Publications

The following publications provide scientific background on, and new results arising from, the Recon4IMD project.

1.

Quinodoz, M., Rodenburg, K., Cvackova, Z., Kaminska, K., de Bruijn, S.E., Iglesias-Romero, A.B., Boonen, E.G.M., Ullah, M., Zomer, N., Folcher, M., Bijon, J., Holtes, L.K., Tsang, S.H., Corradi, Z., Freund, K.B., Shliaga, S., Panneman, D.M., Hitti-Malin, R.J., Ali, M., AlTalbishi, A., Andréasson, S., Ansari, G., Arno, G., Astuti, G.D.N., Ayuso, C., Ayyagari, R., Banfi, S., Banin, E., Barboni, M.T.S., Bauwens, M., Ben-Yosef, T., Birch, D.G., Biswas, P., Blanco-Kelly, F., Bocquet, B., Boon, C.J.F., Branham, K., Britten-Jones, A.C., Bujakowska, K.M., Cadena, E.L., Calzetti, G., Cancellieri, F., Cattaneo, L., Charbel Issa, P., Chadderton, N., Coutinho-Santos, L., Daiger, S.P., De Baere, E., de la Cerda, B., De Roach, J.N., De Zaeytijd, J., Derks, R., Dhaenens, C-M., Dudakova, L., Duncan, J.L., Farrar, G.J., Feltgen, N., Fernández-Caballero, L., Ferraz Sallum, J.M., Gana, S., Garanto, A., Gardner, J.C., Gilissen, C., Goto, K., González-Duarte, R., Griffiths-Jones, S., Haack, T.B., Haer-Wigman, L., Hardcastle, A.J., Hayashi, T., Héon, E., Hoischen, A., Holtan, J.P., Hoyng, C.B., Ibanez IV, M.B.B., Inglehearn, C.F., Iwata, T., Jones, K., Kalatzis, V., Kamakari, S., Karali, M., Kellner, U., Knézy, K., Klaver, C.C.W., Koenekoop, R.K., Kohl, S., Kominami, T., Kühlewein, L., Lamey, T.M., Leroy, B.P., Martín-Gutiérrez, M.P., Martins, N., Mauring, L., Leibu, R., Lin, S., Liskova, P., Lopez, I., López-Rodríguez, V.R.d.J., Mahroo, O.A., Manes, G., McKibbin, M., McLaren, T.L., Meunier, I., Michaelides, M., Millán, J.M., Mizobuchi, K., Mukherjee, R., Nagy, Z.Z., Neveling, K., Ołdak, M., Oorsprong, M., Pan, Y., Papachristou, A., Percesepe, A., Pfau, M., Pierce, E.A., Place, E., Ramesar, R., Rasquin, F.A., Rice, G.I., Roberts, L., Rodríguez-Hidalgo, M., Ruiz-Eddera, J., Sabir, A.H., Sajiki, A.F., Sánchez-Barbero, A.I., Sarma, A.S., Sangermano, R., Santos, C.M., Scarpato, M., Scholl, H.P.N., Sharon, D., Signorini, S.G., Simonelli, F., Sousa, A.B., Stefaniotou, M., Stingl, K., Suga, A., Sullivan, L.S., Szabó, V., Szaflik, J.P., Taurina, G., Toomes, C., Tran, V.H., Tsilimbaris, M.K., Tsoka, P., Vaclavik, V., Vajter, M., Valeina, S., Valente, E.M., Valentine, C., Valero, R., van Aerschot, J., van den Born, L.I., Webster, A.R., Whelan, L., Wissinger, B., Yioti, G.G., Yoshitake, K., Zenteno, J.C., Zeuli, R., Zuleger, T., Landau, C., Jacob, A.I., Cremers, F.P.M., Lee, W., Ellingford, J.M., Stanek, D., Rivolta, C., & Roosing, S. (2025).
De novo and inherited dominant variants in U4 and U6 snRNAs cause retinitis pigmentosa.
Preprint at Cold Spring Harbor Laboratory.
https://doi.org/10.1101/2025.01.06.24317169

2.

