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1

Tulipa gesneriana and Lilium longiflorum PEBP Genes and Their Putative Roles in Flowering Time Control

Leeggangers, Hendrika ACF, Rosilio-Brami, Tamar, Bigas-Nadal, Judit, Rubin, Noam, van Dijk, Aalt DJ, Nunez de Caceres Gonzalez, Francisco F, Saadon-Shitrit, Shani, Nijveen, Harm, Hilhorst, Henk WM, Im

Journal:

Plant and Cell Physiology

Year:

2018

Language:

english

File:

PDF, 2.29 MB

english, 2018

2

Understanding and identifying amino acid repeats

Luo, H., Nijveen, H.

Journal:

Briefings in Bioinformatics

Year:

2014

Language:

english

File:

PDF, 156 KB

english, 2014

3

A footprint of desiccation tolerance in the genome of Xerophyta viscosa

Costa, Maria-Cecília D., Artur, Mariana A. S., Maia, Julio, Jonkheer, Eef, Derks, Martijn F. L., Nijveen, Harm, Williams, Brett, Mundree, Sagadevan G., Jiménez-Gómez, José M., Hesselink, Thamara, Schi

Journal:

Year:

2017

Language:

english

File:

PDF, 5.88 MB

english, 2017

4

Detection of QTLs for genotype Ã environment interactions in tomato seeds and seedlings

Geshnizjani, Nafiseh, Snoek, Basten L., Willems, Leo A.J., Rienstra, Juriaan A., Nijveen, Harm, Hilhorst, Henk W.M., Ligterink, Wilco

Journal:

Plant, Cell & Environment

Year:

2020

File:

PDF, 5.17 MB

2020

5

Network Analysis Prioritizes DEWAX and ICE1 as the Candidate Genes for Major eQTL Hotspots in Seed Germination of Arabidopsis thaliana

Hartanto, Margi, Joosen, Ronny V. L., Snoek, Basten L., Willems, Leo A. J., Sterken, Mark G., de Ridder, Dick, Hilhorst, Henk W. M., Ligterink, Wilco, Nijveen, Harm

Journal:

G3 Genes|Genome|Genetics

Year:

2020

File:

PDF, 3.02 MB

2020

6

HSPVdb—the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands

Harm Nijveen, Michel G. D. Kester, Chopie Hassan, Aurélie Viars, Arnoud H. de Ru, Machiel de Jager, J. H. Fred Falkenburg, Jack A. M. Leunissen, Peter A. van Veelen

Journal:

Year:

2011

Language:

english

File:

PDF, 1.63 MB

english, 2011

7

Constraint-based probabilistic learning of metabolic pathways from tomato volatiles

Anand K. Gavai, Yury Tikunov, Remco Ursem, Arnaud Bovy, Fred van Eeuwijk, Harm Nijveen, Peter J. F. Lucas, Jack A. M. Leunissen

Journal:

Year:

2009

Language:

english

File:

PDF, 566 KB

english, 2009

8

Mutations in the RET proto-oncogene in sporadic medullary thyroid carcinomas

Tineke Stelwagen, Robert M.W. Hofstra, Rein P. Stulp, Harm Nijveen, Giovanni Romeo, Rudy M. Landsvater, Cornelis J.M. Lips, Charles H.C.M. Buys

Journal:

Cancer Genetics and Cytogenetics

Year:

1994

Language:

english

File:

PDF, 92 KB

english, 1994

9

Regulatory Elements in the Rat βB2-crystallin Promoter

Linda Doerwald, Harm Nijveen, Azem Civil, Siebe T van Genesen, Nicolette H Lubsen

Journal:

Experimental Eye Research

Year:

2001

Language:

english

File:

PDF, 227 KB

english, 2001

10

Benchmarking protein classification algorithms via supervised cross-validation

Attila Kertész-Farkas, Somdutta Dhir, Paolo Sonego, Mircea Pacurar, Sergiu Netoteia, Harm Nijveen, Arnold Kuzniar, Jack A.M. Leunissen, András Kocsor, Sándor Pongor

Journal:

Journal of Biochemical and Biophysical Methods

Year:

2008

Language:

english

File:

PDF, 301 KB

english, 2008

11

Birth, Death, and Diversification of Mobile Promoters in Prokaryotes

van Passel, M. W. J., Nijveen, H., Wahl, L. M.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.42 MB

english, 2014

12

Primer3Plus, an enhanced web interface to Primer3

Untergasser, A., Nijveen, H., Rao, X., Bisseling, T., Geurts, R., Leunissen, J. A.M.

Journal:

Nucleic Acids Research

Year:

2007

Language:

english

File:

PDF, 2.48 MB

english, 2007

13

Interaction between parental environment and genotype affects plant and seed performance in Arabidopsis

He, H., de Souza Vidigal, D., Snoek, L. B., Schnabel, S., Nijveen, H., Hilhorst, H., Bentsink, L.

