Tomasz Gambin

Tomasz Gambin

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SeQuiLa-cov: A fast and scalable library for depth of coverage calculations.

Gigascience 2019 08;8(8)

Institute of Computer Science, Warsaw University of Technology, ul. Nowowiejska 15/19, 00-665 Warsaw, Poland.

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http://dx.doi.org/10.1093/gigascience/giz094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6680061PMC
August 2019

A combined immunodeficiency with severe infections, inflammation, and allergy caused by ARPC1B deficiency.

J Allergy Clin Immunol 2019 Jun 13;143(6):2296-2299. Epub 2019 Feb 13.

Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory AMC, University of Amsterdam, Amsterdam, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.jaci.2019.02.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6677392PMC
June 2019

Comparison of kNN and k-means optimization methods of reference set selection for improved CNV callers performance.

BMC Bioinformatics 2019 May 28;20(1):266. Epub 2019 May 28.

Institute of Computer Science, Warsaw University of Technology, ul. Nowowiejska 15/19, Warsaw, 00-665, Poland.

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http://dx.doi.org/10.1186/s12859-019-2889-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6537193PMC
May 2019

Complex Compound Inheritance of Lethal Lung Developmental Disorders Due to Disruption of the TBX-FGF Pathway.

Am J Hum Genet 2019 02 10;104(2):213-228. Epub 2019 Jan 10.

Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA; Institute of Mother and Child, 01-211 Warsaw, Poland. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00029297183046
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http://dx.doi.org/10.1016/j.ajhg.2018.12.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6369446PMC
February 2019

Familial ataxia, tremor, and dementia in a polish family with a novel mutation in the CCDC88C gene.

Mov Disord 2019 01 6;34(1):142-144. Epub 2018 Nov 6.

Department of Neurology and Epileptology, Centre of Postgraduate Medical Education, Warsaw, Poland.

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http://doi.wiley.com/10.1002/mds.27536
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http://dx.doi.org/10.1002/mds.27536DOI Listing
January 2019

CAV3 mutation in a patient with transient hyperCKemia and myalgia.

Neurol Neurochir Pol 2016 Nov - Dec;50(6):468-473. Epub 2016 Jul 9.

Department of Neurology, Medical University of Warsaw, Warsaw, Poland. Electronic address:

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http://dx.doi.org/10.1016/j.pjnns.2016.06.008DOI Listing
February 2017

An Organismal CNV Mutator Phenotype Restricted to Early Human Development.

Cell 2017 02;168(5):830-842.e7

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2017.01.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5407901PMC
February 2017

Primary immunodeficiency diseases: Genomic approaches delineate heterogeneous Mendelian disorders.

Authors:
Asbjørg Stray-Pedersen Hanne Sørmo Sorte Pubudu Samarakoon Tomasz Gambin Ivan K Chinn Zeynep H Coban Akdemir Hans Christian Erichsen Lisa R Forbes Shen Gu Bo Yuan Shalini N Jhangiani Donna M Muzny Olaug Kristin Rødningen Ying Sheng Sarah K Nicholas Lenora M Noroski Filiz O Seeborg Carla M Davis Debra L Canter Emily M Mace Timothy J Vece Carl E Allen Harshal A Abhyankar Philip M Boone Christine R Beck Wojciech Wiszniewski Børre Fevang Pål Aukrust Geir E Tjønnfjord Tobias Gedde-Dahl Henrik Hjorth-Hansen Ingunn Dybedal Ingvild Nordøy Silje F Jørgensen Tore G Abrahamsen Torstein Øverland Anne Grete Bechensteen Vegard Skogen Liv T N Osnes Mari Ann Kulseth Trine E Prescott Cecilie F Rustad Ketil R Heimdal John W Belmont Nicholas L Rider Javier Chinen Tram N Cao Eric A Smith Maria Soledad Caldirola Liliana Bezrodnik Saul Oswaldo Lugo Reyes Francisco J Espinosa Rosales Nina Denisse Guerrero-Cursaru Luis Alberto Pedroza Cecilia M Poli Jose L Franco Claudia M Trujillo Vargas Juan Carlos Aldave Becerra Nicola Wright Thomas B Issekutz Andrew C Issekutz Jordan Abbott Jason W Caldwell Diana K Bayer Alice Y Chan Alessandro Aiuti Caterina Cancrini Eva Holmberg Christina West Magnus Burstedt Ender Karaca Gözde Yesil Hasibe Artac Yavuz Bayram Mehmed Musa Atik Mohammad K Eldomery Mohammad S Ehlayel Stephen Jolles Berit Flatø Alison A Bertuch I Celine Hanson Victor W Zhang Lee-Jun Wong Jianhong Hu Magdalena Walkiewicz Yaping Yang Christine M Eng Eric Boerwinkle Richard A Gibbs William T Shearer Robert Lyle Jordan S Orange James R Lupski

J Allergy Clin Immunol 2017 01 16;139(1):232-245. Epub 2016 Jul 16.

Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex. Electronic address:

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http://dx.doi.org/10.1016/j.jaci.2016.05.042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5222743PMC
January 2017

Benchmarking distributed data warehouse solutions for storing genomic variant information.

Database (Oxford) 2017 01;2017

Institute of Computer Science, Warsaw University of Technology, Nowowiejska 15/19, Warsaw 00-665, Poland.

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http://dx.doi.org/10.1093/database/bax049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5504537PMC
January 2017

A potential founder variant in in three Norwegian families with warts, molluscum contagiosum, and T-cell dysfunction.

Mol Genet Genomic Med 2016 Nov 17;4(6):604-616. Epub 2016 Sep 17.

Baylor-Hopkins Center for Mendelian Genomics (BHCMG) of the Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas; Norwegian National Unit for Newborn ScreeningDivision of Children and Adolescent MedicineOslo University HospitalOsloNorway.

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http://dx.doi.org/10.1002/mgg3.237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5118205PMC
November 2016

Two male sibs with severe micrognathia and a missense variant in MED12.

Eur J Med Genet 2016 Aug 7;59(8):367-72. Epub 2016 Jun 7.

Baylor-Hopkins Center for Mendelian Genomics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Norwegian National Unit for Newborn Screening, Oslo University Hospital, 0424, Oslo, Norway.

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http://dx.doi.org/10.1016/j.ejmg.2016.06.001DOI Listing
August 2016

PEHO Syndrome May Represent Phenotypic Expansion at the Severe End of the Early-Onset Encephalopathies.

Pediatr Neurol 2016 07 9;60:83-7. Epub 2016 Apr 9.

Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas. Electronic address:

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http://dx.doi.org/10.1016/j.pediatrneurol.2016.03.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5125779PMC
July 2016

Evidence against ZNF469 being causative for keratoconus in Polish patients.

Acta Ophthalmol 2016 May 25;94(3):289-94. Epub 2016 Jan 25.

Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland.

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http://dx.doi.org/10.1111/aos.12968DOI Listing
May 2016

Pathogenetics of alveolar capillary dysplasia with misalignment of pulmonary veins.

Authors:
Przemyslaw Szafranski Tomasz Gambin Avinash V Dharmadhikari Kadir Caner Akdemir Shalini N Jhangiani Jennifer Schuette Nihal Godiwala Svetlana A Yatsenko Jessica Sebastian Suneeta Madan-Khetarpal Urvashi Surti Rosanna G Abellar David A Bateman Ashley L Wilson Melinda H Markham Jill Slamon Fernando Santos-Simarro María Palomares Julián Nevado Pablo Lapunzina Brian Hon-Yin Chung Wai-Lap Wong Yoyo Wing Yiu Chu Gary Tsz Kin Mok Eitan Kerem Joel Reiter Namasivayam Ambalavanan Scott A Anderson David R Kelly Joseph Shieh Taryn C Rosenthal Kristin Scheible Laurie Steiner M Anwar Iqbal Margaret L McKinnon Sara Jane Hamilton Kamilla Schlade-Bartusiak Dawn English Glenda Hendson Elizabeth R Roeder Thomas S DeNapoli Rebecca Okashah Littlejohn Daynna J Wolff Carol L Wagner Alison Yeung David Francis Elizabeth K Fiorino Morris Edelman Joyce Fox Denise A Hayes Sandra Janssens Elfride De Baere Björn Menten Anne Loccufier Lieve Vanwalleghem Philippe Moerman Yves Sznajer Amy S Lay Jennifer L Kussmann Jasneek Chawla Diane J Payton Gael E Phillips Erwin Brosens Dick Tibboel Annelies de Klein Isabelle Maystadt Richard Fisher Neil Sebire Alison Male Maya Chopra Jason Pinner Girvan Malcolm Gregory Peters Susan Arbuckle Melissa Lees Zoe Mead Oliver Quarrell Richard Sayers Martina Owens Charles Shaw-Smith Janet Lioy Eileen McKay Nicole de Leeuw Ilse Feenstra Liesbeth Spruijt Frances Elmslie Timothy Thiruchelvam Carlos A Bacino Claire Langston James R Lupski Partha Sen Edwina Popek Paweł Stankiewicz

Hum Genet 2016 May 12;135(5):569-586. Epub 2016 Apr 12.

Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm. R809, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1007/s00439-016-1655-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5518754PMC
May 2016

Multiallelic Positions in the Human Genome: Challenges for Genetic Analyses.

Hum Mutat 2016 Mar 31;37(3):231-234. Epub 2015 Dec 31.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1002/humu.22944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4752396PMC
March 2016

Hutterite-type cataract maps to chromosome 6p21.32-p21.31, cosegregates with a homozygous mutation in LEMD2, and is associated with sudden cardiac death.

Mol Genet Genomic Med 2016 Jan 14;4(1):77-94. Epub 2015 Nov 14.

Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas; Department of PediatricsBaylor College of MedicineHoustonTexas; Texas Children's HospitalHoustonTexas; Department of OphthalmologyBaylor College of MedicineHoustonTexas; Department of MedicineBaylor College of MedicineHoustonTexas.

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http://dx.doi.org/10.1002/mgg3.181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4707028PMC
January 2016

Social cognition, psychopathological symptoms, and family functioning in a sample of inpatient adolescents using variable-centered and person-centered approaches.

J Adolesc 2015 Dec 7;45:31-43. Epub 2015 Sep 7.

Department of Psychology, University of Houston, 126 Heyne Building, Houston, TX 77204, USA; Menninger Clinic, 12301 S. Main St., Houston, TX 77035-6207, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S01401971150020
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http://dx.doi.org/10.1016/j.adolescence.2015.08.010DOI Listing
December 2015

Genes that Affect Brain Structure and Function Identified by Rare Variant Analyses of Mendelian Neurologic Disease.

Neuron 2015 Nov;88(3):499-513

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S08966273150083
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http://dx.doi.org/10.1016/j.neuron.2015.09.048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824012PMC
November 2015

Secondary findings and carrier test frequencies in a large multiethnic sample.

Genome Med 2015 13;7(1):54. Epub 2015 Jun 13.

The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA ; Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030 USA.

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http://dx.doi.org/10.1186/s13073-015-0171-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4507324PMC
July 2015

Alpha-thalassemia mutations in adana province, southern Turkey: genotype-phenotype correlation.

Indian J Hematol Blood Transfus 2015 Jun 13;31(2):223-8. Epub 2014 Jun 13.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA.

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http://dx.doi.org/10.1007/s12288-014-0406-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4375160PMC
June 2015

Homozygous loss-of-function mutations in SOHLH1 in patients with nonsyndromic hypergonadotropic hypogonadism.

J Clin Endocrinol Metab 2015 May 16;100(5):E808-14. Epub 2015 Mar 16.

Department of Molecular and Human Genetics (Y.B., T.Ga., M.M.A., E.K., D.P., J.R.L.), Baylor College of Medicine, Houston, Texas 77030; Department of Medicine, Division of Medical Genetics (S.G., H.U.G., S.B.P., M.L., T.W., M.-C.K.), University of Washington, Seattle, Washington 98195; Department of Pediatric Endocrinology and Diabetes (T.Gu., Z.A., S.T., A.Be.), Marmara University Hospital, Istanbul, Turkey 34899; Department of Pediatric Endocrinology (A.Ab., E.Bob., A.Bu.), Dokuz Eylül University Faculty of Medicine, Izmir, Turkey 35340; Department of Medical Genetics (G.Y.), Bezmialem University, Istanbul, Turkey 34093; Human Genome Sequencing Center (S.N.J., D.M., E.Boe., R.A.G.), Baylor College of Medicine, Houston, Texas 77030; Human Genetics Center (E.Boe.), University of Texas Health Science Center at Houston, Houston, Texas 77030; Department of Pediatrics (J.R.L.), Baylor College of Medicine, Houston, Texas 77030; and Texas Children's Hospital (J.R.L.), Houston, Texas 77030.

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http://dx.doi.org/10.1210/jc.2015-1150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4422898PMC
May 2015

Complex genomic rearrangements at the PLP1 locus include triplication and quadruplication.

PLoS Genet 2015 Mar 6;11(3):e1005050. Epub 2015 Mar 6.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America; Department of Pediatrics and Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America; Texas Children's Hospital, Houston, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4352052PMC
March 2015

Genome-wide analyses of LINE-LINE-mediated nonallelic homologous recombination.

Nucleic Acids Res 2015 Feb 22;43(4):2188-98. Epub 2015 Jan 22.

Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland Mossakowski Medical Research Centre, Polish Academy of Sciences, 5 Pawińskiego street, 02-106 Warsaw, Poland

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http://dx.doi.org/10.1093/nar/gku1394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344489PMC
February 2015

Whole-exome sequencing identifies homozygous GPR161 mutation in a family with pituitary stalk interruption syndrome.