Martin del Pico, E., Psomopoulos, F.E., Portell-Silva, L., Alves, R., Moretti, S., Sufi, S., Bouhraoua, A.K.E., Steinberg, D., Farrell, G., Tsontaki, M., Andrade Buono, R., Beier, S., Garijo, D., Fernández González, J.M., Steeghs-Turchina, M., Anton, M., & Palmblad, M. (2025).

Software Quality Indicators: extraction, categorisation and recommendations from canonical sources.
BioHackrXiv Preprint.
https://doi.org/10.37044/osf.io/etp3g_v1

3.

Laugwitz, L., Buchert, R., Olguín, P., Estiar, M.A., Atanasova, M., Marques Jr., W., Enssle, J., Marsden, B., Avilés, J., González-Gutiérrez, A., Candia, N., Fabiano, M., Morlot, S., Peralta, S., Groh, A., Schillinger, C., Kuehn, C., Sofan, L., Sturm, M., Bender, B., Tomaselli, P.J., Diebold, U., Mueller, A.J., Spranger, S., Fuchs, M., Freua, F., Souto Melo, U., Mattas, L., Ashtiani, S., Suchowersky, O., Groeschel, S., Rouleau, G.A., Yosovich, K., Michelson, M., Leibovitz, Z., Bilal, M., Uctepe, E., Yesilyurt, A., Ozdogan, O., Celik, T., Krägeloh-Mann, I., Riess, O., Rosewich, H., Umair, M., Lev, D., Zuchner, S., Schweizer, U., Lynch, D.S., Gan-Or, Z., & Haack, T.B. (2025).
EEFSEC deficiency: A selenopathy with early-onset neurodegeneration.
The American Journal of Human Genetics, 112, 168–180.
https://doi.org/10.1016/j.ajhg.2024.12.001

4.

Buchert, R., Burkhalter, M.D., Huridou, C., Sofan, L., Roser, T., Cremer, K., Alvi, J.R., Efthymiou, S., Froukh, T., Gulieva, S., Guliyeva, U., Hamdallah, M., Holder-Espinasse, M., Kaiyrzhanov, R., Klingler, D., Koko, M., Matthies, L., Park, J., Sturm, M., Velic, A., Spranger, S., Sultan, T., Engels, H., Lerche, H., Houlden, H., Pagnamenta, A.T., Borggraefe, I., Weber, Y., Bonnen, P.E., Maroofian, R., Riess, O., Weber, J.J., Philipp, M., & Haack, T.B. (2025).
Bi-allelic KICS2 mutations impair KICSTOR complex-mediated mTORC1 regulation, causing intellectual disability and epilepsy.
The American Journal of Human Genetics, 112, 374–393.
https://doi.org/10.1016/j.ajhg.2024.12.019

5.

Lessel, I., Baresic, A., Chinn, I.K., May, J., Goenka, A., Chandler, K.E., Posey, J.E., Afenjar, A., Averdunk, L., Bedeschi, M.F., Besnard, T., Brager, R., Brick, L., Brugger, M., Brunet, T., Byrne, S., de la Calle-Martín, O., Capra, V., Cardenas, P., Chappé, C., Chong, H.J., Cogne, B., Conboy, E., Cope, H., Courtin, T., Deb, W., Dilena, R., Dubourg, C., Elgizouli, M., Fernandes, E., Fitzgerald, K.K., Gangi, S., George-Abraham, J.K., Gucsavas-Calikoglu, M., Haack, T.B., Hadonou, M., Hanker, B., Hüning, I., Iascone, M., Isidor, B., Järvelä, I., Jin, J.J., Jorge, A.A.L., Josifova, D., Kalinauskiene, R., Kamsteeg, E.-J., Keren, B., Kessler, E., Kölbel, H., Kozenko, M., Kubisch, C., Kuechler, A., Leal, S.M., Leppälä, J., Luu, S.M., Lyon, G.J., Madan-Khetarpal, S., Mancardi, M., Marchi, E., Mehta, L., Menendez, B., Morel, C.F., Moyer Harasink, S., Nevay, D.-L., Nigro, V., Odent, S., Oegema, R., Pappas, J., Pastore, M.T., Perilla-Young, Y., Platzer, K., Powell-Hamilton, N., Rabin, R., Rekab, A., Rezende, R.C., Robert, L., Romano, F., Scala, M., Poths, K., Schrauwen, I., Sebastian, J., Short, J., Sidlow, R., Sullivan, J., Szakszon, K., Tan, Q.K.G., Undiagnosed Diseases Network, Wagner, M., Wieczorek, D., Yuan, B., Maeding, N., Strunk, D., Begtrup, A., Banka, S., Lupski, J.R., Tolosa, E., & Lessel, D. (2025).
DNA-binding affinity and specificity determine the phenotypic diversity in BCL11B-related disorders.
The American Journal of Human Genetics, 112, 394–413.
https://doi.org/10.1016/j.ajhg.2024.12.012