Journal:

Journal of Experimental Botany

Year:

2014

Language:

english

File:

PDF, 2.71 MB

english, 2014

14

Discovery of T Cell Epitopes Implementing HLA-Peptidomics into a Reverse Immunology Approach

Hombrink, P., Hassan, C., Kester, M. G. D., de Ru, A. H., van Bergen, C. A. M., Nijveen, H., Drijfhout, J. W., Falkenburg, J. H. F., Heemskerk, M. H. M., van Veelen, P. A.

Journal:

The Journal of Immunology

Year:

2013

Language:

english

File:

PDF, 1.38 MB

english, 2013

15

ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins

Luo, H., Lin, K., David, A., Nijveen, H., Leunissen, J. A. M.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 3.32 MB

english, 2012

16

Promoter propagation in prokaryotes

Matus-Garcia, M., Nijveen, H., van Passel, M. W. J.

Journal:

Nucleic Acids Research

Year:

2012

Language:

english

File:

PDF, 5.12 MB

english, 2012

17

A gene co-expression network predicts functional genes controlling the re-establishment of desiccation tolerance in germinatedArabidopsis thalianaseeds

Costa, Maria Cecília D., Righetti, Karima, Nijveen, Harm, Yazdanpanah, Farzaneh, Ligterink, Wilco, Buitink, Julia, Hilhorst, Henk W. M.

Journal:

Year:

2015

Language:

english

File:

PDF, 2.12 MB

english, 2015

18

Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks

Kuzniar, A., Dhir, S., Nijveen, H., Pongor, S., Leunissen, J. A. M.

Journal:

Year:

2010

Language:

english

File:

PDF, 2.27 MB

english, 2010

19

QualitySNPng: a user-friendly SNP detection and visualization tool

Nijveen, H., van Kaauwen, M., Esselink, D. G., Hoegen, B., Vosman, B.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 1.84 MB

english, 2013

20

Obituary: In memory of Jack Leunissen

Luo, J., Nijveen, H., Attwood, T., Judge, D., Pongor, S., Landsman, D., Bishop, M.

Journal:

Briefings in Bioinformatics

Year:

2013

Language:

english

File:

PDF, 39 KB

english, 2013

21

The Human Leukocyte Antigen-presented Ligandome of B Lymphocytes

Hassan, C., Kester, M. G. D., de Ru, A. H., Hombrink, P., Drijfhout, J. W., Nijveen, H., Leunissen, J. A. M., Heemskerk, M. H. M., Falkenburg, J. H. F., van Veelen, P. A.

Journal:

Molecular & Cellular Proteomics

Year:

2013

Language:

english

File:

PDF, 2.08 MB

english, 2013

22

ProGMap: an integrated annotation resource for protein orthology

Kuzniar, A., Lin, K., He, Y., Nijveen, H., Pongor, S., Leunissen, J. A. M.

Journal:

Nucleic Acids Research

Year:

2009

Language:

english

File:

PDF, 4.89 MB

english, 2009

23

Beyond genomic variation - comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage

Lin, Ke, Zhang, Ningwen, Severing, Edouard I, Nijveen, Harm, Cheng, Feng, Visser, Richard GF, Wang, Xiaowu, de Ridder, Dick, Bonnema, Guusje

Journal:

Year:

2014

Language:

english

File:

PDF, 2.13 MB

english, 2014

24

Promoter reuse in prokaryotes

Nijveen, Harm, Matus-Garcia, Mariana, van Passel, Mark Willem John

Journal:

Mobile Genetic Elements

Year:

2012

Language:

english

File:

PDF, 156 KB

english, 2012

25

TreeDomViewer: a tool for the visualization of phylogeny and protein domain structure

Alako, B. T. F., Rainey, D., Nijveen, H., Leunissen, J. A. M.

Journal:

Nucleic Acids Research

Year:

2006

Language:

english

File:

PDF, 577 KB

english, 2006

26

Effects of Parental Temperature and Nitrate on Seed Performance are Reflected by Partly Overlapping Genetic and Metabolic Pathways

He, Hanzi, Willems, Leo, Batushansky, Albert, Fait, Aaron, Hanson, Johannes, Nijveen, Harm, Hilhorst, Henk W. M., Bentsink, Leónie

Journal:

Plant and Cell Physiology

Year:

2016

Language:

english

File:

PDF, 1.62 MB

english, 2016

27

Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks

Kuzniar, Arnold, Dhir, Somdutta, Nijveen, Harm, Pongor, Sándor, Leunissen, Jack A.M.