J Clin Endocrinol Metab 2015 Jan;100(1):E140-7

Department of Molecular and Human Genetics (E.K., D.P., W.-L.C., Y.B., T.G., M.W., M.M.A., R.A.G., J.R.L.), Baylor College of Medicine, Houston, Texas 77030; Department of Radiology (R.B.), Duzce University Medical School, 81620 Duzce, Turkey; Department of Medical Biology (K.O.Y.), Kahramanmaras Sutcu Imam University, Medical School, 46100 Kahramanmaras, Turkey; Department of Pediatric Endocrinology (I.A., S.B.), Duzce University Medical School, 81620 Duzce, Turkey; Center for Human Genetic Research (S.E.), Massachussetts General Hospital, Boston, Massachussetts 02114; Department of Radiology (A.B.), Duzce Ataturk Community Hospital, 81620 Duzce, Turkey; Department of Medical Biology and Genetics (E.Y.), Duzce University Institute of Health Science, 81620 Duzce, Turkey; Human Genome Sequencing Center (S.N.J., D.M.M., R.A.G.), Baylor College of Medicine, Houston Texas 77030; Department of Pediatrics (J.R.L.), Baylor College of Medicine, Houston, Texas 77030; and Texas Children's Hospital (J.R.L.), Houston, Texas 77030.

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http://dx.doi.org/10.1210/jc.2014-1984DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4283017PMC
January 2015

Whole-exome sequencing links TMCO1 defect syndrome with cerebro-facio-thoracic dysplasia.

Eur J Hum Genet 2014 Sep 15;22(9):1145-8. Epub 2014 Jan 15.

1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [2] Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA [3] Texas Children's Hospital, Houston, TX, USA.

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http://dx.doi.org/10.1038/ejhg.2013.291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4135405PMC
September 2014

Human endogenous retroviral elements promote genome instability via non-allelic homologous recombination.

BMC Biol 2014 Sep 23;12:74. Epub 2014 Sep 23.

Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Rm ABBR-R809, Houston, TX, USA.

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http://dx.doi.org/10.1186/s12915-014-0074-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4195946PMC
September 2014

A drosophila genetic resource of mutants to study mechanisms underlying human genetic diseases.

Cell 2014 Sep;159(1):200-214

Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA; Howard Hughes Medical Institute, Houston, TX 77030, USA; Program in Structural and Computational Biology and Molecular Biophysics, BCM, Houston, TX 77030, USA; Department of Neuroscience, BCM, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.09.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298142PMC
September 2014

Functional performance of aCGH design for clinical cytogenetics.

Comput Biol Med 2013 Jul 16;43(6):775-85. Epub 2013 Mar 16.

Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland.

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http://dx.doi.org/10.1016/j.compbiomed.2013.02.008DOI Listing
July 2013

Multiple samples aCGH analysis for rare CNVs detection.

J Clin Bioinforma 2013 Jun 11;3(1):12. Epub 2013 Jun 11.

Institute of Informatics, University of Warsaw, Warsaw, Poland.

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http://dx.doi.org/10.1186/2043-9113-3-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691624PMC
June 2013

Inverted low-copy repeats and genome instability--a genome-wide analysis.

Hum Mutat 2013 Jan 11;34(1):210-20. Epub 2012 Oct 11.

Institute of Informatics, University of Warsaw, Warsaw, Poland.

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http://dx.doi.org/10.1002/humu.22217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738003PMC
January 2013

Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula.

Gene 2009 Dec 17;448(2):214-20. Epub 2009 Jun 17.

Department of Genetics, Plant Breeding and Seed Science, University of Agriculture in Krakow, Al. 29 Listopada 54, 31-425 Krakow, Poland.

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http://dx.doi.org/10.1016/j.gene.2009.06.004DOI Listing
December 2009

A new classification method using array Comparative Genome Hybridization data, based on the concept of Limited Jumping Emerging Patterns.

BMC Bioinformatics 2009 Jan 30;10 Suppl 1:S64. Epub 2009 Jan 30.

Faculty of Electronics and Information Technology of Warsaw University of Technology, Institute of Computer Science, Nowowiejska 15/19, Warsaw, 00-665, Poland.

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http://dx.doi.org/10.1186/1471-2105-10-S1-S64DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648754PMC
January 2009

Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula.

BMC Genomics 2007 Nov 9;8:409. Epub 2007 Nov 9.

Department of Genetics, Plant Breeding and Seed Science, Agricultural University of Krakow, Al, 29 Listopada 54, 31-425 Krakow, Poland.

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http://dx.doi.org/10.1186/1471-2164-8-409DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2213677PMC
November 2007