6.

Laurie, S., Steyaert, W., de Boer, E., Polavarapu, K., Schuermans, N., Sommer, A.K., Demidov, G., Ellwanger, K., Paramonov, I., Thomas, C., Aretz, S., Baets, J., Benetti, E., Bullich, G., Chinnery, P.F., Clayton-Smith, J., Cohen, E., Danis, D., de Sainte Agathe, J.-M., Denommé-Pichon, A.-S., Diaz-Manera, J., Efthymiou, S., Faivre, L., Fernandez-Callejo, M., Freeberg, M., Garcia-Pelaez, J., Guillot-Noel, L., Haack, T.B., Hanna, M., Hengel, H., Horvath, R., Houlden, H., Jackson, A., Johansson, L., Johari, M., Kamsteeg, E.-J., Kellner, M., Kleefstra, T., Lacombe, D., Lochmüller, H., López-Martín, E., Macaya, A., Marcé-Grau, A., Maver, A., Morsy, H., Muntoni, F., Musacchia, F., Nelson, I., Nigro, V., Olimpio, C., Oliveira, C., Paulasová Schwabová, J., Pauly, M.G., Peterlin, B., Peters, S., Pfundt, R., Piluso, G., Piscia, D., Posada, M., Reich, S., Renieri, A., Ryba, L., Šablauskas, K., Savarese, M., Schöls, L., Schütz, L., Steinke-Lange, V., Stevanin, G., Straub, V., Sturm, M., Swertz, M.A., Tartaglia, M., te Paske, I.B.A.W., Thompson, R., Torella, A., Trainor, C., Udd, B., Van de Vondel, L., van de Warrenburg, B., van Reeuwijk, J., Vandrovcova, J., Vitobello, A., Vos, J., Vyhnálková, E., Wijngaard, R., Wilke, C., William, D., Xu, J., Yaldiz, B., Zalatnai, L., Zurek, B., Solve-RD DITF-GENTURIS, Solve-RD DITF-ITHACA, Solve-RD DITF-EURO-NMD, Solve-RD DITF-RND, Solve-RD consortium, Brookes, A.J., Evangelista, T., Gilissen, C., Graessner, H., Hoogerbrugge, N., Ossowski, S., Riess, O., Schüle, R., Synofzik, M., Verloes, A., Matalonga, L., Brunner, H.G., Lohmann, K., de Voer, R.M., Töpf, A., Vissers, L.E.L.M., Beltran, S., & Hoischen, A. (2025).
Genomic reanalysis of a pan-European rare-disease resource yields new diagnoses.

Nature Medicine, 31, 478–489.
https://doi.org/10.1038/s41591-024-03420-w

7.