Journal:

Year:

2015

Language:

english

File:

PDF, 39 KB

english, 2015

28

Time-series analysis of the transcriptome of the re-establishment of desiccation tolerance by ABA in germinated Arabidopsis thaliana seeds

Costa, Maria Cecília D., Nijveen, Harm, Ligterink, Wilco, Buitink, Julia, Hilhorst, Henk W.M.

Journal:

Year:

2015

File:

PDF, 252 KB

2015

29

Time-series analysis of the transcriptome of the re-establishment of desiccation tolerance by ABA in germinated Arabidopsis thaliana seeds

Costa, Maria Cecília D., Nijveen, Harm, Ligterink, Wilco, Buitink, Julia, Hilhorst, Henk W.M.

Journal:

Year:

2015

Language:

english

File:

PDF, 252 KB

english, 2015

30

Propagation of errors in citation networks: a study involving the entire citation network of a widely cited paper published in, and later retracted from, the journal Nature

van der Vet, Paul E., Nijveen, Harm

Journal:

Research Integrity and Peer Review

Year:

2016

Language:

english

File:

PDF, 1.85 MB

english, 2016

31

Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856

Thompson, O. A., Snoek, L. B., Nijveen, H., Sterken, M. G., Volkers, R. J. M., Brenchley, R., van't Hof, A., Bevers, R. P. J., Cossins, A. R., Yanai, I., Hajnal, A., Schmid, T., Perkins, J. D., Spence

Journal:

Year:

2015

Language:

english

File:

PDF, 5.75 MB

english, 2015

32

Elucidating and mining theTulipaandLiliumtranscriptomes

Moreno-Pachon, Natalia M., Leeggangers, Hendrika A. C. F., Nijveen, Harm, Severing, Edouard, Hilhorst, Henk, Immink, Richard G. H.

Journal:

Plant Molecular Biology

Year:

2016

Language:

english

File:

PDF, 4.32 MB

english, 2016

33

AraQTL - Workbench and Archive for systems genetics in Arabidopsis thaliana

Nijveen, Harm, Ligterink, Wilco, Keurentjes, Joost J.B., Loudet, Olivier, Long, Jiao, Sterken, Mark G., Prins, Pjotr, Hilhorst, Henk W., de Ridder, Dick, Kammenga, Jan E., Snoek, Basten L.

Journal:

The Plant Journal

Year:

2016

Language:

english

File:

PDF, 635 KB

english, 2016

34

Molecular Regulation of Temperature-Dependent Floral Induction in Tulipa gesneriana

Leeggangers, Hendrika A.C.F., Nijveen, Harm, Bigas, Judit Nadal, Hilhorst, Henk W.M., Immink, Richard G.H.

Journal:

PLANT PHYSIOLOGY

Year:

2017

Language:

english

File:

PDF, 1.23 MB

english, 2017

35

Fire Usage and Ancient Hominin Detoxification Genes: Protective Ancestral Variants Dominate While Additional Derived Risk Variants Appear in Modern Humans

Aarts, Jac M. M. J. G., Alink, Gerrit M., Scherjon, Fulco, MacDonald, Katharine, Smith, Alison C., Nijveen, Harm, Roebroeks, Wil, Petraglia, Michael D.

Journal:

Year:

2016

Language:

english

File:

PDF, 354 KB

english, 2016

36

Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population

Serin, Elise A. R., Snoek, L. B., Nijveen, Harm, Willems, Leo A. J., Jiménez-Gómez, Jose M., Hilhorst, Henk W. M., Ligterink, Wilco

Journal:

Frontiers in Genetics

Year:

2017

Language:

english

File:

PDF, 4.60 MB

english, 2017

37

Learning from Co-expression Networks: Possibilities and Challenges

Serin, Elise A. R., Nijveen, Harm, Hilhorst, Henk W. M., Ligterink, Wilco

Journal:

Frontiers in Plant Science

Year:

2016

Language:

english

File:

PDF, 1.18 MB

english, 2016

38

A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters

Witjes, Lotte, Kooke, Rik, van der Hooft, Justin J. J., de Vos, Ric C. H., Keurentjes, Joost J. B., Medema, Marnix H., Nijveen, Harm

Journal:

BMC Research Notes

Year:

2019

Language:

english

File:

PDF, 761 KB

english, 2019

39

Dormancy cycling: Translation related transcripts are the main difference between dormant and non‐dormant seeds in the field

Buijs, Gonda, Vogelzang, Afke, Nijveen, Harm, Bentsink, Leónie

Journal:

The Plant Journal

Year:

2019

File:

PDF, 15.59 MB

2019

40

WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans

Snoek, Basten L, Sterken, Mark G, Hartanto, Margi, van Zuilichem, Albert-Jan, Kammenga, Jan E, de Ridder, Dick, Nijveen, Harm

Journal:

Year:

2020

File:

PDF, 1.04 MB

2020