in the Physical Growth of Children

I. Makałowska, A. Szwed, Magdalena Durda-Masny, 2022, Life.

HuntMi: an efficient and taxon-specific approach in pre-miRNA identification

Marek Sikora, Adam Gudys, Izabela Makalowska, 2013, BMC Bioinformatics.

The Functional Meaning of 5′UTR in Protein-Coding Genes

I. Makałowska, Natalia Ryczek, Aneta Łyś, 2023, International journal of molecular sciences.

Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5’ ends

T. Skrzypczak, I. Makałowska, M. Kubiak, 2021, Scientific Reports.

Overlapping genes in vertebrate genomes

Izabela Makalowska, Wojciech Makalowski, Chiao-Feng Lin, 2005, Comput. Biol. Chem..

RetrogeneDB–a database of plant and animal retrocopies

Jan Kosinski, Izabela Makalowska, Wojciech Rosikiewicz, 2017, Database J. Biol. Databases Curation.

Cloning and characterization of a novel gene, SHPRH, encoding a conserved putative protein with SNF2/helicase and PHD-finger domains from the 6q24 region.

J. Trent, M. Galdzicki, C. Robbins, 2003, Genomics.

OverGeneDB: a database of 5′ end protein coding overlapping genes in human and mouse genomes

Yutaka Suzuki, Izabela Makalowska, Wojciech Rosikiewicz, 2017, Nucleic Acids Res..

Comparative analysis of an unusual gene arrangement in the human chromosome 1.

I. Makałowska, 2008, Gene.

Overlapping genes in the human genome

I. Makałowska, 2005 .

Retroposition as a source of antisense long non-coding RNAs with possible regulatory functions.

M. Szcześniak, I. Makałowska, Oleksii Bryzghalov, 2016, Acta biochimica Polonica.

Cloning and characterization of 13 novel transcripts and the human RGS8 gene from the 1q25 region encompassing the hereditary prostate cancer (HPC1) locus.

K. Klinger, G. Landes, J. Carpten, 2001, Genomics.

Application of the Burrows-Wheeler Transform for Searching for Approximate Tandem Repeats

Andrzej Polanski, Izabela Makalowska, Agnieszka Danek, 2012, PRIB.

Isolation and characterization of the human homeobox gene HOX D1

M. Brownstein, C. Robbins, I. Makałowska, 2004, Molecular Biology Reports.

Origin and evolution of the chicken leukocyte receptor complex.

M. Nei, J. Klein, W. Makałowski, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Rootstock-regulated gene expression patterns in apple tree scions

Naomi S. Altman, C. Praul, R. Crassweller, 2009, Tree Genetics & Genomes.

Identification and characterization of mouse Rab32 by mRNA and protein expression analysis.

J. Trent, C. Robbins, I. Makałowska, 2003, Biochimica et biophysica acta.

Genome Evolution

Igor B. Rogozin, Izabela Makalowska, Wojciech Makalowski, 2011, Adv. Bioinformatics.

CANTATAdb 2.0: Expanding the Collection of Plant Long Noncoding RNAs.

M. Szcześniak, I. Makałowska, Oleksii Bryzghalov, 2019, Methods in molecular biology.

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts

Teruyoshi Hishiki, Katsuhiko Murakami, Yoshihiro Kawahara, 2007, Nucleic Acids Res..

Hypermethylation of TRIM59 and KLF14 Influences Cell Death Signaling in Familial Alzheimer's Disease

M. Skrzypczak, K. Ginalski, B. Pepłońska, 2018, Oxidative medicine and cellular longevity.

lncEvo: automated identification and conservation study of long noncoding RNAs

M. Szcześniak, I. Makałowska, Oleksii Bryzghalov, 2021, BMC Bioinform..

Overactive BRCA1 Affects Presenilin 1 in Induced Pluripotent Stem Cell-Derived Neurons in Alzheimer's Disease.

M. Skrzypczak, K. Ginalski, B. Pepłońska, 2018, Journal of Alzheimer's disease : JAD.

Novel functions of a retroposed gene.

I. Makałowska, M. Kubiak, 2023, Trends in genetics : TIG.

Contig map of the Parkinson's disease region on 4q21-q23.

A. Dehejia, M. Polymeropoulos, R. Nussbaum, 1998, DNA Research.

Phytophthora Database: A Forensic Database Supporting the Identification and Monitoring of Phytophthora.

O. K. Ribeiro, D. Geiser, N. Veeraraghavan, 2008, Plant Disease.

Oncogenes and cell proliferation. Web alert.

T. Wolfsberg, W. Makałowski, I. Makałowska, 1998, Current Opinion in Genetics and Development.

Characterization of the mitochondrial genome of Rousettus leschenaulti

S. Sugano, Yutaka Suzuki, W. Makałowski, 2014, Mitochondrial DNA.

Comparative Profiling of miRNAs and Target Gene Identification in Distant-Grafting between Tomato and Lycium (Goji Berry)

A. Laganà, M. Poidinger, I. Makałowska, 2016, Front. Plant Sci..

ChloroplastDB: the Chloroplast Genome Database

Alexander Richter, James Leebens-Mack, Liying Cui, 2005, Nucleic Acids Res..

Novel function of U7 snRNA in the repression of HERV1/LTR12s and lincRNAs in human cells

M. Szcześniak, I. Makałowska, Elżbieta Wanowska, 2023, bioRxiv.

Identification of six novel genes by experimental validation of GeneMachine predicted genes.

Izabela Makalowska, Ping Hu, Andreas D Baxevanis, 2002, Gene.

Inter-population Differences in Retrogene Loss and Expression in Humans

A. Polański, S. Deorowicz, I. Makałowska, 2015, PLoS genetics.

Rootstock-regulated gene expression patterns associated with fire blight resistance in apple

Noemi O. Halbrendt, Naomi S. Altman, C. Praul, 2012, BMC Genomics.

ERISdb: a database of plant splice sites and splicing signals.

M. Szcześniak, I. Makałowska, Michał Kabza, 2013, Plant & cell physiology.

Bioinformatics

W. Makałowski, I. Makałowska, Victoria Shabardina, 2018, eLS.

Retroposition as a source of antisense long non-coding RNAs with possible regulatory functions.

M. Szcześniak, I. Makałowska, Oleksii Bryzghalov, 2016, Acta biochimica Polonica.