Nava, C., Cogne, B., Santini, A., Leitão, E., Lecoquierre, F., Chen, Y., Stenton, S.L., Besnard, T., Heide, S., Baer, S., Jakhar, A., Neuser, S., Keren, B., Faudet, A., Forlani, S., Faoucher, M., Uguen, K., Platzer, K., Afenjar, A., Alessandri, J.-L., Andres, S., Angelini, C., Aral, B., Arveiler, B., Attie-Bitach, T., Aubert Mucca, M., Banneau, G., Barakat, T.S., Barcia, G., Baulac, S., Beneteau, C., Benkerdou, F., Bernard, V., Bézieau, S., Bonneau, D., Bonnet-Dupeyron, M.-N., Boussion, S., Boute, O., Brischoux-Boucher, E., Bryen, S.J., Buratti, J., Busa, T., Caliebe, A., Capri, Y., Cassinari, K., Caumes, R., Cenni, C., Chambon, P., Charles, P., Christodoulou, J., Colson, C., Conrad, S., Cospain, A., Coursimault, J., Courtin, T., Couse, M., Coutton, C., Creveaux, I., D’Gama, A.M., Dauriat, B., de Sainte Agathe, J.-M., Del Gobbo, G., Delahaye-Duriez, A., Delanne, J., Denommé-Pichon, A.-S., Dieux-Coeslier, A., Do Souto Ferreira, L., Doco-Fenzy, M., Drukewitz, S., Duboc, V., Dubourg, C., Duffourd, Y., Dyment, D., El Chehadeh, S., Elmaleh, M., Faivre, L., Fennelly, S., Fischer, H., Fradin, M., Galludec Vaillant, C., Ganne, B., Ghoumid, J., Goel, H., Gokce-Samar, Z., Goldenberg, A., Gonfreville Robert, R., Gorokhova, S., Goujon, L., Granier, V., Gras, M., Greally, J.M., Greiten, B., Gueguen, P., Guerrot, A.-M., Guha, S., Guimier, A., Haack, T.B., Hadj Abdallah, H., Halleb, Y., Harbuz, R., Harris, M., Hentschel, J., Héron, B., Hitz, M.-P., Innes, A.M., Jadas, V., Januel, L., Jean-Marçais, N., Jobanputra, V., Jobic, F., Jornea, L., Jost, C., Julia, S., Kaiser, F.J., Kaschta, D., Kaya, S., Ketteler, P., Khadija, B., Kilpert, F., Knopp, C., Kraft, F., Krey, I., Lackmy, M., Laffargue, F., Lambert, L., Lamont, R., Laugel, V., Laurie, S., Lauzon, J.L., Lebreton, L., Lebrun, M., Legendre, M., Leguern, E., Lehalle, D., Lejeune, E., Lesca, G., Lesieur-Sebellin, M., Levy, J., Linglart, A., Lyonnet, S., Lüthy, K., Ma, A.S., Mach, C., Mandel, J.-L., Mansour-Hendili, L., Marcadier, J., Marin, V., Margot, H., Marquet, V., May, A., Mayr, J.A., Meridda, C., Michaud, V., Michot, C., Nadeau, G., Naudion, S., Nguyen, L., Nizon, M., Nowak, F., Odent, S., Olin, V., Osei-Owusu, I.A., Osmond, M., Õunap, K., Pasquier, L., Passemard, S., Pauly, M., Patat, O., Pensec, M., Perrin-Sabourin, L., Petit, F., Philippe, C., Planes, M., Poduri, A., Poirsier, C., Pouzet, A., Prince, B., Prouteau, C., Pujol, A., Racine, C., Rama, M., Ramond, F., Ranguin, K., Raway, M., Reis, A., Renaud, M., Revencu, N., Richard, A.-C., Riera-Navarro, L., Rius, R., Rodriguez, D., Rodriguez-Palmero, A., Rondeau, S., Roser-Unruh, A., Rougeot Jung, C., Safraou, H., Satre, V., Saugier-Veber, P., Sauvestre, C., Schaefer, E., Shao, W., Schanze, I., Schlump, J.-U., Schlüter Martin, A., Schluth-Bolard, C., Schuhmann, S., Schröder, C., Sebastin, M., Sigaudy, S., Spielmann, M., Spodenkiewicz, M., St Clair, L., Steffann, J., Stoeva, R., Surowy, H., Tarnopolsky, M.A., Todosi, C., Toutain, A., Tran Mau-Them, F., Unterlauft, A., Van-Gils, J., Vanlerberghe, C., Vasileiou, G., Vera, G., Verdel, A., Verloes, A., Vial, Y., Vignal, C., Vincent, M., Vincent-Delorme, C., Vincent-Devulder, A., Vitobello, A., Weber, S., Willems, M., Zaafrane-Khachnaoui, K., Zacher, P., Zeltner, L., Ziegler, A., Galej, W.P., Dollfus, H., Thauvin, C., Boycott, K.M., Marijon, P., Lermine, A., Malan, V., Rio, M., Kuechler, A., Isidor, B., Drunat, S., Smol, T., Chatron, N., Piton, A., Nicolas, G., Wagner, M., Abou Jamra, R., Héron, D., Mignot, C., Blanc, P., O’Donnell-Luria, A., Whiffin, N., Charbonnier, C., Charenton, C., Thevenon, J., & Depienne, C. (2025).

Dominant variants in major spliceosome U4 and U5 small nuclear RNA genes cause neurodevelopmental disorders through splicing disruption.
Nature Genetics, 57, 1374–1388.
https://doi.org/10.1038/s41588-025-02184-4

8.

Scherer, N., Fässler, D., Borisov, O., Cheng, Y., Schlosser, P., Wuttke, M., Haug, S., Li, Y., Telkämper, F., Patil, S., Meiselbach, H., Wong, C., Berger, U., Sekula, P., Hoppmann, A., Schultheiss, U.T., Mozaffari, S., Xi, Y., Graham, R., Schmidts, M., Köttgen, M., Oefner, P.J., Knauf, F., Eckardt, K.-U., Grünert, S.C., Estrada, K., Thiele, I., Hertel, J., & Köttgen, A. (2025).
Coupling metabolomics and exome sequencing reveals graded effects of rare damaging heterozygous variants on gene function and human traits.
Nature Genetics, 57, 193–205.
https://doi.org/10.1038/s41588-024-01965-7

9.

Luo, X., El Assal, D.C., Liu, Y., Ranjbar, S., and Fleming, R.M.T. (2025).
Constraint-based modeling of bioenergetic differences between synaptic and non-synaptic components of dopaminergic neurons in Parkinson’s disease.
Frontiers in Computational Neuroscience, 19.
https://doi.org/10.3389/fncom.2025.1594330

10.

Park, J., Dufke, C., Fleszar, Z., Schlotterbek, M., Buena-Atienza, E., Stühn, L.G., Gross, C., Sturm, M., Ossowski, S., Schöls, L., Riess, O., & Haack, T.B. (2025).

Long-Read Sequencing Identifies Mosaic Sequence Variations in Friedreich’s Ataxia-GAA Repeats.
International Journal of Molecular Sciences, 26, 4969.
https://doi.org/10.3390/ijms26114969

11.

Huang, L., Preciat, G., Alarcon-Gil, J., Moreno, E.L., Wegrzyn, A., Thiele, I., Schymanski, E.L., Harms, A., Fleming, R.M.T., and Hankemeier, T. (2024).
fluxTrAM: Integration of tracer-based metabolomics data into atomically resolved genome-scale metabolic networks for metabolic flux analysis.
Preprint at Cold Spring Harbor Laboratory.
https://doi.org/10.1101/2024.11.26.625485

12.

Zaunseder, E., Mohammad, F.K., Mütze, U., Kölker, S., Heuveline, V., and Thiele, I. (2024).
Dynamic whole-body models for infant metabolism.
Preprint at Cold Spring Harbor Laboratory.
https://doi.org/10.1101/2024.11.25.625291

13.

Lai, P.-T., Coudert, E., Aimo, L., Axelsen, K., Breuza, L., De Castro, E., Feuermann, M., Morgat, A., Pourcel, L., Pedruzzi, I., et al. (2024).
EnzChemRED, a rich enzyme chemistry relation extraction dataset.
Scientific Data, 11.
https://doi.org/10.1038/s41597-024-03835-7

Journal of Inherited Metabolic Disease, 46(5), 824–838.
https://doi.org/10.1002/jimd.12663

17.

Thiele, I., Sahoo, S., Heinken, A., Hertel, J., Heirendt, L., Aurich, M.K., & Fleming, R.M.T. (2020).
Personalized whole-body models integrate metabolism, physiology, and the gut microbiome.
Molecular Systems Biology, 16(5), e8982.
https://doi.org/10.15252/msb.20198982

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